Starting phenix.real_space_refine on Fri Feb 16 21:52:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0y_32249/02_2024/7w0y_32249_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0y_32249/02_2024/7w0y_32249.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0y_32249/02_2024/7w0y_32249_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0y_32249/02_2024/7w0y_32249_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0y_32249/02_2024/7w0y_32249_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0y_32249/02_2024/7w0y_32249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0y_32249/02_2024/7w0y_32249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0y_32249/02_2024/7w0y_32249_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0y_32249/02_2024/7w0y_32249_updated.pdb" } resolution = 3.4 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 46 5.49 5 Mg 1 5.21 5 S 482 5.16 5 C 44089 2.51 5 N 11238 2.21 5 O 12208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "J GLU 311": "OE1" <-> "OE2" Residue "J GLU 336": "OE1" <-> "OE2" Residue "J GLU 351": "OE1" <-> "OE2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "M GLU 54": "OE1" <-> "OE2" Residue "M GLU 136": "OE1" <-> "OE2" Residue "M GLU 283": "OE1" <-> "OE2" Residue "M GLU 284": "OE1" <-> "OE2" Residue "M GLU 320": "OE1" <-> "OE2" Residue "M GLU 369": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P GLU 167": "OE1" <-> "OE2" Residue "P GLU 222": "OE1" <-> "OE2" Residue "P GLU 240": "OE1" <-> "OE2" Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 212": "OE1" <-> "OE2" Residue "Q GLU 335": "OE1" <-> "OE2" Residue "Q GLU 336": "OE1" <-> "OE2" Residue "Q GLU 370": "OE1" <-> "OE2" Residue "Q GLU 460": "OE1" <-> "OE2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "T GLU 105": "OE1" <-> "OE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "W GLU 56": "OE1" <-> "OE2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X GLU 129": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "a GLU 97": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "a GLU 111": "OE1" <-> "OE2" Residue "a GLU 130": "OE1" <-> "OE2" Residue "a GLU 153": "OE1" <-> "OE2" Residue "b GLU 122": "OE1" <-> "OE2" Residue "c GLU 47": "OE1" <-> "OE2" Residue "c GLU 60": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c GLU 177": "OE1" <-> "OE2" Residue "d GLU 53": "OE1" <-> "OE2" Residue "d GLU 67": "OE1" <-> "OE2" Residue "d GLU 78": "OE1" <-> "OE2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "d GLU 101": "OE1" <-> "OE2" Residue "d GLU 117": "OE1" <-> "OE2" Residue "d GLU 130": "OE1" <-> "OE2" Residue "d PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "f GLU 64": "OE1" <-> "OE2" Residue "g GLU 19": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "h GLU 55": "OE1" <-> "OE2" Residue "h GLU 59": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "i GLU 269": "OE1" <-> "OE2" Residue "l GLU 60": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 102": "OE1" <-> "OE2" Residue "l GLU 207": "OE1" <-> "OE2" Residue "l GLU 238": "OE1" <-> "OE2" Residue "l GLU 397": "OE1" <-> "OE2" Residue "l GLU 503": "OE1" <-> "OE2" Residue "l GLU 559": "OE1" <-> "OE2" Residue "m PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 81": "OE1" <-> "OE2" Residue "o GLU 46": "OE1" <-> "OE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "o GLU 118": "OE1" <-> "OE2" Residue "p GLU 28": "OE1" <-> "OE2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p GLU 123": "OE1" <-> "OE2" Residue "p GLU 131": "OE1" <-> "OE2" Residue "p GLU 136": "OE1" <-> "OE2" Residue "p GLU 142": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s GLU 143": "OE1" <-> "OE2" Residue "s GLU 202": "OE1" <-> "OE2" Residue "s GLU 206": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "u GLU 6": "OE1" <-> "OE2" Residue "u GLU 17": "OE1" <-> "OE2" Residue "u GLU 80": "OE1" <-> "OE2" Residue "u GLU 139": "OE1" <-> "OE2" Residue "u GLU 155": "OE1" <-> "OE2" Residue "v GLU 101": "OE1" <-> "OE2" Residue "v GLU 116": "OE1" <-> "OE2" Residue "v GLU 119": "OE1" <-> "OE2" Residue "v GLU 121": "OE1" <-> "OE2" Residue "w GLU 79": "OE1" <-> "OE2" Residue "w GLU 88": "OE1" <-> "OE2" Residue "w TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 226": "OE1" <-> "OE2" Residue "w GLU 238": "OE1" <-> "OE2" Residue "w TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 248": "OE1" <-> "OE2" Residue "w GLU 254": "OE1" <-> "OE2" Residue "w GLU 274": "OE1" <-> "OE2" Residue "w GLU 303": "OE1" <-> "OE2" Residue "w GLU 316": "OE1" <-> "OE2" Residue "w GLU 345": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 68093 Number of models: 1 Model: "" Number of chains: 68 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5289 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 32, 'TRANS': 657} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1654 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3451 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'2MR:plan-2': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 566 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1018 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} 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: "W" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1167 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 704 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 580 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 60} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 633 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 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: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 815 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 577} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "m" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1295 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 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: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1530 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 160} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "r" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3629 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "s" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2501 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 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: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1053 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "w" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2575 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'PEE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {' UQ': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "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: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 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: "j" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 290 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "m" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 168 Unusual residues: {' UQ': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 41 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: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 127 Unusual residues: {'ADP': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2718 SG CYS A 382 47.759 49.109 177.833 1.00 19.21 S ATOM 3060 SG CYS A 425 47.380 45.873 183.658 1.00 24.35 S ATOM 2738 SG CYS A 385 44.733 44.560 178.072 1.00 26.69 S ATOM 2699 SG CYS A 379 42.631 49.746 181.840 1.00 28.23 S ATOM 3961 SG CYS B 113 35.420 63.561 142.856 1.00 28.56 S ATOM 3980 SG CYS B 116 40.770 61.331 146.488 1.00 26.50 S ATOM 4003 SG CYS B 119 41.568 63.891 140.969 1.00 17.42 S ATOM 4332 SG CYS B 162 38.982 58.095 141.963 1.00 22.44 S ATOM 4030 SG CYS B 123 47.474 66.647 136.165 1.00 31.65 S ATOM 4256 SG CYS B 152 45.636 64.619 130.415 1.00 15.61 S ATOM 4303 SG CYS B 158 43.845 61.028 135.395 1.00 25.15 S ATOM 4282 SG CYS B 155 49.919 61.364 133.667 1.00 25.60 S ATOM 5724 SG CYS C 166 52.218 64.541 126.001 1.00 23.46 S ATOM 4996 SG CYS C 72 52.446 65.733 119.699 1.00 6.05 S ATOM 4990 SG CYS C 71 57.860 64.449 122.558 1.00 22.14 S ATOM 5494 SG CYS C 136 54.509 69.650 124.779 1.00 12.83 S ATOM 14927 SG CYS M 131 40.184 61.958 158.727 1.00 31.30 S ATOM 14906 SG CYS M 128 43.861 57.301 155.656 1.00 14.65 S ATOM 14967 SG CYS M 137 45.561 60.959 160.414 1.00 13.53 S ATOM 15299 SG CYS M 179 44.565 61.354 171.679 1.00 12.09 S ATOM 15653 SG CYS M 226 41.345 63.903 167.482 1.00 24.82 S ATOM 15323 SG CYS M 182 39.115 64.122 173.589 1.00 19.97 S ATOM 15276 SG CYS M 176 39.051 58.411 170.371 1.00 19.68 S ATOM 14524 SG CYS M 78 56.354 57.142 175.395 1.00 20.41 S ATOM 14625 SG CYS M 92 54.563 59.082 177.939 1.00 21.13 S ATOM 14413 SG CYS M 64 50.174 59.106 175.447 1.00 6.32 S ATOM 14499 SG CYS M 75 51.327 57.010 172.607 1.00 7.35 S ATOM 21455 SG CYS O 135 32.359 31.797 186.958 1.00 43.43 S ATOM 21489 SG CYS O 140 32.194 28.402 188.109 1.00 53.52 S ATOM 21769 SG CYS O 176 36.717 33.494 189.603 1.00 47.51 S ATOM 21792 SG CYS O 180 37.165 30.054 190.235 1.00 49.01 S ATOM 28506 SG CYS T 86 28.514 50.566 151.434 1.00 21.60 S ATOM 28684 SG CYS T 111 29.693 53.786 152.084 1.00 26.72 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 402 " occ=0.66 ... (25 atoms not shown) pdb=" PB ADP w 402 " occ=0.66 Time building chain proxies: 27.16, per 1000 atoms: 0.40 Number of scatterers: 68093 At special positions: 0 Unit cell: (210.543, 215.914, 234.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 482 16.00 P 46 15.00 Mg 1 11.99 O 12208 8.00 N 11238 7.00 C 44089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, 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 u 46 " - pdb=" SG CYS u 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.62 Conformation dependent library (CDL) restraints added in 9.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb=" SF4 C 301 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb=" SF4 M 801 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15530 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 349 helices and 29 sheets defined 52.4% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.64 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 95 through 102 removed outlier: 4.295A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.550A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 296 through 303 removed outlier: 3.560A pdb=" N HIS A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.311A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 Processing helix chain 'A' and resid 427 through 456 Proline residue: A 434 - end of helix removed outlier: 3.659A pdb=" N ARG A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.561A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 206 removed outlier: 5.494A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'C' and resid 43 through 59 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 111 through 122 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'E' and resid 25 through 50 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.233A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.364A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 39 removed outlier: 4.761A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 95 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 4.039A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 78 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 20 through 22 No H-bonds generated for 'chain 'I' and resid 20 through 22' Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 59 through 61 No H-bonds generated for 'chain 'I' and resid 59 through 61' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 75 removed outlier: 4.147A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.612A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 120 Processing helix chain 'J' and resid 141 through 144 No H-bonds generated for 'chain 'J' and resid 141 through 144' Processing helix chain 'J' and resid 147 through 158 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 223 removed outlier: 3.832A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 253 Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.889A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 322 Processing helix chain 'J' and resid 336 through 338 No H-bonds generated for 'chain 'J' and resid 336 through 338' Processing helix chain 'J' and resid 345 through 347 No H-bonds generated for 'chain 'J' and resid 345 through 347' Processing helix chain 'J' and resid 350 through 356 removed outlier: 5.641A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 80 Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.462A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 73 removed outlier: 3.932A pdb=" N LYS L 73 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 140 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.829A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 128 through 130 No H-bonds generated for 'chain 'M' and resid 128 through 130' Processing helix chain 'M' and resid 138 through 145 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.622A pdb=" N ILE M 222 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 292 Processing helix chain 'M' and resid 294 through 298 Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.613A pdb=" N SER M 332 " --> pdb=" O GLY M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 359 Processing helix chain 'M' and resid 382 through 384 No H-bonds generated for 'chain 'M' and resid 382 through 384' Processing helix chain 'M' and resid 390 through 396 removed outlier: 3.778A pdb=" N VAL M 394 " --> pdb=" O THR M 390 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU M 395 " --> pdb=" O ILE M 391 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU M 396 " --> pdb=" O ALA M 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 390 through 396' Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 Processing helix chain 'M' and resid 461 through 468 removed outlier: 3.525A pdb=" N ILE M 465 " --> pdb=" O PRO M 461 " (cutoff:3.500A) Processing helix chain 'M' and resid 480 through 482 No H-bonds generated for 'chain 'M' and resid 480 through 482' Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 522 through 528 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 557 through 559 No H-bonds generated for 'chain 'M' and resid 557 through 559' Processing helix chain 'M' and resid 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 671 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 703 Processing helix chain 'M' and resid 706 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.726A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 removed outlier: 3.654A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 90 removed outlier: 4.269A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix removed outlier: 3.873A pdb=" N ASN O 90 " --> pdb=" O GLN O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 208 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.663A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 173 removed outlier: 3.903A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 41 through 47 removed outlier: 4.258A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 91 No H-bonds generated for 'chain 'Q' and resid 89 through 91' Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.794A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 139 Processing helix chain 'Q' and resid 144 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 3.589A pdb=" N TRP Q 202 " --> pdb=" O THR Q 198 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 262 removed outlier: 3.667A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG Q 254 " --> pdb=" O ASN Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.504A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 311 through 313 No H-bonds generated for 'chain 'Q' and resid 311 through 313' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 371 No H-bonds generated for 'chain 'Q' and resid 368 through 371' Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 433 Processing helix chain 'Q' and resid 435 through 438 No H-bonds generated for 'chain 'Q' and resid 435 through 438' Processing helix chain 'Q' and resid 444 through 453 Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'S' and resid 2 through 31 Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix removed outlier: 4.480A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 55 Processing helix chain 'S' and resid 66 through 69 Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'U' and resid 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 83 Processing helix chain 'V' and resid 4 through 10 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 32 through 100 Proline residue: W 73 - end of helix removed outlier: 3.730A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP W 100 " --> pdb=" O ILE W 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 122 through 125 No H-bonds generated for 'chain 'W' and resid 122 through 125' Processing helix chain 'W' and resid 130 through 137 Processing helix chain 'W' and resid 139 through 142 No H-bonds generated for 'chain 'W' and resid 139 through 142' Processing helix chain 'X' and resid 76 through 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: 3.960A pdb=" N LEU Y 81 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) 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: 3.772A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 54 removed outlier: 3.510A pdb=" N ALA Z 50 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER Z 54 " --> pdb=" O TRP Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 89 removed outlier: 4.240A pdb=" N GLU Z 89 " --> pdb=" O GLU Z 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 3.872A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 109 through 112' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 25 Processing helix chain 'b' and resid 69 through 74 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 129 through 149 Processing helix chain 'd' and resid 29 through 58 removed outlier: 4.531A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix removed outlier: 3.532A pdb=" N LYS d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) 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: 3.835A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.461A 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 99 through 107 Processing helix chain 'e' and resid 116 through 131 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 removed outlier: 3.760A 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 43 Processing helix chain 'h' and resid 48 through 54 removed outlier: 4.057A 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 'h' and resid 96 through 98 No H-bonds generated for 'chain 'h' and resid 96 through 98' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 Proline residue: i 42 - end of helix 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: 4.309A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 145 removed outlier: 3.812A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.840A 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 151 through 171 removed outlier: 3.847A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.146A 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: 3.626A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 252 Processing helix chain 'i' and resid 258 through 272 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 276 through 300 removed outlier: 3.699A pdb=" N THR i 280 " --> pdb=" O ILE i 276 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.063A 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 Proline residue: j 74 - end of helix removed outlier: 5.729A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.356A 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 50 Processing helix chain 'k' and resid 54 through 85 removed outlier: 4.258A 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 'k' and resid 95 through 97 No H-bonds generated for 'chain 'k' and resid 95 through 97' Processing helix chain 'l' and resid 3 through 15 removed outlier: 3.676A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) Processing helix chain 'l' and resid 17 through 22 Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.473A 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: 3.869A 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 192 removed outlier: 3.959A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 204 Processing helix chain 'l' and resid 210 through 224 Processing helix chain 'l' and resid 227 through 229 No H-bonds generated for 'chain 'l' and resid 227 through 229' Processing helix chain 'l' and resid 231 through 238 removed outlier: 4.125A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.339A 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 253 through 262 removed outlier: 4.251A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.190A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.567A 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: 4.091A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.884A 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 381 Processing helix chain 'l' and resid 387 through 401 removed outlier: 3.817A pdb=" N SER l 391 " --> pdb=" O THR l 387 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.658A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 469 removed outlier: 6.018A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.415A 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: 3.840A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR l 509 " --> pdb=" O ASN l 505 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 526 through 533 Proline residue: l 530 - end of helix removed outlier: 4.223A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 25 through 46 Processing helix chain 'm' and resid 50 through 74 removed outlier: 3.513A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 87 through 109 Processing helix chain 'm' and resid 124 through 127 removed outlier: 3.508A pdb=" N ILE m 127 " --> pdb=" O ASP m 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 124 through 127' Processing helix chain 'm' and resid 138 through 148 removed outlier: 4.191A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TYR m 147 " --> pdb=" O ILE m 143 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER m 148 " --> pdb=" O ALA m 144 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 4 through 32 removed outlier: 6.374A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix Processing helix chain 'o' and resid 20 through 22 No H-bonds generated for 'chain 'o' and resid 20 through 22' Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.775A 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 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 50 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 142 removed outlier: 4.699A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 4.719A 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 17 Proline residue: r 7 - end of helix Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 20 through 42 removed outlier: 4.184A pdb=" N ILE r 23 " --> pdb=" O HIS r 20 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N TRP r 24 " --> pdb=" O ASN r 21 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN r 26 " --> pdb=" O ILE r 23 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS r 30 " --> pdb=" O ALA r 27 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 Proline residue: r 74 - end of helix removed outlier: 4.538A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.722A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.281A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.294A 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 142 through 171 removed outlier: 3.726A pdb=" N GLY r 156 " --> pdb=" O TYR r 152 " (cutoff:3.500A) Proline residue: r 159 - end of helix Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.479A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.211A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 235 through 246 removed outlier: 3.838A pdb=" N GLY r 239 " --> pdb=" O LEU r 236 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 Processing helix chain 'r' and resid 259 through 278 removed outlier: 3.565A pdb=" N SER r 273 " --> pdb=" O MET r 269 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG r 278 " --> pdb=" O SER r 274 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.590A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 350 No H-bonds generated for 'chain 'r' and resid 348 through 350' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 392 through 415 Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 31 Proline residue: s 12 - end of helix removed outlier: 3.652A 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: 4.312A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 122 removed outlier: 3.557A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.166A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.735A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) 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 210 through 213 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 Processing helix chain 's' and resid 293 through 311 Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 10 through 13 Processing helix chain 'u' and resid 22 through 35 removed outlier: 4.936A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 77 removed outlier: 3.688A pdb=" N CYS u 56 " --> pdb=" O PRO u 53 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU u 57 " --> pdb=" O ARG u 54 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLU u 58 " --> pdb=" O ARG u 55 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU u 59 " --> pdb=" O CYS u 56 " (cutoff:3.500A) Processing helix chain 'u' and resid 80 through 91 Processing helix chain 'u' and resid 102 through 113 Processing helix chain 'v' and resid 3 through 10 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 124 Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 93 through 97 removed outlier: 3.689A pdb=" N THR w 97 " --> pdb=" O TYR w 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 93 through 97' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 163 through 175 removed outlier: 5.115A pdb=" N PHE w 167 " --> pdb=" O TYR w 164 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL w 168 " --> pdb=" O SER w 165 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG w 175 " --> pdb=" O ALA w 172 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.127A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 243 Processing helix chain 'w' and resid 245 through 251 removed outlier: 4.221A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 260 through 264 removed outlier: 3.958A pdb=" N GLU w 264 " --> pdb=" O ALA w 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 260 through 264' Processing helix chain 'w' and resid 266 through 275 removed outlier: 3.663A pdb=" N TYR w 275 " --> pdb=" O GLU w 271 " (cutoff:3.500A) Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 305 Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 345 through 347 No H-bonds generated for 'chain 'w' and resid 345 through 347' Processing sheet with id= A, first strand: chain 'A' and resid 240 through 244 removed outlier: 7.476A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 99 through 103 removed outlier: 4.624A pdb=" N HIS B 101 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 168 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 5.863A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.669A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 57 removed outlier: 6.995A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.569A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 228 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= O, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 365 through 368 removed outlier: 4.510A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.026A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= S, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.476A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.551A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.741A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 6.353A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 77 through 79 Processing sheet with id= Z, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= AA, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.568A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.880A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'w' and resid 84 through 86 2928 hydrogen bonds defined for protein. 8109 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: 25.22 Time building geometry restraints manager: 25.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27720 1.40 - 1.62: 41098 1.62 - 1.84: 880 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 69778 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.260 0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.288 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.633 -0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.298 0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C3' ADP w 402 " pdb=" C4' ADP w 402 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 ... (remaining 69773 not shown) Histogram of bond angle deviations from ideal: 73.61 - 86.00: 76 86.00 - 98.39: 3 98.39 - 110.77: 24145 110.77 - 123.16: 67092 123.16 - 135.55: 3017 Bond angle restraints: 94333 Sorted by residual: angle pdb=" N GLN F 62 " pdb=" CA GLN F 62 " pdb=" C GLN F 62 " ideal model delta sigma weight residual 108.22 119.12 -10.90 9.00e-01 1.23e+00 1.47e+02 angle pdb=" C GLN F 62 " pdb=" N PRO F 63 " pdb=" CA PRO F 63 " ideal model delta sigma weight residual 119.84 131.75 -11.91 1.25e+00 6.40e-01 9.08e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 123.35 -15.61 1.95e+00 2.62e-01 6.38e+01 angle pdb=" N GLN F 25 " pdb=" CA GLN F 25 " pdb=" C GLN F 25 " ideal model delta sigma weight residual 111.28 119.54 -8.26 1.09e+00 8.42e-01 5.74e+01 angle pdb=" N VAL F 61 " pdb=" CA VAL F 61 " pdb=" C VAL F 61 " ideal model delta sigma weight residual 110.42 117.24 -6.82 9.60e-01 1.09e+00 5.05e+01 ... (remaining 94328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 40674 35.98 - 71.96: 1678 71.96 - 107.95: 130 107.95 - 143.93: 21 143.93 - 179.91: 7 Dihedral angle restraints: 42510 sinusoidal: 18420 harmonic: 24090 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual -102.41 77.50 -179.91 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP w 402 " pdb=" O5' ADP w 402 " pdb=" PA ADP w 402 " pdb=" O2A ADP w 402 " ideal model delta sinusoidal sigma weight residual -60.00 107.09 -167.08 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" CB CYS u 78 " pdb=" SG CYS u 78 " pdb=" SG CYS u 110 " pdb=" CB CYS u 110 " ideal model delta sinusoidal sigma weight residual -86.00 -132.74 46.74 1 1.00e+01 1.00e-02 3.02e+01 ... (remaining 42507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 9251 0.073 - 0.147: 883 0.147 - 0.220: 39 0.220 - 0.293: 9 0.293 - 0.367: 5 Chirality restraints: 10187 Sorted by residual: chirality pdb=" C3B NDP J 401 " pdb=" C2B NDP J 401 " pdb=" C4B NDP J 401 " pdb=" O3B NDP J 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.38 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA PHE s 19 " pdb=" N PHE s 19 " pdb=" C PHE s 19 " pdb=" CB PHE s 19 " 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=" CA PHE Q 174 " pdb=" N PHE Q 174 " pdb=" C PHE Q 174 " pdb=" CB PHE Q 174 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 10184 not shown) Planarity restraints: 11760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 403 " 0.337 2.00e-02 2.50e+03 3.14e-01 1.24e+03 pdb=" C18 UQ s 403 " -0.317 2.00e-02 2.50e+03 pdb=" C19 UQ s 403 " -0.385 2.00e-02 2.50e+03 pdb=" C20 UQ s 403 " 0.003 2.00e-02 2.50e+03 pdb=" C21 UQ s 403 " 0.363 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ J 402 " -0.067 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C11 UQ J 402 " 0.026 2.00e-02 2.50e+03 pdb=" C7 UQ J 402 " -0.309 2.00e-02 2.50e+03 pdb=" C8 UQ J 402 " 0.566 2.00e-02 2.50e+03 pdb=" C9 UQ J 402 " -0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 403 " -0.045 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C11 UQ s 403 " 0.028 2.00e-02 2.50e+03 pdb=" C7 UQ s 403 " -0.288 2.00e-02 2.50e+03 pdb=" C8 UQ s 403 " 0.553 2.00e-02 2.50e+03 pdb=" C9 UQ s 403 " -0.249 2.00e-02 2.50e+03 ... (remaining 11757 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1683 2.70 - 3.25: 66859 3.25 - 3.80: 110594 3.80 - 4.35: 148994 4.35 - 4.90: 247461 Nonbonded interactions: 575591 Sorted by model distance: nonbonded pdb=" N GLU J 365 " pdb=" OE1 GLU J 365 " model vdw 2.148 2.520 nonbonded pdb=" N GLU M 535 " pdb=" OE1 GLU M 535 " model vdw 2.188 2.520 nonbonded pdb=" N GLU Z 15 " pdb=" OE1 GLU Z 15 " model vdw 2.193 2.520 nonbonded pdb=" OG1 THR M 405 " pdb=" OE1 GLU M 410 " model vdw 2.204 2.440 nonbonded pdb=" OE2 GLU l 353 " pdb=" N ASP l 355 " model vdw 2.204 2.520 ... (remaining 575586 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 69 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 156 or resid 201)) selection = (chain 'X' and (resid 69 through 122 or (resid 123 and (name N or name CA or nam \ e C or name O or name CB )) or resid 124 through 149 or (resid 150 through 153 a \ nd (name N or name CA or name C or name O or name CB )) or resid 154 through 156 \ or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.66 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 9.110 Check model and map are aligned: 0.780 Set scattering table: 0.500 Process input model: 168.510 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.360 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: 0.020 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 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 0.319 69778 Z= 0.497 Angle : 0.805 17.540 94333 Z= 0.411 Chirality : 0.044 0.367 10187 Planarity : 0.008 0.314 11760 Dihedral : 18.566 179.910 26959 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.48 % Rotamer: Outliers : 0.22 % Allowed : 17.45 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 1.17 (0.09), residues: 8172 helix: 1.77 (0.08), residues: 4275 sheet: -0.04 (0.24), residues: 446 loop : -0.34 (0.11), residues: 3451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.011 0.001 HIS G 103 PHE 0.029 0.001 PHE i 292 TYR 0.024 0.001 TYR r 406 ARG 0.005 0.000 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1141 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1125 time to evaluate : 6.027 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 76 ASN cc_start: 0.8309 (p0) cc_final: 0.8068 (p0) REVERT: G 103 HIS cc_start: 0.3520 (m-70) cc_final: 0.3227 (m90) REVERT: X 85 TYR cc_start: 0.8435 (t80) cc_final: 0.8223 (t80) REVERT: e 111 ASP cc_start: 0.6515 (t70) cc_final: 0.6201 (t0) REVERT: s 24 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8223 (tm-30) outliers start: 16 outliers final: 12 residues processed: 1132 average time/residue: 0.7117 time to fit residues: 1377.1731 Evaluate side-chains 1121 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1108 time to evaluate : 6.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 137 CYS Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain Q residue 173 LEU Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 76 MET Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain u residue 126 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 679 optimal weight: 0.8980 chunk 610 optimal weight: 2.9990 chunk 338 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 411 optimal weight: 1.9990 chunk 325 optimal weight: 0.8980 chunk 630 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 383 optimal weight: 9.9990 chunk 469 optimal weight: 9.9990 chunk 731 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN E 99 GLN ** J 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 182 ASN W 76 GLN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 7 ASN k 57 ASN ** l 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN s 235 ASN ** u 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 77 HIS w 85 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 69778 Z= 0.183 Angle : 0.529 14.968 94333 Z= 0.261 Chirality : 0.041 0.190 10187 Planarity : 0.004 0.056 11760 Dihedral : 14.511 179.957 10830 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 1.91 % Allowed : 16.42 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 1.18 (0.09), residues: 8172 helix: 1.76 (0.08), residues: 4258 sheet: -0.03 (0.24), residues: 446 loop : -0.28 (0.11), residues: 3468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.006 0.001 HIS r 30 PHE 0.030 0.001 PHE i 292 TYR 0.022 0.001 TYR r 406 ARG 0.007 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1335 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1199 time to evaluate : 6.116 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 76 ASN cc_start: 0.8235 (p0) cc_final: 0.7992 (p0) REVERT: P 201 ASP cc_start: 0.8724 (p0) cc_final: 0.8519 (p0) REVERT: Q 73 LYS cc_start: 0.7847 (mtpp) cc_final: 0.7623 (mtmm) REVERT: Q 84 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6268 (m-80) REVERT: T 78 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6800 (mt-10) REVERT: V 104 ARG cc_start: 0.7750 (mmm160) cc_final: 0.7534 (mmm160) REVERT: X 83 VAL cc_start: 0.7963 (t) cc_final: 0.7709 (p) REVERT: X 85 TYR cc_start: 0.8210 (t80) cc_final: 0.7949 (t80) REVERT: a 76 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7681 (mp) REVERT: e 83 ASP cc_start: 0.8348 (t0) cc_final: 0.8058 (t0) REVERT: l 383 MET cc_start: 0.8654 (tpp) cc_final: 0.8223 (tpp) REVERT: m 65 LEU cc_start: 0.8839 (tt) cc_final: 0.8542 (tp) REVERT: n 29 ARG cc_start: 0.6872 (mtp-110) cc_final: 0.5673 (mtt180) REVERT: o 88 LEU cc_start: 0.8525 (mt) cc_final: 0.8313 (mt) REVERT: p 151 THR cc_start: 0.8594 (m) cc_final: 0.8298 (m) REVERT: s 224 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7523 (m-80) REVERT: s 288 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9097 (tp) REVERT: u 134 ASP cc_start: 0.6678 (m-30) cc_final: 0.6371 (m-30) REVERT: w 272 ASP cc_start: 0.7464 (t0) cc_final: 0.7202 (t0) outliers start: 136 outliers final: 75 residues processed: 1278 average time/residue: 0.6406 time to fit residues: 1389.7936 Evaluate side-chains 1197 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1117 time to evaluate : 5.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 288 ASP Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 84 PHE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain W residue 135 SER Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 84 ASP Chi-restraints excluded: chain i residue 21 MET Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 328 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 170 ILE Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 26 ASN Chi-restraints excluded: chain r residue 78 MET Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 339 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 288 LEU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain v residue 59 CYS Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 90 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 406 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 608 optimal weight: 9.9990 chunk 497 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 732 optimal weight: 1.9990 chunk 791 optimal weight: 0.0010 chunk 652 optimal weight: 0.1980 chunk 726 optimal weight: 2.9990 chunk 249 optimal weight: 0.0970 chunk 587 optimal weight: 6.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN G 142 GLN ** J 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 514 ASN N 122 GLN Q 454 GLN T 123 HIS W 76 GLN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 83 GLN c 127 ASN ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 7 ASN ** l 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 541 ASN m 46 ASN ** p 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 169 ASN s 32 GLN s 235 ASN ** u 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 69778 Z= 0.161 Angle : 0.504 10.468 94333 Z= 0.250 Chirality : 0.040 0.186 10187 Planarity : 0.004 0.055 11760 Dihedral : 13.717 179.187 10810 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.37 % Favored : 96.59 % Rotamer: Outliers : 2.00 % Allowed : 17.33 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 1.23 (0.09), residues: 8172 helix: 1.80 (0.08), residues: 4263 sheet: -0.01 (0.24), residues: 456 loop : -0.27 (0.11), residues: 3453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.008 0.001 HIS T 123 PHE 0.030 0.001 PHE i 292 TYR 0.022 0.001 TYR r 406 ARG 0.005 0.000 ARG m 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1322 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1179 time to evaluate : 7.406 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 CYS cc_start: 0.8838 (m) cc_final: 0.8469 (m) REVERT: A 383 THR cc_start: 0.9346 (m) cc_final: 0.9086 (p) REVERT: G 139 MET cc_start: 0.4417 (ttt) cc_final: 0.4216 (ttt) REVERT: I 7 VAL cc_start: 0.7381 (OUTLIER) cc_final: 0.7163 (t) REVERT: M 358 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8534 (mp) REVERT: M 468 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: Q 73 LYS cc_start: 0.7871 (mtpp) cc_final: 0.7611 (mtmm) REVERT: Q 84 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.6279 (m-80) REVERT: Q 438 MET cc_start: 0.8759 (mtm) cc_final: 0.8522 (mtp) REVERT: T 78 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6765 (mt-10) REVERT: X 83 VAL cc_start: 0.8053 (t) cc_final: 0.7782 (p) REVERT: X 85 TYR cc_start: 0.8221 (t80) cc_final: 0.7971 (t80) REVERT: a 76 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7664 (mp) REVERT: e 83 ASP cc_start: 0.8307 (t0) cc_final: 0.8017 (t0) REVERT: i 46 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7625 (ttpt) REVERT: j 109 LYS cc_start: 0.8543 (mmtt) cc_final: 0.7872 (mmmt) REVERT: l 383 MET cc_start: 0.8665 (tpp) cc_final: 0.8310 (tpp) REVERT: l 587 TYR cc_start: 0.8189 (m-10) cc_final: 0.7759 (m-10) REVERT: m 65 LEU cc_start: 0.8899 (tt) cc_final: 0.8594 (tp) REVERT: n 29 ARG cc_start: 0.6804 (mtp-110) cc_final: 0.5677 (mtt180) REVERT: o 88 LEU cc_start: 0.8558 (mt) cc_final: 0.8350 (mt) REVERT: p 151 THR cc_start: 0.8549 (m) cc_final: 0.8227 (m) REVERT: r 244 MET cc_start: 0.9266 (mtt) cc_final: 0.9064 (mtt) REVERT: r 273 SER cc_start: 0.9259 (t) cc_final: 0.9040 (m) REVERT: s 234 MET cc_start: 0.8748 (mmp) cc_final: 0.8330 (mmt) REVERT: s 288 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9121 (tp) REVERT: u 134 ASP cc_start: 0.6460 (m-30) cc_final: 0.6161 (m-30) REVERT: w 272 ASP cc_start: 0.7379 (t0) cc_final: 0.7053 (t0) outliers start: 143 outliers final: 84 residues processed: 1266 average time/residue: 0.6429 time to fit residues: 1384.1600 Evaluate side-chains 1202 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1110 time to evaluate : 6.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain M residue 288 ASP Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 84 PHE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 137 ASP Chi-restraints excluded: chain Q residue 278 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain W residue 135 SER Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 137 MET Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 84 ASP Chi-restraints excluded: chain i residue 46 LYS Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 294 THR Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 170 ILE Chi-restraints excluded: chain r residue 14 MET Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 26 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 288 LEU Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 90 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 2.9990 chunk 550 optimal weight: 9.9990 chunk 380 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 349 optimal weight: 0.9990 chunk 491 optimal weight: 6.9990 chunk 734 optimal weight: 8.9990 chunk 778 optimal weight: 8.9990 chunk 383 optimal weight: 7.9990 chunk 696 optimal weight: 8.9990 chunk 209 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN A 458 GLN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 122 HIS ** J 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 GLN O 69 ASN O 187 GLN Q 60 HIS S 44 GLN W 76 GLN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 83 GLN c 160 GLN d 55 GLN ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN i 235 ASN j 10 ASN k 7 ASN ** l 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 580 GLN m 46 ASN ** p 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 169 ASN s 235 ASN s 287 HIS s 304 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 69778 Z= 0.365 Angle : 0.614 10.834 94333 Z= 0.307 Chirality : 0.045 0.214 10187 Planarity : 0.005 0.057 11760 Dihedral : 13.591 178.515 10805 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.07 % Favored : 95.88 % Rotamer: Outliers : 3.17 % Allowed : 17.45 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.09), residues: 8172 helix: 1.40 (0.08), residues: 4278 sheet: -0.06 (0.25), residues: 420 loop : -0.45 (0.10), residues: 3474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP u 86 HIS 0.007 0.001 HIS r 422 PHE 0.032 0.002 PHE i 292 TYR 0.022 0.002 TYR r 406 ARG 0.006 0.001 ARG n 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1394 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1168 time to evaluate : 7.177 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 73 GLN cc_start: 0.8245 (tp-100) cc_final: 0.7724 (tp40) REVERT: I 7 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7148 (t) REVERT: I 106 LEU cc_start: 0.8867 (tp) cc_final: 0.8510 (tp) REVERT: J 36 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8620 (tt) REVERT: M 358 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8507 (mp) REVERT: Q 73 LYS cc_start: 0.7830 (mtpp) cc_final: 0.7589 (mtmm) REVERT: T 41 THR cc_start: 0.9162 (p) cc_final: 0.8902 (t) REVERT: T 78 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7179 (mt-10) REVERT: V 140 LYS cc_start: 0.8879 (pttt) cc_final: 0.8653 (ptmt) REVERT: X 83 VAL cc_start: 0.8085 (t) cc_final: 0.7826 (p) REVERT: X 115 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: a 76 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8004 (mp) REVERT: b 93 LYS cc_start: 0.8345 (mttt) cc_final: 0.8103 (mptt) REVERT: c 111 MET cc_start: 0.9208 (ttp) cc_final: 0.8983 (ttm) REVERT: e 83 ASP cc_start: 0.8445 (t0) cc_final: 0.8137 (t0) REVERT: e 116 GLU cc_start: 0.7585 (mp0) cc_final: 0.7298 (mp0) REVERT: i 159 MET cc_start: 0.8744 (mmm) cc_final: 0.8537 (mmm) REVERT: i 335 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8566 (mt) REVERT: j 109 LYS cc_start: 0.8630 (mmtt) cc_final: 0.7824 (mmmt) REVERT: l 383 MET cc_start: 0.8749 (tpp) cc_final: 0.8448 (tpp) REVERT: l 593 ILE cc_start: 0.8915 (mm) cc_final: 0.8631 (mt) REVERT: m 46 ASN cc_start: 0.8845 (m-40) cc_final: 0.8629 (m110) REVERT: m 65 LEU cc_start: 0.9041 (tt) cc_final: 0.8740 (tp) REVERT: m 78 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7942 (ttt) REVERT: n 29 ARG cc_start: 0.7022 (mtp-110) cc_final: 0.5875 (mtt180) REVERT: o 88 LEU cc_start: 0.8622 (mt) cc_final: 0.8382 (mt) REVERT: p 59 LYS cc_start: 0.8664 (mptt) cc_final: 0.8270 (tttm) REVERT: p 160 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6887 (tp30) REVERT: r 294 MET cc_start: 0.8964 (mmp) cc_final: 0.8739 (mmp) REVERT: r 415 GLN cc_start: 0.8756 (mm-40) cc_final: 0.7822 (mp10) REVERT: s 224 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7521 (m-80) REVERT: w 272 ASP cc_start: 0.7505 (t0) cc_final: 0.7200 (t0) outliers start: 226 outliers final: 152 residues processed: 1311 average time/residue: 0.6431 time to fit residues: 1431.5602 Evaluate side-chains 1280 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1119 time to evaluate : 6.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 168 LYS Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 138 ASP Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 288 ASP Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 48 ASN Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 120 THR Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 200 ASP Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 278 VAL Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain U residue 55 VAL Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain X residue 115 GLN Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Z residue 25 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 137 MET Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 90 VAL Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 84 ASP Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 258 SER Chi-restraints excluded: chain i residue 285 THR Chi-restraints excluded: chain i residue 289 ASN Chi-restraints excluded: chain i residue 335 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 20 ILE Chi-restraints excluded: chain j residue 33 LYS Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain l residue 31 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 508 THR Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 78 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain o residue 110 ASP Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 144 THR Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 26 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 78 MET Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 265 SER Chi-restraints excluded: chain r residue 339 SER Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 136 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain v residue 59 CYS Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain w residue 44 VAL Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 116 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 9.9990 chunk 441 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 579 optimal weight: 10.0000 chunk 321 optimal weight: 0.7980 chunk 664 optimal weight: 7.9990 chunk 537 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 397 optimal weight: 0.0970 chunk 698 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN G 142 GLN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 GLN T 123 HIS ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 HIS c 160 GLN d 140 GLN h 21 GLN ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 235 ASN j 10 ASN k 7 ASN ** l 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 69778 Z= 0.257 Angle : 0.551 11.483 94333 Z= 0.276 Chirality : 0.042 0.199 10187 Planarity : 0.004 0.062 11760 Dihedral : 13.197 178.442 10805 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 2.90 % Allowed : 18.21 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.09), residues: 8172 helix: 1.46 (0.08), residues: 4277 sheet: -0.20 (0.25), residues: 434 loop : -0.44 (0.11), residues: 3461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.012 0.001 HIS u 77 PHE 0.032 0.001 PHE i 292 TYR 0.023 0.001 TYR r 406 ARG 0.006 0.000 ARG n 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1395 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1188 time to evaluate : 6.092 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8846 (mtmt) REVERT: F 73 GLN cc_start: 0.8227 (tp-100) cc_final: 0.7715 (tp40) REVERT: I 70 MET cc_start: 0.8592 (tmt) cc_final: 0.8184 (tmt) REVERT: J 36 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8565 (tt) REVERT: M 358 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8522 (mp) REVERT: O 158 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.5833 (pp) REVERT: Q 73 LYS cc_start: 0.7810 (mtpp) cc_final: 0.7583 (mtmm) REVERT: Q 197 MET cc_start: 0.8642 (ptp) cc_final: 0.8240 (ptp) REVERT: Q 438 MET cc_start: 0.8896 (mtm) cc_final: 0.8638 (mtp) REVERT: T 41 THR cc_start: 0.9156 (p) cc_final: 0.8899 (t) REVERT: T 78 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7108 (mt-10) REVERT: X 83 VAL cc_start: 0.8050 (t) cc_final: 0.7783 (p) REVERT: X 115 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: a 76 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7981 (mp) REVERT: b 9 LYS cc_start: 0.8645 (mmmt) cc_final: 0.8364 (mmmt) REVERT: b 93 LYS cc_start: 0.8412 (mttt) cc_final: 0.8105 (mptt) REVERT: b 99 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: c 111 MET cc_start: 0.9204 (ttp) cc_final: 0.9000 (ttm) REVERT: e 83 ASP cc_start: 0.8378 (t0) cc_final: 0.8073 (t0) REVERT: i 21 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8560 (mtm) REVERT: i 68 MET cc_start: 0.9318 (OUTLIER) cc_final: 0.9068 (mmt) REVERT: j 33 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8855 (tptm) REVERT: j 109 LYS cc_start: 0.8627 (mmtt) cc_final: 0.7855 (mmmt) REVERT: l 383 MET cc_start: 0.8754 (tpp) cc_final: 0.8476 (tpp) REVERT: l 504 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8601 (mm) REVERT: l 593 ILE cc_start: 0.8863 (mm) cc_final: 0.8592 (mt) REVERT: m 65 LEU cc_start: 0.9000 (tt) cc_final: 0.8714 (tp) REVERT: n 29 ARG cc_start: 0.6907 (mtp-110) cc_final: 0.5813 (mtt180) REVERT: o 88 LEU cc_start: 0.8619 (mt) cc_final: 0.8400 (mt) REVERT: p 59 LYS cc_start: 0.8590 (mptt) cc_final: 0.8016 (tttm) REVERT: p 64 LEU cc_start: 0.8636 (tp) cc_final: 0.8402 (tp) REVERT: p 160 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6868 (tp30) REVERT: r 415 GLN cc_start: 0.8758 (mm-40) cc_final: 0.7805 (mp10) REVERT: s 224 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: w 272 ASP cc_start: 0.7564 (t0) cc_final: 0.7139 (t0) outliers start: 207 outliers final: 139 residues processed: 1315 average time/residue: 0.6441 time to fit residues: 1438.4974 Evaluate side-chains 1279 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1127 time to evaluate : 6.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 168 LYS Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 138 ASP Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 288 ASP Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 158 ILE Chi-restraints excluded: chain O residue 200 ASP Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 278 VAL Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 447 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 115 GLN Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 137 MET Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 84 ASP Chi-restraints excluded: chain i residue 21 MET Chi-restraints excluded: chain i residue 46 LYS Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 258 SER Chi-restraints excluded: chain i residue 289 ASN Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 33 LYS Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain m residue 169 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain o residue 110 ASP Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 144 THR Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 26 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 339 SER Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 34 ARG Chi-restraints excluded: chain s residue 136 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain v residue 59 CYS Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 90 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 4.9990 chunk 700 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 456 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 778 optimal weight: 9.9990 chunk 646 optimal weight: 6.9990 chunk 360 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 chunk 408 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 381 GLN A 393 ASN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 GLN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 235 ASN j 10 ASN k 7 ASN ** l 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 46 ASN ** p 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN s 235 ASN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 235 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 69778 Z= 0.315 Angle : 0.581 10.692 94333 Z= 0.291 Chirality : 0.043 0.206 10187 Planarity : 0.005 0.059 11760 Dihedral : 13.038 178.261 10805 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.10 % Favored : 95.85 % Rotamer: Outliers : 3.39 % Allowed : 18.35 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.09), residues: 8172 helix: 1.36 (0.08), residues: 4287 sheet: -0.21 (0.25), residues: 428 loop : -0.52 (0.10), residues: 3457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.010 0.001 HIS u 77 PHE 0.033 0.002 PHE i 292 TYR 0.022 0.002 TYR r 406 ARG 0.006 0.000 ARG n 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1407 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1165 time to evaluate : 6.066 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 CYS cc_start: 0.8919 (m) cc_final: 0.8557 (m) REVERT: B 151 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8853 (mtmt) REVERT: F 73 GLN cc_start: 0.8262 (tp-100) cc_final: 0.7759 (tp40) REVERT: J 36 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8570 (tt) REVERT: M 358 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8508 (mp) REVERT: O 89 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: O 158 ILE cc_start: 0.6510 (OUTLIER) cc_final: 0.5836 (pp) REVERT: Q 73 LYS cc_start: 0.7757 (mtpp) cc_final: 0.7539 (mtmm) REVERT: Q 197 MET cc_start: 0.8625 (ptp) cc_final: 0.8226 (ptp) REVERT: Q 438 MET cc_start: 0.8945 (mtm) cc_final: 0.8685 (mtp) REVERT: T 78 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7244 (mt-10) REVERT: X 83 VAL cc_start: 0.8043 (t) cc_final: 0.7796 (p) REVERT: X 115 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7703 (tm-30) REVERT: a 76 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8088 (mp) REVERT: b 9 LYS cc_start: 0.8675 (mmmt) cc_final: 0.8395 (mmmt) REVERT: b 93 LYS cc_start: 0.8472 (mttt) cc_final: 0.8097 (mptt) REVERT: b 99 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: c 111 MET cc_start: 0.9224 (ttp) cc_final: 0.9022 (ttm) REVERT: e 83 ASP cc_start: 0.8399 (t0) cc_final: 0.8089 (t0) REVERT: h 73 MET cc_start: 0.7860 (tpp) cc_final: 0.7610 (tpp) REVERT: i 21 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8549 (mtm) REVERT: i 335 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8550 (mt) REVERT: j 33 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.9029 (tptm) REVERT: j 109 LYS cc_start: 0.8650 (mmtt) cc_final: 0.7868 (mmmt) REVERT: l 383 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8500 (tpp) REVERT: l 504 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8595 (mm) REVERT: l 587 TYR cc_start: 0.8416 (m-10) cc_final: 0.7894 (m-10) REVERT: l 593 ILE cc_start: 0.8890 (mm) cc_final: 0.8631 (mt) REVERT: m 65 LEU cc_start: 0.9028 (tt) cc_final: 0.8738 (tp) REVERT: n 29 ARG cc_start: 0.6997 (mtp-110) cc_final: 0.5893 (mtt180) REVERT: o 88 LEU cc_start: 0.8601 (mt) cc_final: 0.8369 (mt) REVERT: p 16 VAL cc_start: 0.8830 (t) cc_final: 0.8604 (m) REVERT: p 59 LYS cc_start: 0.8610 (mptt) cc_final: 0.8198 (tttm) REVERT: p 64 LEU cc_start: 0.8707 (tp) cc_final: 0.8456 (tp) REVERT: p 160 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6850 (tp30) REVERT: r 415 GLN cc_start: 0.8770 (mm-40) cc_final: 0.7793 (mp10) REVERT: s 100 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9046 (mt) REVERT: s 224 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7432 (m-80) REVERT: u 118 VAL cc_start: 0.8246 (t) cc_final: 0.7937 (p) REVERT: w 272 ASP cc_start: 0.7625 (t0) cc_final: 0.7138 (t0) outliers start: 242 outliers final: 179 residues processed: 1327 average time/residue: 0.6526 time to fit residues: 1476.7162 Evaluate side-chains 1315 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1120 time to evaluate : 6.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 168 LYS Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 138 ASP Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 288 ASP Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 48 ASN Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 158 ILE Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain P residue 214 ASP Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 278 VAL Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 447 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 115 GLN Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Z residue 25 GLU Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 137 MET Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain f residue 56 ILE Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 84 ASP Chi-restraints excluded: chain h residue 98 HIS Chi-restraints excluded: chain i residue 11 MET Chi-restraints excluded: chain i residue 21 MET Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 258 SER Chi-restraints excluded: chain i residue 285 THR Chi-restraints excluded: chain i residue 289 ASN Chi-restraints excluded: chain i residue 335 LEU Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 33 LYS Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain l residue 31 LEU Chi-restraints excluded: chain l residue 127 THR Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 374 ILE Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 11 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain m residue 169 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain o residue 110 ASP Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 115 TYR Chi-restraints excluded: chain p residue 144 THR Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 26 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 339 SER Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 34 ARG Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 136 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain v residue 59 CYS Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain w residue 44 VAL Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 287 ASP Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 443 optimal weight: 2.9990 chunk 568 optimal weight: 3.9990 chunk 440 optimal weight: 7.9990 chunk 655 optimal weight: 9.9990 chunk 434 optimal weight: 6.9990 chunk 775 optimal weight: 0.5980 chunk 485 optimal weight: 3.9990 chunk 473 optimal weight: 0.9990 chunk 358 optimal weight: 0.3980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 381 GLN I 13 ASN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN M 460 HIS N 122 GLN Q 60 HIS ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 235 ASN j 10 ASN k 7 ASN ** l 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN u 77 HIS ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 69778 Z= 0.182 Angle : 0.525 14.846 94333 Z= 0.262 Chirality : 0.041 0.189 10187 Planarity : 0.004 0.061 11760 Dihedral : 12.576 178.028 10805 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.56 % Favored : 96.39 % Rotamer: Outliers : 2.80 % Allowed : 19.12 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.09), residues: 8172 helix: 1.56 (0.08), residues: 4261 sheet: -0.23 (0.24), residues: 459 loop : -0.40 (0.11), residues: 3452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP u 86 HIS 0.008 0.001 HIS u 77 PHE 0.031 0.001 PHE i 292 TYR 0.023 0.001 TYR r 406 ARG 0.007 0.000 ARG n 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1381 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1181 time to evaluate : 6.099 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 CYS cc_start: 0.8924 (m) cc_final: 0.8597 (m) REVERT: A 390 ASP cc_start: 0.8215 (t0) cc_final: 0.7938 (t0) REVERT: C 195 ARG cc_start: 0.8089 (mmt90) cc_final: 0.7344 (mtm110) REVERT: F 73 GLN cc_start: 0.8278 (tp-100) cc_final: 0.7717 (tp40) REVERT: I 70 MET cc_start: 0.8602 (tmt) cc_final: 0.8358 (tmt) REVERT: M 100 TRP cc_start: 0.8690 (OUTLIER) cc_final: 0.8478 (m-10) REVERT: M 358 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8531 (mp) REVERT: O 89 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: O 158 ILE cc_start: 0.6338 (OUTLIER) cc_final: 0.5764 (pp) REVERT: P 240 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8254 (tp30) REVERT: Q 52 MET cc_start: 0.7658 (mmt) cc_final: 0.7261 (mmt) REVERT: Q 73 LYS cc_start: 0.7696 (mtpp) cc_final: 0.7480 (mtmm) REVERT: Q 197 MET cc_start: 0.8589 (ptp) cc_final: 0.8144 (ptp) REVERT: Q 438 MET cc_start: 0.8908 (mtm) cc_final: 0.8649 (mtp) REVERT: T 78 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7111 (mt-10) REVERT: W 50 MET cc_start: 0.8898 (mmm) cc_final: 0.8643 (mmt) REVERT: X 83 VAL cc_start: 0.7986 (t) cc_final: 0.7729 (p) REVERT: X 115 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: Z 30 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7149 (mt-10) REVERT: a 76 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7998 (mp) REVERT: b 9 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8317 (mmmt) REVERT: b 93 LYS cc_start: 0.8433 (mttt) cc_final: 0.8079 (mptt) REVERT: b 99 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: d 99 ASP cc_start: 0.9164 (m-30) cc_final: 0.8478 (m-30) REVERT: e 83 ASP cc_start: 0.8313 (t70) cc_final: 0.7991 (t0) REVERT: h 73 MET cc_start: 0.7766 (tpp) cc_final: 0.7508 (mpp) REVERT: i 21 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8530 (mtm) REVERT: i 274 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6860 (tp30) REVERT: j 109 LYS cc_start: 0.8581 (mmtt) cc_final: 0.7764 (mmmt) REVERT: l 340 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.7819 (t80) REVERT: l 383 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8214 (tpp) REVERT: l 504 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8541 (mm) REVERT: l 587 TYR cc_start: 0.8384 (m-10) cc_final: 0.7912 (m-10) REVERT: l 593 ILE cc_start: 0.8852 (mm) cc_final: 0.8594 (mt) REVERT: m 65 LEU cc_start: 0.8970 (tt) cc_final: 0.8700 (tp) REVERT: n 29 ARG cc_start: 0.6807 (mtp-110) cc_final: 0.5753 (mtt180) REVERT: o 30 ARG cc_start: 0.7704 (mmt-90) cc_final: 0.7460 (tpp-160) REVERT: o 88 LEU cc_start: 0.8586 (mt) cc_final: 0.8386 (mt) REVERT: p 59 LYS cc_start: 0.8509 (mptt) cc_final: 0.8163 (tttm) REVERT: p 64 LEU cc_start: 0.8604 (tp) cc_final: 0.8376 (tp) REVERT: p 160 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6810 (tp30) REVERT: r 415 GLN cc_start: 0.8767 (mm-40) cc_final: 0.7822 (mp10) REVERT: s 100 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9009 (mt) REVERT: s 174 MET cc_start: 0.8743 (tpp) cc_final: 0.8529 (tpp) REVERT: s 224 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7441 (m-80) REVERT: u 118 VAL cc_start: 0.8237 (t) cc_final: 0.7942 (p) REVERT: v 96 VAL cc_start: 0.8927 (m) cc_final: 0.8546 (t) REVERT: w 272 ASP cc_start: 0.7605 (t0) cc_final: 0.7111 (t0) outliers start: 200 outliers final: 148 residues processed: 1310 average time/residue: 0.6431 time to fit residues: 1430.0593 Evaluate side-chains 1306 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1142 time to evaluate : 6.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 100 TRP Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 138 ASP Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 288 ASP Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 48 ASN Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain O residue 158 ILE Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 137 ASP Chi-restraints excluded: chain Q residue 278 VAL Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 447 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 115 GLN Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 137 MET Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain f residue 56 ILE Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 84 ASP Chi-restraints excluded: chain h residue 98 HIS Chi-restraints excluded: chain i residue 21 MET Chi-restraints excluded: chain i residue 46 LYS Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 258 SER Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 285 THR Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 41 CYS Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 169 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain o residue 110 ASP Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 115 TYR Chi-restraints excluded: chain p residue 144 THR Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 26 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 339 SER Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 34 ARG Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 136 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain v residue 59 CYS Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 287 ASP Chi-restraints excluded: chain w residue 333 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 480 optimal weight: 5.9990 chunk 309 optimal weight: 0.5980 chunk 463 optimal weight: 6.9990 chunk 233 optimal weight: 0.6980 chunk 152 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 493 optimal weight: 3.9990 chunk 528 optimal weight: 4.9990 chunk 383 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 609 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN M 677 GLN Q 60 HIS W 76 GLN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 83 GLN ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 235 ASN k 7 ASN ** l 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 14 GLN p 141 GLN s 235 ASN u 77 HIS ** 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: 0.8455 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 69778 Z= 0.237 Angle : 0.549 15.062 94333 Z= 0.273 Chirality : 0.042 0.196 10187 Planarity : 0.004 0.058 11760 Dihedral : 12.373 178.050 10805 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 2.84 % Allowed : 19.25 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.09), residues: 8172 helix: 1.50 (0.08), residues: 4264 sheet: -0.07 (0.25), residues: 431 loop : -0.43 (0.11), residues: 3477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.010 0.001 HIS u 77 PHE 0.032 0.001 PHE i 292 TYR 0.022 0.001 TYR r 406 ARG 0.008 0.000 ARG m 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1368 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1165 time to evaluate : 6.201 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 CYS cc_start: 0.8918 (m) cc_final: 0.8577 (m) REVERT: B 151 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8883 (mtmt) REVERT: F 73 GLN cc_start: 0.8274 (tp-100) cc_final: 0.7713 (tp40) REVERT: H 71 GLN cc_start: 0.8566 (tt0) cc_final: 0.8335 (tt0) REVERT: I 70 MET cc_start: 0.8599 (tmt) cc_final: 0.8334 (tmt) REVERT: M 100 TRP cc_start: 0.8694 (OUTLIER) cc_final: 0.8478 (m-10) REVERT: M 358 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8507 (mp) REVERT: O 89 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: O 150 GLU cc_start: 0.7091 (pp20) cc_final: 0.6801 (pp20) REVERT: O 158 ILE cc_start: 0.6455 (OUTLIER) cc_final: 0.5818 (pp) REVERT: P 240 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8261 (tp30) REVERT: Q 52 MET cc_start: 0.7667 (mmt) cc_final: 0.7274 (mmt) REVERT: Q 197 MET cc_start: 0.8592 (ptp) cc_final: 0.8147 (ptp) REVERT: Q 438 MET cc_start: 0.8922 (mtm) cc_final: 0.8651 (mtp) REVERT: T 78 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: W 50 MET cc_start: 0.8897 (mmm) cc_final: 0.8662 (mmt) REVERT: W 89 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7531 (mt-10) REVERT: X 83 VAL cc_start: 0.8021 (t) cc_final: 0.7774 (p) REVERT: X 115 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: Y 50 LEU cc_start: 0.8281 (mp) cc_final: 0.8034 (mp) REVERT: a 76 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8007 (mp) REVERT: b 9 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8293 (mmmt) REVERT: b 93 LYS cc_start: 0.8491 (mttt) cc_final: 0.8114 (mptt) REVERT: b 99 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: e 83 ASP cc_start: 0.8343 (t70) cc_final: 0.8052 (t0) REVERT: i 21 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8553 (mtm) REVERT: i 68 MET cc_start: 0.9318 (OUTLIER) cc_final: 0.8989 (mmt) REVERT: j 33 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8867 (tptm) REVERT: j 109 LYS cc_start: 0.8607 (mmtt) cc_final: 0.7773 (mmmt) REVERT: l 340 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.7824 (t80) REVERT: l 383 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8238 (tpp) REVERT: l 416 THR cc_start: 0.8263 (m) cc_final: 0.7990 (m) REVERT: l 504 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8535 (mm) REVERT: l 512 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7585 (tttm) REVERT: l 587 TYR cc_start: 0.8394 (m-10) cc_final: 0.7900 (m-10) REVERT: l 593 ILE cc_start: 0.8873 (mm) cc_final: 0.8620 (mt) REVERT: m 65 LEU cc_start: 0.8991 (tt) cc_final: 0.8708 (tp) REVERT: n 29 ARG cc_start: 0.6906 (mtp-110) cc_final: 0.5799 (mtt180) REVERT: o 30 ARG cc_start: 0.7701 (mmt-90) cc_final: 0.7446 (tpp-160) REVERT: o 88 LEU cc_start: 0.8584 (mt) cc_final: 0.8376 (mt) REVERT: p 59 LYS cc_start: 0.8489 (mptt) cc_final: 0.8149 (tttm) REVERT: p 64 LEU cc_start: 0.8687 (tp) cc_final: 0.8439 (tp) REVERT: p 160 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6823 (tp30) REVERT: r 415 GLN cc_start: 0.8773 (mm-40) cc_final: 0.7853 (mp10) REVERT: s 100 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9012 (mt) REVERT: s 224 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7434 (m-80) REVERT: u 118 VAL cc_start: 0.8259 (t) cc_final: 0.7950 (p) REVERT: v 96 VAL cc_start: 0.9001 (m) cc_final: 0.8618 (t) REVERT: v 101 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6607 (tm-30) REVERT: w 272 ASP cc_start: 0.7650 (t0) cc_final: 0.7169 (t0) outliers start: 203 outliers final: 166 residues processed: 1298 average time/residue: 0.6581 time to fit residues: 1454.0340 Evaluate side-chains 1324 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1139 time to evaluate : 5.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 100 TRP Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 138 ASP Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 288 ASP Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 48 ASN Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 158 ILE Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 214 ASP Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 278 VAL Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 447 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 20 ASP Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 115 GLN Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 137 MET Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain f residue 56 ILE Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 84 ASP Chi-restraints excluded: chain h residue 98 HIS Chi-restraints excluded: chain i residue 21 MET Chi-restraints excluded: chain i residue 46 LYS Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 258 SER Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 285 THR Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 33 LYS Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain l residue 127 THR Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 374 ILE Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 512 LYS Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 41 CYS Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain m residue 169 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain o residue 110 ASP Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 115 TYR Chi-restraints excluded: chain p residue 144 THR Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 26 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 339 SER Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 34 ARG Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 136 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain v residue 59 CYS Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 287 ASP Chi-restraints excluded: chain w residue 333 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 1.9990 chunk 743 optimal weight: 1.9990 chunk 678 optimal weight: 1.9990 chunk 723 optimal weight: 0.8980 chunk 435 optimal weight: 10.0000 chunk 314 optimal weight: 0.8980 chunk 567 optimal weight: 4.9990 chunk 221 optimal weight: 0.9980 chunk 653 optimal weight: 10.0000 chunk 683 optimal weight: 0.9980 chunk 720 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN I 73 GLN ** J 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN N 122 GLN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 83 GLN ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 235 ASN l 59 GLN ** l 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 13 GLN p 14 GLN s 194 ASN s 235 ASN u 77 HIS ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 69778 Z= 0.158 Angle : 0.518 16.891 94333 Z= 0.257 Chirality : 0.040 0.184 10187 Planarity : 0.004 0.060 11760 Dihedral : 11.869 177.679 10805 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.37 % Favored : 96.59 % Rotamer: Outliers : 2.59 % Allowed : 19.55 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 1.05 (0.09), residues: 8172 helix: 1.64 (0.08), residues: 4258 sheet: -0.07 (0.25), residues: 441 loop : -0.34 (0.11), residues: 3473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP u 86 HIS 0.009 0.001 HIS u 77 PHE 0.031 0.001 PHE i 292 TYR 0.024 0.001 TYR r 406 ARG 0.007 0.000 ARG n 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1375 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1190 time to evaluate : 6.103 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 CYS cc_start: 0.8920 (m) cc_final: 0.8616 (m) REVERT: A 390 ASP cc_start: 0.8163 (t0) cc_final: 0.7927 (t0) REVERT: B 151 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.9022 (mttt) REVERT: F 73 GLN cc_start: 0.8269 (tp-100) cc_final: 0.7703 (tp40) REVERT: I 73 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.6200 (pt0) REVERT: M 653 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8871 (mt) REVERT: O 89 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: O 150 GLU cc_start: 0.7099 (pp20) cc_final: 0.6851 (pp20) REVERT: O 158 ILE cc_start: 0.6353 (OUTLIER) cc_final: 0.5744 (pp) REVERT: P 240 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8214 (tp30) REVERT: Q 52 MET cc_start: 0.7626 (mmt) cc_final: 0.7311 (mmt) REVERT: Q 197 MET cc_start: 0.8457 (ptp) cc_final: 0.8093 (ptp) REVERT: Q 438 MET cc_start: 0.8888 (mtm) cc_final: 0.8625 (mtp) REVERT: T 78 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7133 (mt-10) REVERT: W 50 MET cc_start: 0.8850 (mmm) cc_final: 0.8570 (mmt) REVERT: X 77 GLU cc_start: 0.7410 (pm20) cc_final: 0.7150 (pm20) REVERT: X 83 VAL cc_start: 0.7983 (t) cc_final: 0.7719 (p) REVERT: X 115 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: Y 50 LEU cc_start: 0.8241 (mp) cc_final: 0.7997 (mp) REVERT: Z 30 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7173 (mt-10) REVERT: Z 34 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7865 (mm-30) REVERT: a 76 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7832 (mp) REVERT: b 9 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8223 (mmmt) REVERT: b 93 LYS cc_start: 0.8448 (mttt) cc_final: 0.8086 (mptt) REVERT: b 99 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: c 173 ASP cc_start: 0.6495 (m-30) cc_final: 0.6074 (m-30) REVERT: d 32 TYR cc_start: 0.7911 (t80) cc_final: 0.7642 (t80) REVERT: d 99 ASP cc_start: 0.9136 (m-30) cc_final: 0.8537 (m-30) REVERT: d 143 TYR cc_start: 0.8976 (m-10) cc_final: 0.8722 (m-10) REVERT: e 83 ASP cc_start: 0.8266 (t70) cc_final: 0.8006 (t0) REVERT: i 21 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8577 (mtm) REVERT: i 68 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.8932 (mmt) REVERT: j 109 LYS cc_start: 0.8570 (mmtt) cc_final: 0.7738 (mmmt) REVERT: k 31 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8416 (mp) REVERT: l 340 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.7841 (t80) REVERT: l 383 MET cc_start: 0.8662 (tpp) cc_final: 0.8252 (tpp) REVERT: l 416 THR cc_start: 0.8145 (m) cc_final: 0.7875 (m) REVERT: l 499 MET cc_start: 0.7282 (ptp) cc_final: 0.6997 (ptt) REVERT: l 504 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8548 (mm) REVERT: l 512 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7609 (tttm) REVERT: l 587 TYR cc_start: 0.8337 (m-10) cc_final: 0.7962 (m-10) REVERT: l 593 ILE cc_start: 0.8816 (mm) cc_final: 0.8550 (mt) REVERT: m 65 LEU cc_start: 0.8931 (tt) cc_final: 0.8666 (tp) REVERT: n 29 ARG cc_start: 0.6813 (mtp-110) cc_final: 0.5589 (mtt180) REVERT: o 30 ARG cc_start: 0.7696 (mmt-90) cc_final: 0.7474 (tpp-160) REVERT: p 59 LYS cc_start: 0.8445 (mptt) cc_final: 0.8144 (tttm) REVERT: p 64 LEU cc_start: 0.8606 (tp) cc_final: 0.8356 (tp) REVERT: p 160 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6783 (tp30) REVERT: r 415 GLN cc_start: 0.8746 (mm-40) cc_final: 0.7810 (mp10) REVERT: s 100 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8994 (mt) REVERT: s 174 MET cc_start: 0.8682 (tpp) cc_final: 0.8462 (tpp) REVERT: s 224 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7310 (m-80) REVERT: u 118 VAL cc_start: 0.8239 (t) cc_final: 0.7943 (p) REVERT: v 96 VAL cc_start: 0.8993 (m) cc_final: 0.8600 (t) REVERT: v 101 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6673 (tm-30) REVERT: w 272 ASP cc_start: 0.7608 (t0) cc_final: 0.7120 (t0) outliers start: 185 outliers final: 132 residues processed: 1315 average time/residue: 0.6499 time to fit residues: 1452.8294 Evaluate side-chains 1295 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1145 time to evaluate : 7.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 73 GLN Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 138 ASP Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 288 ASP Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 653 LEU Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 48 ASN Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 158 ILE Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 137 ASP Chi-restraints excluded: chain Q residue 278 VAL Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 447 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 115 GLN Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 137 MET Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 56 ILE Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 84 ASP Chi-restraints excluded: chain i residue 21 MET Chi-restraints excluded: chain i residue 46 LYS Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 258 SER Chi-restraints excluded: chain i residue 285 THR Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 374 ILE Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 512 LYS Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 41 CYS Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 169 MET Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 115 TYR Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 26 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 265 SER Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain r residue 449 LEU Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain v residue 59 CYS Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 333 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 474 optimal weight: 4.9990 chunk 764 optimal weight: 5.9990 chunk 466 optimal weight: 10.0000 chunk 362 optimal weight: 4.9990 chunk 531 optimal weight: 4.9990 chunk 801 optimal weight: 6.9990 chunk 738 optimal weight: 0.9990 chunk 638 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 493 optimal weight: 3.9990 chunk 391 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 HIS ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN W 76 GLN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 83 GLN ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 235 ASN ** l 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 541 ASN ** p 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 77 HIS ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 69778 Z= 0.269 Angle : 0.630 59.200 94333 Z= 0.340 Chirality : 0.043 0.290 10187 Planarity : 0.004 0.065 11760 Dihedral : 11.872 177.680 10805 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.43 % Favored : 96.52 % Rotamer: Outliers : 2.33 % Allowed : 19.79 % Favored : 77.88 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.19 % 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: 1.02 (0.09), residues: 8172 helix: 1.61 (0.08), residues: 4263 sheet: -0.08 (0.25), residues: 441 loop : -0.34 (0.11), residues: 3468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 100 HIS 0.008 0.001 HIS u 77 PHE 0.031 0.001 PHE i 292 TYR 0.023 0.001 TYR r 406 ARG 0.006 0.000 ARG n 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1315 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1149 time to evaluate : 6.046 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 CYS cc_start: 0.8904 (m) cc_final: 0.8603 (m) REVERT: A 390 ASP cc_start: 0.8180 (t0) cc_final: 0.7939 (t0) REVERT: B 151 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.9025 (mttt) REVERT: F 73 GLN cc_start: 0.8275 (tp-100) cc_final: 0.7708 (tp40) REVERT: I 73 GLN cc_start: 0.6057 (OUTLIER) cc_final: 0.5716 (pt0) REVERT: M 358 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8512 (mp) REVERT: M 653 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8876 (mt) REVERT: O 89 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: O 150 GLU cc_start: 0.7097 (pp20) cc_final: 0.6863 (pp20) REVERT: O 158 ILE cc_start: 0.6380 (OUTLIER) cc_final: 0.5758 (pp) REVERT: P 240 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8219 (tp30) REVERT: Q 52 MET cc_start: 0.7662 (mmt) cc_final: 0.7337 (mmt) REVERT: Q 197 MET cc_start: 0.8505 (ptp) cc_final: 0.8098 (ptp) REVERT: Q 438 MET cc_start: 0.8898 (mtm) cc_final: 0.8634 (mtp) REVERT: T 78 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7159 (mt-10) REVERT: W 50 MET cc_start: 0.8867 (mmm) cc_final: 0.8576 (mmt) REVERT: X 77 GLU cc_start: 0.7416 (pm20) cc_final: 0.7155 (pm20) REVERT: X 83 VAL cc_start: 0.7989 (t) cc_final: 0.7723 (p) REVERT: X 115 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7953 (mm-40) REVERT: Y 50 LEU cc_start: 0.8251 (mp) cc_final: 0.8009 (mp) REVERT: Z 30 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7172 (mt-10) REVERT: Z 34 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7865 (mm-30) REVERT: a 76 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7840 (mp) REVERT: b 9 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8226 (mmmt) REVERT: b 93 LYS cc_start: 0.8458 (mttt) cc_final: 0.8094 (mptt) REVERT: b 99 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: c 173 ASP cc_start: 0.6503 (m-30) cc_final: 0.6097 (m-30) REVERT: d 99 ASP cc_start: 0.9159 (m-30) cc_final: 0.8501 (m-30) REVERT: d 143 TYR cc_start: 0.8982 (m-10) cc_final: 0.8725 (m-10) REVERT: e 83 ASP cc_start: 0.8282 (t70) cc_final: 0.7978 (t0) REVERT: i 21 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8582 (mtm) REVERT: i 68 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8940 (mmt) REVERT: j 109 LYS cc_start: 0.8589 (mmtt) cc_final: 0.7744 (mmmt) REVERT: k 31 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8422 (mp) REVERT: l 340 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.7849 (t80) REVERT: l 383 MET cc_start: 0.8666 (tpp) cc_final: 0.8258 (tpp) REVERT: l 416 THR cc_start: 0.8160 (m) cc_final: 0.7881 (m) REVERT: l 499 MET cc_start: 0.7296 (ptp) cc_final: 0.7004 (ptt) REVERT: l 504 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8557 (mm) REVERT: l 587 TYR cc_start: 0.8344 (m-10) cc_final: 0.7968 (m-10) REVERT: l 593 ILE cc_start: 0.8816 (mm) cc_final: 0.8556 (mt) REVERT: m 65 LEU cc_start: 0.8966 (tt) cc_final: 0.8697 (tp) REVERT: n 29 ARG cc_start: 0.6609 (mtp-110) cc_final: 0.5604 (mtt180) REVERT: o 30 ARG cc_start: 0.7702 (mmt-90) cc_final: 0.7479 (tpp-160) REVERT: p 59 LYS cc_start: 0.8443 (mptt) cc_final: 0.8146 (tttm) REVERT: p 64 LEU cc_start: 0.8612 (tp) cc_final: 0.8370 (tp) REVERT: p 160 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6788 (tp30) REVERT: r 415 GLN cc_start: 0.8753 (mm-40) cc_final: 0.7822 (mp10) REVERT: s 100 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8996 (mt) REVERT: s 174 MET cc_start: 0.8683 (tpp) cc_final: 0.8470 (tpp) REVERT: s 224 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: u 118 VAL cc_start: 0.8246 (t) cc_final: 0.7946 (p) REVERT: v 96 VAL cc_start: 0.8989 (m) cc_final: 0.8606 (t) REVERT: v 101 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6683 (tm-30) REVERT: w 272 ASP cc_start: 0.7673 (t0) cc_final: 0.7181 (t0) outliers start: 166 outliers final: 143 residues processed: 1263 average time/residue: 0.6431 time to fit residues: 1381.7231 Evaluate side-chains 1308 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1147 time to evaluate : 6.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 73 GLN Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 138 ASP Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 288 ASP Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 653 LEU Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 48 ASN Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain O residue 158 ILE Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 137 ASP Chi-restraints excluded: chain Q residue 278 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 447 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 20 ASP Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 115 GLN Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 137 MET Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 56 ILE Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 84 ASP Chi-restraints excluded: chain i residue 21 MET Chi-restraints excluded: chain i residue 46 LYS Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 285 THR Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain l residue 127 THR Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 294 THR Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 374 ILE Chi-restraints excluded: chain l residue 411 MET Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 11 THR Chi-restraints excluded: chain m residue 41 CYS Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 169 MET Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 115 TYR Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 26 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 265 SER Chi-restraints excluded: chain s residue 34 ARG Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain v residue 59 CYS Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 333 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 507 optimal weight: 0.0020 chunk 680 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 588 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 639 optimal weight: 0.7980 chunk 267 optimal weight: 9.9990 chunk 656 optimal weight: 0.0870 chunk 80 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 overall best weight: 0.5366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 83 GLN ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 235 ASN ** l 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 77 HIS ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104578 restraints weight = 107542.153| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.39 r_work: 0.2982 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 69778 Z= 0.269 Angle : 0.630 59.185 94333 Z= 0.340 Chirality : 0.043 0.290 10187 Planarity : 0.004 0.065 11760 Dihedral : 11.872 177.680 10805 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.43 % Favored : 96.52 % Rotamer: Outliers : 2.27 % Allowed : 19.89 % Favored : 77.84 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.19 % 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: 1.02 (0.09), residues: 8172 helix: 1.61 (0.08), residues: 4263 sheet: -0.08 (0.25), residues: 441 loop : -0.34 (0.11), residues: 3468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 100 HIS 0.008 0.001 HIS u 77 PHE 0.031 0.001 PHE i 292 TYR 0.023 0.001 TYR r 406 ARG 0.006 0.000 ARG n 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20693.56 seconds wall clock time: 361 minutes 40.31 seconds (21700.31 seconds total)