Starting phenix.real_space_refine on Thu Mar 14 23:35:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzw_32231/03_2024/7vzw_32231_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzw_32231/03_2024/7vzw_32231.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzw_32231/03_2024/7vzw_32231_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzw_32231/03_2024/7vzw_32231_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzw_32231/03_2024/7vzw_32231_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzw_32231/03_2024/7vzw_32231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzw_32231/03_2024/7vzw_32231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzw_32231/03_2024/7vzw_32231_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzw_32231/03_2024/7vzw_32231_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 45 5.49 5 Mg 1 5.21 5 S 482 5.16 5 C 44166 2.51 5 N 11232 2.21 5 O 12210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 134": "OD1" <-> "OD2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "B ASP 55": "OD1" <-> "OD2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B ASP 137": "OD1" <-> "OD2" Residue "B ASP 165": "OD1" <-> "OD2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B ASP 208": "OD1" <-> "OD2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 52": "OD1" <-> "OD2" Residue "C ASP 101": "OD1" <-> "OD2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 61": "OD1" <-> "OD2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G ASP 91": "OD1" <-> "OD2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G ASP 134": "OD1" <-> "OD2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H ASP 64": "OD1" <-> "OD2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "I ASP 109": "OD1" <-> "OD2" Residue "J GLU 87": "OE1" <-> "OE2" Residue "J PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J ASP 173": "OD1" <-> "OD2" Residue "J GLU 190": "OE1" <-> "OE2" Residue "J PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 234": "OE1" <-> "OE2" Residue "J TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 317": "OD1" <-> "OD2" Residue "J GLU 336": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "L ASP 119": "OD1" <-> "OD2" Residue "L PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 132": "OE1" <-> "OE2" Residue "M PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 255": "OD1" <-> "OD2" Residue "M ASP 288": "OD1" <-> "OD2" Residue "M GLU 310": "OE1" <-> "OE2" Residue "M ASP 364": "OD1" <-> "OD2" Residue "M ASP 509": "OD1" <-> "OD2" Residue "M GLU 660": "OE1" <-> "OE2" Residue "M ASP 698": "OD1" <-> "OD2" Residue "M GLU 716": "OE1" <-> "OE2" Residue "N TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 76": "OD1" <-> "OD2" Residue "N ASP 96": "OD1" <-> "OD2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "N TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 43": "OD1" <-> "OD2" Residue "O ASP 50": "OD1" <-> "OD2" Residue "O ASP 54": "OD1" <-> "OD2" Residue "O TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 146": "OD1" <-> "OD2" Residue "O ASP 206": "OD1" <-> "OD2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P ASP 91": "OD1" <-> "OD2" Residue "P TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 148": "OD1" <-> "OD2" Residue "P PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 234": "OD1" <-> "OD2" Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q ASP 70": "OD1" <-> "OD2" Residue "Q TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 148": "OE1" <-> "OE2" Residue "Q GLU 246": "OE1" <-> "OE2" Residue "Q ASP 360": "OD1" <-> "OD2" Residue "Q ASP 455": "OD1" <-> "OD2" Residue "Q PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 57": "OD1" <-> "OD2" Residue "T GLU 64": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "T GLU 105": "OE1" <-> "OE2" Residue "U PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 60": "OD1" <-> "OD2" Residue "U ASP 65": "OD1" <-> "OD2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "V GLU 82": "OE1" <-> "OE2" Residue "V TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 9": "OD1" <-> "OD2" Residue "W TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "X ASP 111": "OD1" <-> "OD2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X GLU 123": "OE1" <-> "OE2" Residue "X ASP 124": "OD1" <-> "OD2" Residue "X GLU 125": "OE1" <-> "OE2" Residue "X ASP 132": "OD1" <-> "OD2" Residue "X ASP 134": "OD1" <-> "OD2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Y ASP 76": "OD1" <-> "OD2" Residue "Z GLU 25": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "Z ASP 43": "OD1" <-> "OD2" Residue "Z TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 100": "OD1" <-> "OD2" Residue "a GLU 143": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 148": "OE1" <-> "OE2" Residue "a TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 25": "OD1" <-> "OD2" Residue "b TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 108": "OD1" <-> "OD2" Residue "b PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 35": "OD1" <-> "OD2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c ASP 80": "OD1" <-> "OD2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c ASP 96": "OD1" <-> "OD2" Residue "c GLU 148": "OE1" <-> "OE2" Residue "c ASP 173": "OD1" <-> "OD2" Residue "c GLU 177": "OE1" <-> "OE2" Residue "d ASP 6": "OD1" <-> "OD2" Residue "d GLU 12": "OE1" <-> "OE2" Residue "d ASP 38": "OD1" <-> "OD2" Residue "d ASP 42": "OD1" <-> "OD2" Residue "d TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 73": "OD1" <-> "OD2" Residue "d ASP 81": "OD1" <-> "OD2" Residue "d ASP 99": "OD1" <-> "OD2" Residue "d GLU 108": "OE1" <-> "OE2" Residue "d GLU 119": "OE1" <-> "OE2" Residue "d PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 145": "OD1" <-> "OD2" Residue "e GLU 57": "OE1" <-> "OE2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e ASP 79": "OD1" <-> "OD2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "f ASP 65": "OD1" <-> "OD2" Residue "g ASP 91": "OD1" <-> "OD2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g ASP 102": "OD1" <-> "OD2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "h ASP 5": "OD1" <-> "OD2" Residue "h GLU 39": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 59": "OE1" <-> "OE2" Residue "h ASP 61": "OD1" <-> "OD2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 269": "OE1" <-> "OE2" Residue "i GLU 274": "OE1" <-> "OE2" Residue "i TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 105": "OE1" <-> "OE2" Residue "k ASP 88": "OD1" <-> "OD2" Residue "k TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 83": "OD1" <-> "OD2" Residue "l ASP 111": "OD1" <-> "OD2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 238": "OE1" <-> "OE2" Residue "l PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 138": "OE1" <-> "OE2" Residue "m GLU 139": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "n GLU 48": "OE1" <-> "OE2" Residue "o GLU 22": "OE1" <-> "OE2" Residue "o GLU 28": "OE1" <-> "OE2" Residue "o ASP 53": "OD1" <-> "OD2" Residue "o TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "o ASP 122": "OD1" <-> "OD2" Residue "p ASP 49": "OD1" <-> "OD2" Residue "p GLU 123": "OE1" <-> "OE2" Residue "p ASP 162": "OD1" <-> "OD2" Residue "p GLU 176": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 335": "OE1" <-> "OE2" Residue "s TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 192": "OE1" <-> "OE2" Residue "s GLU 204": "OE1" <-> "OE2" Residue "s GLU 206": "OE1" <-> "OE2" Residue "s GLU 214": "OE1" <-> "OE2" Residue "s ASP 248": "OD1" <-> "OD2" Residue "s PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 80": "OE1" <-> "OE2" Residue "u ASP 90": "OD1" <-> "OD2" Residue "u GLU 139": "OE1" <-> "OE2" Residue "u TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 149": "OE1" <-> "OE2" Residue "u GLU 153": "OE1" <-> "OE2" Residue "u ASP 157": "OD1" <-> "OD2" Residue "v TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "v GLU 45": "OE1" <-> "OE2" Residue "v ASP 72": "OD1" <-> "OD2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "v TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 101": "OE1" <-> "OE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "v GLU 105": "OE1" <-> "OE2" Residue "w ASP 63": "OD1" <-> "OD2" Residue "w GLU 79": "OE1" <-> "OE2" Residue "w ASP 145": "OD1" <-> "OD2" Residue "w GLU 251": "OE1" <-> "OE2" Residue "w ASP 265": "OD1" <-> "OD2" Residue "w GLU 303": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 68165 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3326 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} 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: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 690 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1735 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 192} 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: "Q" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3459 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 566 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1161 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "X" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 694 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 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: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2706 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "j" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4816 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 28, 'TRANS': 577} Chain: "m" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1291 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 34 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: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1526 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 160} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "w" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2579 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 170 Unusual residues: {' UQ': 1, 'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "I" 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: "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: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} 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: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 194 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'PLX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 336 Unusual residues: {'CDL': 2, 'PEE': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "m" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "r" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 203 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 130 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2714 SG CYS A 382 48.776 49.883 175.075 1.00 67.32 S ATOM 3056 SG CYS A 425 48.007 46.659 180.821 1.00 63.05 S ATOM 2734 SG CYS A 385 45.344 45.517 175.100 1.00 70.71 S ATOM 2695 SG CYS A 379 43.526 50.709 178.911 1.00 56.06 S ATOM 3957 SG CYS B 113 37.373 64.137 139.599 1.00 61.41 S ATOM 3976 SG CYS B 116 42.579 61.855 143.331 1.00 42.91 S ATOM 3999 SG CYS B 119 43.505 64.418 137.806 1.00 50.10 S ATOM 4328 SG CYS B 162 40.856 58.639 138.662 1.00 54.71 S ATOM 4026 SG CYS B 123 49.690 66.938 133.094 1.00 62.51 S ATOM 4252 SG CYS B 152 47.941 64.849 127.295 1.00 53.15 S ATOM 4299 SG CYS B 158 45.888 61.348 132.154 1.00 55.38 S ATOM 4278 SG CYS B 155 51.913 61.487 130.832 1.00 57.81 S ATOM 5720 SG CYS C 166 54.343 64.452 122.926 1.00 50.05 S ATOM 4992 SG CYS C 72 54.790 65.642 116.676 1.00 58.33 S ATOM 4986 SG CYS C 71 60.101 64.176 119.658 1.00 50.04 S ATOM 5490 SG CYS C 136 56.936 69.552 121.651 1.00 55.07 S ATOM 14942 SG CYS M 131 41.943 62.706 155.475 1.00 61.17 S ATOM 14921 SG CYS M 128 45.357 57.832 152.572 1.00 48.95 S ATOM 14982 SG CYS M 137 47.531 61.344 157.650 1.00 51.19 S ATOM 15314 SG CYS M 179 45.872 62.168 168.729 1.00 54.32 S ATOM 15668 SG CYS M 226 42.863 64.717 164.357 1.00 61.37 S ATOM 15338 SG CYS M 182 40.475 65.051 170.412 1.00 50.57 S ATOM 15291 SG CYS M 176 40.279 59.356 167.248 1.00 49.49 S ATOM 14539 SG CYS M 78 57.596 57.669 172.519 1.00 53.69 S ATOM 14640 SG CYS M 92 55.701 59.822 174.859 1.00 62.14 S ATOM 14428 SG CYS M 64 51.410 59.709 172.628 1.00 62.96 S ATOM 14514 SG CYS M 75 52.461 57.635 169.752 1.00 65.40 S ATOM 21477 SG CYS O 135 32.401 33.012 183.897 1.00 76.34 S ATOM 21511 SG CYS O 140 32.343 29.684 185.191 1.00 73.42 S ATOM 21791 SG CYS O 176 36.795 34.581 186.529 1.00 92.83 S ATOM 21814 SG CYS O 180 37.342 31.272 187.561 1.00 77.63 S ATOM 28550 SG CYS T 86 30.050 51.317 148.065 1.00 67.96 S ATOM 28728 SG CYS T 111 31.105 54.697 148.817 1.00 60.35 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.63 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.63 Time building chain proxies: 26.51, per 1000 atoms: 0.39 Number of scatterers: 68165 At special positions: 0 Unit cell: (216.988, 214.84, 232.027, 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 45 15.00 Mg 1 11.99 O 12210 8.00 N 11232 7.00 C 44166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.03 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: 20.77 Conformation dependent library (CDL) restraints added in 9.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " 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 135 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " 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="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb=" SF4 B 302 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " 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="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " 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="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " 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: 339 helices and 29 sheets defined 51.6% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.83 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 59 removed outlier: 3.679A pdb=" N SER A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 95 through 102 removed outlier: 4.466A 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 148 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 204 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: 3.614A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 376 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.316A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.977A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 Proline residue: A 434 - end of helix removed outlier: 3.553A 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: 3.515A 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: 5.403A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.217A 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 42 through 60 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 111 through 122 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 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: 4.327A 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: 4.342A 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 47 removed outlier: 4.788A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG F 40 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL F 42 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU F 43 " --> pdb=" O ARG F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 95 Processing helix chain 'G' and resid 76 through 88 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 4.005A 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 77 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 65 through 75 Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.730A 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 119 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 223 removed outlier: 3.571A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 4.912A 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: 3.926A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 323 Processing helix chain 'J' and resid 335 through 338 Processing helix chain 'J' and resid 350 through 356 removed outlier: 5.560A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 95 removed outlier: 4.455A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' 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: 3.881A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 138 through 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 219 through 225 removed outlier: 3.929A 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: 3.577A pdb=" N SER M 332 " --> pdb=" O GLY M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 361 removed outlier: 3.812A pdb=" N VAL M 361 " --> pdb=" O LEU M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 378 through 380 No H-bonds generated for 'chain 'M' and resid 378 through 380' Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 392 through 395 removed outlier: 3.525A pdb=" N GLU M 395 " --> pdb=" O ALA M 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 392 through 395' 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 Processing helix chain 'M' and resid 478 through 481 Processing helix chain 'M' and resid 486 through 503 Processing helix chain 'M' and resid 522 through 528 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 557 through 559 No H-bonds generated for 'chain 'M' and resid 557 through 559' Processing helix chain 'M' and resid 589 through 591 No H-bonds generated for 'chain 'M' and resid 589 through 591' 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 673 removed outlier: 3.539A pdb=" N LYS M 673 " --> pdb=" O ASN M 669 " (cutoff:3.500A) Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 4 through 17 removed outlier: 3.662A 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: 3.641A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.304A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 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 210 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.559A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 4.743A 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 174 removed outlier: 3.975A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 41 through 48 removed outlier: 4.271A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY Q 48 " --> pdb=" O ALA Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 126 Processing helix chain 'Q' and resid 133 through 139 removed outlier: 3.968A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 3.991A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 241 through 262 removed outlier: 3.664A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.842A 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: 4.339A 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 438 removed outlier: 4.458A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) 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 30 Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 42 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 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 82 No H-bonds generated for 'chain 'U' and resid 79 through 82' Processing helix chain 'V' and resid 3 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 removed outlier: 3.568A pdb=" N THR W 42 " --> pdb=" O VAL W 38 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU W 43 " --> pdb=" O GLY W 39 " (cutoff:3.500A) Proline residue: W 73 - end of helix removed outlier: 3.703A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASP W 100 " --> pdb=" O ILE W 96 " (cutoff:3.500A) 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 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 through 81 Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' 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: 3.724A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 54 removed outlier: 3.844A 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 86 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 111 No H-bonds generated for 'chain 'a' and resid 109 through 111' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 26 Processing helix chain 'b' and resid 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 148 Processing helix chain 'd' and resid 29 through 57 removed outlier: 4.764A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 116 Processing helix chain 'd' and resid 121 through 124 No H-bonds generated for 'chain 'd' and resid 121 through 124' Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 174 Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 106 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: 3.793A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 7 through 10 No H-bonds generated for 'chain 'h' and resid 7 through 10' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 44 Processing helix chain 'h' and resid 49 through 53 removed outlier: 3.606A pdb=" N GLU h 53 " --> pdb=" O GLY h 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 49 through 53' 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: 4.228A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.744A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 169 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: 3.736A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 271 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.377A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 23 Processing helix chain 'j' and resid 56 through 80 removed outlier: 4.175A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU j 68 " --> pdb=" O LEU j 64 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.538A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.434A 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 21 Processing helix chain 'k' and resid 27 through 51 Processing helix chain 'k' and resid 55 through 85 removed outlier: 3.875A pdb=" N MET k 58 " --> pdb=" O LEU k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix Processing helix chain 'k' and resid 90 through 92 No H-bonds generated for 'chain 'k' and resid 90 through 92' Processing helix chain 'l' and resid 3 through 13 removed outlier: 3.746A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 17 through 23 removed outlier: 4.941A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.574A 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: 3.859A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 132 Processing helix chain 'l' and resid 137 through 155 Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.860A 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: 4.163A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.421A 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 252 through 262 removed outlier: 4.433A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.074A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 272 through 294 removed outlier: 4.395A 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: 4.058A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.927A 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 389 through 400 removed outlier: 4.821A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.707A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 469 removed outlier: 5.796A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.292A 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: 3.713A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.295A 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: 4.138A 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 577 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 27 through 46 Processing helix chain 'm' and resid 50 through 74 Processing helix chain 'm' and resid 87 through 109 Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.194A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 4 through 34 removed outlier: 6.367A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.809A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 23 No H-bonds generated for 'chain 'o' and resid 20 through 23' Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.697A 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 51 removed outlier: 4.293A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 74 Processing helix chain 'p' and resid 93 through 96 removed outlier: 4.357A pdb=" N CYS p 96 " --> pdb=" O ARG p 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 93 through 96' 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: 4.709A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 171 No H-bonds generated for 'chain 'p' and resid 168 through 171' Processing helix chain 'r' and resid 2 through 16 Proline residue: r 7 - end of helix Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.254A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 80 Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 89 through 110 Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.718A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 140 through 171 removed outlier: 4.093A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 4.148A pdb=" N THR r 171 " --> pdb=" O GLN r 168 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.471A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.348A 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: 4.489A pdb=" N GLY r 239 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY r 240 " --> 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 277 removed outlier: 3.777A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 283 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.517A 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 32 Proline residue: s 12 - end of helix removed outlier: 3.665A 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: 4.480A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 3.855A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.106A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.681A 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 204 through 207 No H-bonds generated for 'chain 's' and resid 204 through 207' Processing helix chain 's' and resid 210 through 212 No H-bonds generated for 'chain 's' and resid 210 through 212' Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 284 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 27 Processing helix chain 'u' and resid 29 through 35 Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 79 through 91 Processing helix chain 'u' and resid 102 through 114 Processing helix chain 'v' and resid 3 through 10 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 94 through 96 No H-bonds generated for 'chain 'w' and resid 94 through 96' 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 165 No H-bonds generated for 'chain 'w' and resid 163 through 165' Processing helix chain 'w' and resid 167 through 175 Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.166A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.736A 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 251 removed outlier: 5.150A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix removed outlier: 3.836A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 266 through 274 Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 309 removed outlier: 5.006A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 345 through 347 No H-bonds generated for 'chain 'w' and resid 345 through 347' Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 239 through 244 removed outlier: 3.640A pdb=" N THR A 241 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.064A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.293A 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: 6.634A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.613A 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: 6.902A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.887A 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 264 removed outlier: 7.983A pdb=" N PHE J 263 " --> pdb=" O ALA J 198 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU J 164 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE J 201 " --> pdb=" O LEU J 164 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS J 166 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N SER J 168 " --> pdb=" O PRO J 203 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.732A 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 200 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: 4.470A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.179A 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: 8.185A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.491A 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: 6.568A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.539A 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: 6.723A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.733A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.877A 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 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 83 through 86 Processing sheet with id= Z, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= AA, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.426A 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: 7.024A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'w' and resid 84 through 86 2913 hydrogen bonds defined for protein. 8166 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.19 Time building geometry restraints manager: 22.87 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: 27725 1.40 - 1.62: 41169 1.62 - 1.84: 874 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 69848 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.297 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C18 UQ J 402 " pdb=" C19 UQ J 402 " ideal model delta sigma weight residual 1.336 1.555 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C18 UQ C 304 " pdb=" C19 UQ C 304 " ideal model delta sigma weight residual 1.336 1.555 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C13 UQ C 304 " pdb=" C14 UQ C 304 " ideal model delta sigma weight residual 1.335 1.549 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C13 UQ J 402 " pdb=" C14 UQ J 402 " ideal model delta sigma weight residual 1.335 1.545 -0.210 2.00e-02 2.50e+03 1.11e+02 ... (remaining 69843 not shown) Histogram of bond angle deviations from ideal: 73.63 - 85.78: 76 85.78 - 97.92: 1 97.92 - 110.07: 11480 110.07 - 122.22: 73126 122.22 - 134.37: 9720 Bond angle restraints: 94403 Sorted by residual: angle pdb=" N ARG P 125 " pdb=" CA ARG P 125 " pdb=" C ARG P 125 " ideal model delta sigma weight residual 111.28 120.88 -9.60 1.09e+00 8.42e-01 7.76e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 123.03 -15.29 1.95e+00 2.62e-01 6.13e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 117.14 -13.30 1.91e+00 2.73e-01 4.82e+01 angle pdb=" C51 CDL l 702 " pdb=" CB5 CDL l 702 " pdb=" OB6 CDL l 702 " ideal model delta sigma weight residual 111.33 120.41 -9.08 1.32e+00 5.72e-01 4.72e+01 angle pdb=" C51 CDL m 201 " pdb=" CB5 CDL m 201 " pdb=" OB6 CDL m 201 " ideal model delta sigma weight residual 111.33 120.34 -9.01 1.32e+00 5.72e-01 4.64e+01 ... (remaining 94398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 40639 35.79 - 71.59: 1622 71.59 - 107.38: 102 107.38 - 143.18: 15 143.18 - 178.97: 12 Dihedral angle restraints: 42390 sinusoidal: 18299 harmonic: 24091 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 257.59 82.44 175.15 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 99.70 -159.69 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -144.11 58.11 1 1.00e+01 1.00e-02 4.53e+01 ... (remaining 42387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 9314 0.073 - 0.146: 859 0.146 - 0.219: 24 0.219 - 0.292: 8 0.292 - 0.364: 2 Chirality restraints: 10207 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 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C3D NDP J 401 " pdb=" C2D NDP J 401 " pdb=" C4D NDP J 401 " pdb=" O3D NDP J 401 " both_signs ideal model delta sigma weight residual False -2.71 -2.40 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ARG P 125 " pdb=" N ARG P 125 " pdb=" C ARG P 125 " pdb=" CB ARG P 125 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 10204 not shown) Planarity restraints: 11765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ J 402 " -0.438 2.00e-02 2.50e+03 3.87e-01 1.87e+03 pdb=" C18 UQ J 402 " 0.465 2.00e-02 2.50e+03 pdb=" C19 UQ J 402 " 0.407 2.00e-02 2.50e+03 pdb=" C20 UQ J 402 " -0.017 2.00e-02 2.50e+03 pdb=" C21 UQ J 402 " -0.418 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ J 402 " -0.002 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C11 UQ J 402 " -0.042 2.00e-02 2.50e+03 pdb=" C7 UQ J 402 " -0.310 2.00e-02 2.50e+03 pdb=" C8 UQ J 402 " 0.575 2.00e-02 2.50e+03 pdb=" C9 UQ J 402 " -0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C42 UQ C 304 " -0.303 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C43 UQ C 304 " 0.564 2.00e-02 2.50e+03 pdb=" C44 UQ C 304 " -0.229 2.00e-02 2.50e+03 pdb=" C45 UQ C 304 " -0.060 2.00e-02 2.50e+03 pdb=" C46 UQ C 304 " 0.029 2.00e-02 2.50e+03 ... (remaining 11762 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5826 2.74 - 3.28: 66520 3.28 - 3.82: 114139 3.82 - 4.36: 139499 4.36 - 4.90: 242510 Nonbonded interactions: 568494 Sorted by model distance: nonbonded pdb=" OD2 ASP S 51 " pdb=" OG SER u 22 " model vdw 2.197 2.440 nonbonded pdb=" OE2 GLU X 125 " pdb=" OH TYR Y 44 " model vdw 2.198 2.440 nonbonded pdb=" OG1 THR g 2 " pdb=" OG SER g 5 " model vdw 2.200 2.440 nonbonded pdb=" OH TYR c 62 " pdb=" OD1 ASP c 74 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR X 85 " pdb=" NE1 TRP Z 22 " model vdw 2.210 2.520 ... (remaining 568489 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 69 through 93 or (resid 94 through 97 and (name N or name \ CA or name C or name O or name CB )) or resid 98 through 156 or resid 201)) selection = (chain 'X' and (resid 69 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB )) or resid 108 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=0.63 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.040 Extract box with map and model: 10.170 Check model and map are aligned: 0.760 Set scattering table: 0.470 Process input model: 153.890 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 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 69848 Z= 0.495 Angle : 0.787 17.082 94403 Z= 0.385 Chirality : 0.043 0.364 10207 Planarity : 0.010 0.387 11765 Dihedral : 18.015 178.969 26833 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 0.27 % Allowed : 14.93 % Favored : 84.80 % 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 (0.10), residues: 8172 helix: 1.92 (0.08), residues: 4259 sheet: -0.00 (0.24), residues: 464 loop : -0.56 (0.11), residues: 3449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP u 86 HIS 0.008 0.001 HIS r 30 PHE 0.029 0.001 PHE i 292 TYR 0.021 0.001 TYR l 587 ARG 0.022 0.000 ARG v 21 *********************** 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 1127 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1108 time to evaluate : 6.823 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: E 42 GLU cc_start: 0.8591 (tp30) cc_final: 0.8383 (tp30) REVERT: L 165 SER cc_start: 0.9336 (t) cc_final: 0.8920 (p) REVERT: M 501 ARG cc_start: 0.8135 (ttm-80) cc_final: 0.7709 (ttp-170) REVERT: S 4 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8395 (mm-30) REVERT: V 39 TYR cc_start: 0.8974 (m-80) cc_final: 0.8667 (m-80) REVERT: Z 30 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: h 65 GLU cc_start: 0.8741 (tp30) cc_final: 0.8470 (tp30) REVERT: i 179 MET cc_start: 0.9405 (mmm) cc_final: 0.8900 (mmt) REVERT: j 52 SER cc_start: 0.9161 (t) cc_final: 0.8868 (m) REVERT: n 32 ASP cc_start: 0.8772 (t0) cc_final: 0.8500 (t0) REVERT: p 3 PHE cc_start: 0.8854 (m-80) cc_final: 0.8595 (m-80) REVERT: s 233 MET cc_start: 0.9431 (tmm) cc_final: 0.9223 (tmm) REVERT: s 277 TYR cc_start: 0.8951 (m-80) cc_final: 0.8572 (m-80) outliers start: 19 outliers final: 11 residues processed: 1114 average time/residue: 0.6780 time to fit residues: 1280.8896 Evaluate side-chains 1098 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1086 time to evaluate : 5.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain v residue 47 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 679 optimal weight: 4.9990 chunk 610 optimal weight: 0.7980 chunk 338 optimal weight: 0.7980 chunk 208 optimal weight: 0.1980 chunk 411 optimal weight: 4.9990 chunk 325 optimal weight: 0.7980 chunk 630 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 383 optimal weight: 1.9990 chunk 469 optimal weight: 1.9990 chunk 731 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN L 109 ASN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 247 GLN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 77 HIS v 47 ASN v 110 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.0403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 69848 Z= 0.142 Angle : 0.481 10.513 94403 Z= 0.238 Chirality : 0.039 0.185 10207 Planarity : 0.004 0.082 11765 Dihedral : 14.780 176.597 10680 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.54 % Favored : 96.41 % Rotamer: Outliers : 1.57 % Allowed : 14.14 % Favored : 84.30 % 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: 1.30 (0.10), residues: 8172 helix: 2.04 (0.08), residues: 4242 sheet: 0.02 (0.24), residues: 471 loop : -0.51 (0.11), residues: 3459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP u 86 HIS 0.006 0.001 HIS r 30 PHE 0.027 0.001 PHE i 292 TYR 0.020 0.001 TYR r 406 ARG 0.005 0.000 ARG m 173 *********************** 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 1259 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1147 time to evaluate : 5.893 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8289 (t70) REVERT: B 55 ASP cc_start: 0.8480 (m-30) cc_final: 0.7864 (m-30) REVERT: E 89 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7896 (mt-10) REVERT: M 501 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.7605 (mtm180) REVERT: M 530 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8076 (t80) REVERT: P 161 LYS cc_start: 0.9237 (mmtm) cc_final: 0.9037 (mmtt) REVERT: Q 57 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7575 (pm20) REVERT: Q 455 ASP cc_start: 0.8615 (t0) cc_final: 0.8292 (t0) REVERT: V 39 TYR cc_start: 0.8917 (m-80) cc_final: 0.8588 (m-80) REVERT: W 5 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8240 (tptm) REVERT: h 13 ASP cc_start: 0.9088 (t0) cc_final: 0.8827 (t0) REVERT: h 65 GLU cc_start: 0.8834 (tp30) cc_final: 0.8360 (tp30) REVERT: i 322 GLN cc_start: 0.6676 (mm-40) cc_final: 0.6198 (mm-40) REVERT: j 52 SER cc_start: 0.9163 (t) cc_final: 0.8850 (m) REVERT: l 70 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8967 (m) REVERT: l 145 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8563 (mm-30) REVERT: l 426 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8164 (tt) REVERT: l 544 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8853 (mmm) REVERT: p 3 PHE cc_start: 0.8925 (m-80) cc_final: 0.8670 (m-80) REVERT: s 277 TYR cc_start: 0.8903 (m-80) cc_final: 0.8587 (m-80) REVERT: s 289 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9217 (mm) REVERT: u 12 ASP cc_start: 0.8546 (m-30) cc_final: 0.8301 (m-30) REVERT: v 52 MET cc_start: 0.8334 (mmm) cc_final: 0.8072 (mmt) REVERT: w 120 ASP cc_start: 0.8673 (t0) cc_final: 0.8165 (t0) REVERT: w 145 ASP cc_start: 0.8353 (m-30) cc_final: 0.8071 (m-30) REVERT: w 227 MET cc_start: 0.8553 (mpp) cc_final: 0.8085 (mpp) REVERT: w 241 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.5930 (t80) outliers start: 112 outliers final: 58 residues processed: 1213 average time/residue: 0.6534 time to fit residues: 1347.2755 Evaluate side-chains 1168 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1102 time to evaluate : 5.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain J residue 369 VAL Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 89 LEU Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 80 ASP Chi-restraints excluded: chain d residue 151 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 96 SER Chi-restraints excluded: chain i residue 140 SER Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 335 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 45 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 55 MET Chi-restraints excluded: chain m residue 102 CYS Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain n residue 54 GLU Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain s residue 289 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain v residue 15 LYS Chi-restraints excluded: chain v residue 65 GLN Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 241 TYR 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: 9.9990 chunk 608 optimal weight: 5.9990 chunk 497 optimal weight: 0.6980 chunk 201 optimal weight: 1.9990 chunk 732 optimal weight: 4.9990 chunk 791 optimal weight: 10.0000 chunk 652 optimal weight: 0.9990 chunk 726 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 587 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN H 110 ASN ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 ASN P 247 GLN d 54 GLN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 51 ASN v 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.0488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 69848 Z= 0.206 Angle : 0.494 10.539 94403 Z= 0.245 Chirality : 0.040 0.189 10207 Planarity : 0.004 0.066 11765 Dihedral : 14.024 178.043 10659 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 2.18 % Allowed : 14.12 % Favored : 83.69 % 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: 1.25 (0.10), residues: 8172 helix: 1.99 (0.08), residues: 4261 sheet: 0.03 (0.24), residues: 461 loop : -0.53 (0.11), residues: 3450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP u 86 HIS 0.006 0.001 HIS r 30 PHE 0.030 0.001 PHE i 292 TYR 0.021 0.001 TYR l 587 ARG 0.007 0.000 ARG L 78 *********************** 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 1281 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1125 time to evaluate : 6.966 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7062 (tt0) REVERT: B 54 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.7966 (t) REVERT: B 55 ASP cc_start: 0.8498 (m-30) cc_final: 0.7832 (m-30) REVERT: G 103 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.7620 (m-70) REVERT: M 58 MET cc_start: 0.9097 (tmt) cc_final: 0.8809 (tmt) REVERT: M 107 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7824 (tp30) REVERT: M 501 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7584 (mtm180) REVERT: M 530 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.8198 (t80) REVERT: M 562 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8520 (mppt) REVERT: M 636 TYR cc_start: 0.9325 (OUTLIER) cc_final: 0.9081 (p90) REVERT: P 161 LYS cc_start: 0.9261 (mmtm) cc_final: 0.8927 (mttm) REVERT: Q 57 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: S 59 ARG cc_start: 0.8344 (mtt90) cc_final: 0.7983 (mtm-85) REVERT: W 5 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8251 (tptm) REVERT: W 7 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8925 (tptp) REVERT: b 9 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8609 (tmtt) REVERT: g 109 LYS cc_start: 0.8325 (mttm) cc_final: 0.7886 (mmtp) REVERT: h 5 ASP cc_start: 0.8916 (t0) cc_final: 0.8644 (t0) REVERT: h 13 ASP cc_start: 0.9102 (t0) cc_final: 0.8793 (t0) REVERT: h 65 GLU cc_start: 0.8923 (tp30) cc_final: 0.8598 (tp30) REVERT: j 52 SER cc_start: 0.9219 (t) cc_final: 0.8892 (m) REVERT: l 145 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8575 (mm-30) REVERT: l 544 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8866 (mmm) REVERT: m 87 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8156 (mtpt) REVERT: o 110 ASP cc_start: 0.8543 (m-30) cc_final: 0.8136 (m-30) REVERT: p 3 PHE cc_start: 0.8926 (m-80) cc_final: 0.8631 (m-80) REVERT: p 160 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7564 (tp30) REVERT: r 139 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8728 (mp10) REVERT: r 168 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.8655 (tt0) REVERT: s 22 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8686 (tp) REVERT: s 277 TYR cc_start: 0.8925 (m-80) cc_final: 0.8559 (m-80) REVERT: u 12 ASP cc_start: 0.8550 (m-30) cc_final: 0.8285 (m-30) REVERT: v 52 MET cc_start: 0.8345 (mmm) cc_final: 0.8018 (mmt) REVERT: w 120 ASP cc_start: 0.8744 (t0) cc_final: 0.8427 (t0) REVERT: w 145 ASP cc_start: 0.8502 (m-30) cc_final: 0.8271 (m-30) REVERT: w 227 MET cc_start: 0.8629 (mpp) cc_final: 0.8414 (mpp) REVERT: w 241 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.6211 (t80) outliers start: 156 outliers final: 94 residues processed: 1218 average time/residue: 0.6678 time to fit residues: 1375.9750 Evaluate side-chains 1200 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1091 time to evaluate : 5.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 369 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 562 LYS Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 637 ASP Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 50 MET Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 89 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 80 ASP Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain d residue 151 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 96 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain i residue 140 SER Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 82 SER Chi-restraints excluded: chain l residue 45 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 305 SER Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 55 MET Chi-restraints excluded: chain m residue 102 CYS Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 54 GLU Chi-restraints excluded: chain o residue 30 ARG Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 53 ASN Chi-restraints excluded: chain p residue 160 GLU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 168 GLN Chi-restraints excluded: chain r residue 171 THR Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain v residue 65 GLN Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 0.9980 chunk 550 optimal weight: 5.9990 chunk 380 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 349 optimal weight: 4.9990 chunk 491 optimal weight: 0.6980 chunk 734 optimal weight: 7.9990 chunk 778 optimal weight: 5.9990 chunk 383 optimal weight: 4.9990 chunk 696 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN F 25 GLN H 110 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 ASN i 83 GLN l 135 ASN l 199 GLN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 366 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 69848 Z= 0.370 Angle : 0.565 10.867 94403 Z= 0.283 Chirality : 0.044 0.209 10207 Planarity : 0.004 0.060 11765 Dihedral : 13.652 175.865 10657 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.22 % Favored : 95.72 % Rotamer: Outliers : 2.50 % Allowed : 14.64 % Favored : 82.86 % 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: 1.02 (0.09), residues: 8172 helix: 1.80 (0.08), residues: 4259 sheet: -0.09 (0.24), residues: 455 loop : -0.64 (0.11), residues: 3458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP u 86 HIS 0.007 0.001 HIS i 232 PHE 0.034 0.002 PHE i 292 TYR 0.028 0.002 TYR l 587 ARG 0.006 0.000 ARG g 21 *********************** 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 1281 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1102 time to evaluate : 7.347 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.7058 (tm-30) REVERT: B 55 ASP cc_start: 0.8544 (m-30) cc_final: 0.7932 (m-30) REVERT: G 92 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8349 (mtpp) REVERT: H 48 THR cc_start: 0.9378 (t) cc_final: 0.9136 (p) REVERT: K 74 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7687 (mmm-85) REVERT: K 81 TYR cc_start: 0.9409 (m-10) cc_final: 0.9121 (m-10) REVERT: M 58 MET cc_start: 0.9136 (tmt) cc_final: 0.8919 (tmt) REVERT: M 107 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: M 530 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.8328 (t80) REVERT: Q 57 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7594 (pm20) REVERT: S 59 ARG cc_start: 0.8440 (mtt90) cc_final: 0.8029 (mtm-85) REVERT: V 44 LYS cc_start: 0.8660 (mmtp) cc_final: 0.8401 (mmtp) REVERT: V 106 ARG cc_start: 0.7415 (tpp-160) cc_final: 0.6362 (mtt-85) REVERT: W 5 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8244 (tptm) REVERT: W 7 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8908 (tptp) REVERT: W 125 TYR cc_start: 0.9476 (m-80) cc_final: 0.8842 (m-80) REVERT: b 9 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8472 (tmtt) REVERT: g 109 LYS cc_start: 0.8272 (mttm) cc_final: 0.7932 (mmtp) REVERT: h 5 ASP cc_start: 0.9010 (t0) cc_final: 0.8574 (t0) REVERT: h 13 ASP cc_start: 0.9110 (t0) cc_final: 0.8846 (t0) REVERT: i 40 MET cc_start: 0.9066 (tpp) cc_final: 0.8127 (tpp) REVERT: j 52 SER cc_start: 0.9272 (t) cc_final: 0.8964 (m) REVERT: j 101 SER cc_start: 0.9363 (OUTLIER) cc_final: 0.8965 (p) REVERT: l 145 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8630 (mm-30) REVERT: m 87 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8251 (mtpt) REVERT: o 110 ASP cc_start: 0.8541 (m-30) cc_final: 0.8101 (m-30) REVERT: p 160 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7619 (tp30) REVERT: r 139 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8690 (mp10) REVERT: r 168 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8746 (tt0) REVERT: w 241 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.6256 (t80) outliers start: 179 outliers final: 127 residues processed: 1206 average time/residue: 0.6710 time to fit residues: 1367.8630 Evaluate side-chains 1221 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1082 time to evaluate : 5.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 369 VAL Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 434 SER Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain U residue 15 LYS Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 69 ILE Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 50 MET Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 89 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 121 LYS Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 122 THR Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 151 SER Chi-restraints excluded: chain e residue 96 SER Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain i residue 54 GLU Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 140 SER Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 82 SER Chi-restraints excluded: chain l residue 45 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 55 MET Chi-restraints excluded: chain m residue 102 CYS Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain m residue 141 MET Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 54 GLU Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 160 GLU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 168 GLN Chi-restraints excluded: chain r residue 171 THR Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 243 MET Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 253 LEU Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain v residue 15 LYS Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 0.8980 chunk 441 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 579 optimal weight: 5.9990 chunk 321 optimal weight: 0.6980 chunk 664 optimal weight: 0.9980 chunk 537 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 397 optimal weight: 5.9990 chunk 698 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 99 GLN F 25 GLN L 88 GLN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 133 GLN d 134 GLN e 86 ASN l 2 ASN l 59 GLN l 135 ASN l 175 ASN l 199 GLN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 366 ASN v 44 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 69848 Z= 0.241 Angle : 0.514 10.573 94403 Z= 0.258 Chirality : 0.041 0.195 10207 Planarity : 0.004 0.060 11765 Dihedral : 13.152 175.436 10657 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.85 % Favored : 96.08 % Rotamer: Outliers : 2.45 % Allowed : 15.13 % Favored : 82.42 % 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: 1.84 (0.08), residues: 4247 sheet: -0.08 (0.24), residues: 453 loop : -0.62 (0.11), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP u 86 HIS 0.005 0.001 HIS r 30 PHE 0.029 0.001 PHE i 292 TYR 0.021 0.001 TYR l 587 ARG 0.005 0.000 ARG m 173 *********************** 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 1274 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1099 time to evaluate : 6.024 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: A 327 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8984 (pt) REVERT: B 54 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8181 (t) REVERT: B 55 ASP cc_start: 0.8537 (m-30) cc_final: 0.7902 (m-30) REVERT: G 92 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8391 (mtpp) REVERT: G 103 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.7452 (m-70) REVERT: G 106 LYS cc_start: 0.8601 (mtmt) cc_final: 0.8360 (mtmt) REVERT: J 322 VAL cc_start: 0.9477 (OUTLIER) cc_final: 0.9275 (p) REVERT: K 74 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7693 (mmm-85) REVERT: K 81 TYR cc_start: 0.9386 (m-10) cc_final: 0.9117 (m-10) REVERT: M 58 MET cc_start: 0.9138 (tmt) cc_final: 0.8925 (tmt) REVERT: M 107 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7768 (tp30) REVERT: M 530 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.8326 (t80) REVERT: M 562 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8546 (mppt) REVERT: Q 57 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7711 (pm20) REVERT: S 59 ARG cc_start: 0.8415 (mtt90) cc_final: 0.8022 (mtm-85) REVERT: V 44 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8320 (mmtp) REVERT: W 5 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8197 (tptm) REVERT: W 7 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8870 (tptp) REVERT: b 9 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8459 (tmtt) REVERT: b 103 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8796 (mtt180) REVERT: c 140 MET cc_start: 0.8898 (mmt) cc_final: 0.8675 (mmt) REVERT: c 173 ASP cc_start: 0.8720 (t0) cc_final: 0.8412 (t0) REVERT: g 109 LYS cc_start: 0.8308 (mttm) cc_final: 0.7863 (mmtp) REVERT: h 5 ASP cc_start: 0.8983 (t0) cc_final: 0.8557 (t0) REVERT: h 13 ASP cc_start: 0.9134 (t0) cc_final: 0.8900 (t0) REVERT: l 145 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8596 (mm-30) REVERT: l 401 MET cc_start: 0.8755 (ptm) cc_final: 0.8470 (ptm) REVERT: m 87 LYS cc_start: 0.8750 (ttmm) cc_final: 0.8231 (mtpt) REVERT: o 110 ASP cc_start: 0.8523 (m-30) cc_final: 0.8056 (m-30) REVERT: p 160 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7602 (tp30) REVERT: r 139 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8660 (mp10) REVERT: r 168 GLN cc_start: 0.9367 (OUTLIER) cc_final: 0.8728 (tt0) REVERT: r 437 MET cc_start: 0.9368 (OUTLIER) cc_final: 0.9108 (mmt) REVERT: r 441 ILE cc_start: 0.9090 (tp) cc_final: 0.8874 (tp) REVERT: v 15 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8689 (tttp) REVERT: w 120 ASP cc_start: 0.8827 (t0) cc_final: 0.8223 (t0) REVERT: w 227 MET cc_start: 0.8610 (mpp) cc_final: 0.8223 (mpp) REVERT: w 241 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.6312 (t80) outliers start: 175 outliers final: 123 residues processed: 1205 average time/residue: 0.6638 time to fit residues: 1354.9220 Evaluate side-chains 1219 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1077 time to evaluate : 5.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 369 VAL Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 434 SER Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 562 LYS Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 50 MET Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 89 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 103 ARG Chi-restraints excluded: chain b residue 121 LYS Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 80 ASP Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 12 GLU Chi-restraints excluded: chain d residue 151 SER Chi-restraints excluded: chain e residue 96 SER Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 140 SER Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 82 SER Chi-restraints excluded: chain l residue 45 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 55 MET Chi-restraints excluded: chain m residue 102 CYS Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 126 VAL Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 54 GLU Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 53 ASN Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain p residue 160 GLU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 168 GLN Chi-restraints excluded: chain r residue 171 THR Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 205 VAL Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain r residue 437 MET Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain v residue 15 LYS Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 0.8980 chunk 700 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 456 optimal weight: 5.9990 chunk 192 optimal weight: 0.0980 chunk 778 optimal weight: 0.0070 chunk 646 optimal weight: 6.9990 chunk 360 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 257 optimal weight: 0.9990 chunk 408 optimal weight: 9.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 99 GLN F 25 GLN J 356 HIS L 88 GLN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 247 GLN d 134 GLN l 2 ASN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 44 GLN v 54 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 69848 Z= 0.140 Angle : 0.477 11.882 94403 Z= 0.239 Chirality : 0.039 0.187 10207 Planarity : 0.004 0.057 11765 Dihedral : 12.358 174.005 10657 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 1.96 % Allowed : 15.79 % Favored : 82.25 % 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: 1.25 (0.10), residues: 8172 helix: 1.98 (0.08), residues: 4270 sheet: 0.04 (0.24), residues: 459 loop : -0.53 (0.11), residues: 3443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP u 86 HIS 0.008 0.000 HIS r 30 PHE 0.027 0.001 PHE i 292 TYR 0.021 0.001 TYR r 406 ARG 0.007 0.000 ARG v 21 *********************** 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 1277 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1137 time to evaluate : 6.058 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: A 327 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8986 (pt) REVERT: B 54 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8068 (t) REVERT: B 55 ASP cc_start: 0.8489 (m-30) cc_final: 0.7824 (m-30) REVERT: E 42 GLU cc_start: 0.8498 (tp30) cc_final: 0.8251 (tp30) REVERT: E 89 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8169 (mt-10) REVERT: G 92 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8422 (mtpp) REVERT: G 103 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7330 (m-70) REVERT: G 106 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8326 (mtmt) REVERT: H 79 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8192 (mt-10) REVERT: K 74 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7715 (mmm-85) REVERT: K 81 TYR cc_start: 0.9350 (m-10) cc_final: 0.9059 (m-10) REVERT: M 58 MET cc_start: 0.9108 (tmt) cc_final: 0.8852 (tmt) REVERT: M 107 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7732 (tp30) REVERT: M 530 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8120 (t80) REVERT: M 562 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8527 (mppt) REVERT: S 59 ARG cc_start: 0.8391 (mtt90) cc_final: 0.8012 (mtm-85) REVERT: T 51 ARG cc_start: 0.9022 (mtm180) cc_final: 0.8763 (mtm180) REVERT: W 5 LYS cc_start: 0.8572 (mmmt) cc_final: 0.8228 (tptp) REVERT: W 7 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8852 (tptp) REVERT: Z 30 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7733 (mt-10) REVERT: b 9 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8520 (tmtt) REVERT: c 140 MET cc_start: 0.8860 (mmt) cc_final: 0.8654 (mmt) REVERT: c 173 ASP cc_start: 0.8572 (t0) cc_final: 0.8197 (t0) REVERT: g 109 LYS cc_start: 0.8353 (mttm) cc_final: 0.8031 (mmtp) REVERT: h 5 ASP cc_start: 0.8973 (t0) cc_final: 0.8645 (t0) REVERT: h 13 ASP cc_start: 0.9138 (t0) cc_final: 0.8845 (t0) REVERT: i 40 MET cc_start: 0.8832 (tpp) cc_final: 0.8223 (tpp) REVERT: i 258 SER cc_start: 0.9546 (t) cc_final: 0.9318 (m) REVERT: j 52 SER cc_start: 0.9236 (t) cc_final: 0.8891 (m) REVERT: l 145 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8624 (mm-30) REVERT: l 544 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8869 (mmm) REVERT: m 87 LYS cc_start: 0.8618 (ttmm) cc_final: 0.8115 (mtpt) REVERT: o 110 ASP cc_start: 0.8517 (m-30) cc_final: 0.8053 (m-30) REVERT: p 160 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7491 (tp30) REVERT: r 168 GLN cc_start: 0.9364 (OUTLIER) cc_final: 0.8668 (tt0) REVERT: r 441 ILE cc_start: 0.9037 (tp) cc_final: 0.8833 (tp) REVERT: s 22 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8665 (tp) REVERT: s 24 GLU cc_start: 0.8999 (tt0) cc_final: 0.8772 (tt0) REVERT: s 224 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8272 (t80) REVERT: s 277 TYR cc_start: 0.8927 (m-80) cc_final: 0.8647 (m-80) REVERT: w 120 ASP cc_start: 0.8703 (t0) cc_final: 0.8099 (t0) REVERT: w 227 MET cc_start: 0.8574 (mpp) cc_final: 0.8346 (mpp) REVERT: w 241 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.6351 (t80) outliers start: 140 outliers final: 100 residues processed: 1219 average time/residue: 0.6636 time to fit residues: 1370.6868 Evaluate side-chains 1220 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1104 time to evaluate : 7.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 369 VAL Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 434 SER Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 562 LYS Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 451 ILE Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 89 LEU Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 80 ASP Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 151 SER Chi-restraints excluded: chain e residue 90 VAL Chi-restraints excluded: chain e residue 96 SER Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 140 SER Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 285 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 45 THR Chi-restraints excluded: chain l residue 61 MET Chi-restraints excluded: chain l residue 104 SER Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 503 GLU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 126 VAL Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 54 GLU Chi-restraints excluded: chain p residue 53 ASN Chi-restraints excluded: chain p residue 160 GLU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 168 GLN Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 443 optimal weight: 0.2980 chunk 568 optimal weight: 4.9990 chunk 440 optimal weight: 4.9990 chunk 655 optimal weight: 0.9990 chunk 434 optimal weight: 9.9990 chunk 775 optimal weight: 0.8980 chunk 485 optimal weight: 6.9990 chunk 473 optimal weight: 8.9990 chunk 358 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN F 25 GLN I 29 GLN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN T 63 ASN d 134 GLN g 14 GLN l 135 ASN l 199 GLN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 366 ASN v 54 GLN v 110 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 69848 Z= 0.303 Angle : 0.539 11.983 94403 Z= 0.268 Chirality : 0.042 0.210 10207 Planarity : 0.004 0.058 11765 Dihedral : 12.256 175.537 10656 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.96 % Favored : 95.99 % Rotamer: Outliers : 2.38 % Allowed : 15.68 % Favored : 81.95 % 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: 1.10 (0.10), residues: 8172 helix: 1.84 (0.08), residues: 4288 sheet: -0.01 (0.24), residues: 459 loop : -0.58 (0.11), residues: 3425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP u 86 HIS 0.006 0.001 HIS i 232 PHE 0.033 0.001 PHE i 292 TYR 0.025 0.001 TYR l 587 ARG 0.010 0.000 ARG v 21 *********************** 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 1266 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1096 time to evaluate : 6.509 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7004 (tm-30) REVERT: A 327 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8993 (pt) REVERT: B 54 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8211 (t) REVERT: B 55 ASP cc_start: 0.8504 (m-30) cc_final: 0.7868 (m-30) REVERT: F 89 ARG cc_start: 0.8752 (ttp80) cc_final: 0.8206 (mtm110) REVERT: G 92 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8437 (mtpp) REVERT: G 103 HIS cc_start: 0.8069 (OUTLIER) cc_final: 0.7423 (m-70) REVERT: G 106 LYS cc_start: 0.8616 (mtmt) cc_final: 0.8356 (mtmt) REVERT: H 48 THR cc_start: 0.9378 (t) cc_final: 0.9147 (p) REVERT: H 89 SER cc_start: 0.9152 (m) cc_final: 0.8833 (p) REVERT: K 74 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7726 (mmm-85) REVERT: K 81 TYR cc_start: 0.9423 (m-10) cc_final: 0.9171 (m-10) REVERT: M 107 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7974 (tp30) REVERT: M 530 TYR cc_start: 0.9034 (OUTLIER) cc_final: 0.8226 (t80) REVERT: S 59 ARG cc_start: 0.8423 (mtt90) cc_final: 0.8039 (mtm-85) REVERT: V 44 LYS cc_start: 0.8605 (mmtp) cc_final: 0.8342 (mmtp) REVERT: W 5 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8194 (tptm) REVERT: W 7 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8888 (tptp) REVERT: W 10 MET cc_start: 0.9442 (mmm) cc_final: 0.8954 (mmm) REVERT: W 72 MET cc_start: 0.8949 (ttm) cc_final: 0.8517 (mtt) REVERT: W 125 TYR cc_start: 0.9473 (m-80) cc_final: 0.8912 (m-80) REVERT: X 82 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8014 (mtt180) REVERT: Z 30 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: Z 49 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: Z 59 ASN cc_start: 0.8142 (p0) cc_final: 0.7880 (p0) REVERT: b 9 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8493 (tmtt) REVERT: b 103 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8755 (mtt180) REVERT: c 173 ASP cc_start: 0.8737 (t0) cc_final: 0.8478 (t70) REVERT: g 109 LYS cc_start: 0.8329 (mttm) cc_final: 0.7897 (mmtp) REVERT: h 5 ASP cc_start: 0.9025 (t0) cc_final: 0.8660 (t0) REVERT: h 13 ASP cc_start: 0.9151 (t0) cc_final: 0.8863 (t0) REVERT: i 40 MET cc_start: 0.8984 (tpp) cc_final: 0.8242 (tpp) REVERT: i 258 SER cc_start: 0.9565 (t) cc_final: 0.9305 (m) REVERT: j 52 SER cc_start: 0.9280 (t) cc_final: 0.9021 (t) REVERT: j 63 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9050 (mt) REVERT: l 145 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8637 (mm-30) REVERT: l 544 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8884 (mmm) REVERT: m 87 LYS cc_start: 0.8762 (ttmm) cc_final: 0.8246 (mtpt) REVERT: n 54 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: o 110 ASP cc_start: 0.8513 (m-30) cc_final: 0.8043 (m-30) REVERT: p 160 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7591 (tp30) REVERT: r 168 GLN cc_start: 0.9389 (OUTLIER) cc_final: 0.8735 (tt0) REVERT: r 441 ILE cc_start: 0.9090 (tp) cc_final: 0.8870 (tp) REVERT: w 120 ASP cc_start: 0.8832 (t0) cc_final: 0.8210 (t0) REVERT: w 145 ASP cc_start: 0.8542 (m-30) cc_final: 0.8273 (m-30) REVERT: w 227 MET cc_start: 0.8605 (mpp) cc_final: 0.8363 (mpp) REVERT: w 241 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.6336 (t80) outliers start: 170 outliers final: 124 residues processed: 1209 average time/residue: 0.6645 time to fit residues: 1358.8126 Evaluate side-chains 1225 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1081 time to evaluate : 5.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 369 VAL Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 434 SER Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 610 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain U residue 15 LYS Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 50 MET Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 82 ARG Chi-restraints excluded: chain X residue 89 LEU Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 103 ARG Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 80 ASP Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 122 THR Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 151 SER Chi-restraints excluded: chain e residue 96 SER Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 140 SER Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 285 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 63 LEU Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 82 SER Chi-restraints excluded: chain l residue 45 THR Chi-restraints excluded: chain l residue 61 MET Chi-restraints excluded: chain l residue 104 SER Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 355 ASP Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 55 MET Chi-restraints excluded: chain m residue 102 CYS Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 126 VAL Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 54 GLU Chi-restraints excluded: chain o residue 56 ARG Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 160 GLU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 168 GLN Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 205 VAL Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain s residue 139 THR Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 354 LEU 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: 0.8980 chunk 463 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 152 optimal weight: 0.1980 chunk 150 optimal weight: 0.1980 chunk 493 optimal weight: 0.8980 chunk 528 optimal weight: 0.9980 chunk 383 optimal weight: 0.9980 chunk 72 optimal weight: 0.2980 chunk 609 optimal weight: 5.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 99 GLN I 29 GLN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 247 GLN g 14 GLN j 26 GLN l 135 ASN l 199 GLN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 251 ASN r 366 ASN v 54 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 69848 Z= 0.135 Angle : 0.483 13.720 94403 Z= 0.241 Chirality : 0.039 0.216 10207 Planarity : 0.004 0.056 11765 Dihedral : 11.685 173.532 10656 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 1.75 % Allowed : 16.43 % Favored : 81.82 % 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: 1.26 (0.10), residues: 8172 helix: 2.00 (0.08), residues: 4267 sheet: 0.09 (0.25), residues: 458 loop : -0.53 (0.11), residues: 3447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP l 144 HIS 0.006 0.000 HIS r 30 PHE 0.026 0.001 PHE i 292 TYR 0.023 0.001 TYR r 406 ARG 0.010 0.000 ARG v 21 *********************** 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 1241 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1116 time to evaluate : 6.208 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7037 (tt0) REVERT: A 327 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8987 (pt) REVERT: B 54 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8097 (t) REVERT: B 55 ASP cc_start: 0.8504 (m-30) cc_final: 0.7847 (m-30) REVERT: E 42 GLU cc_start: 0.8465 (tp30) cc_final: 0.8213 (tp30) REVERT: G 92 LYS cc_start: 0.8826 (ttmm) cc_final: 0.8462 (mtpp) REVERT: G 103 HIS cc_start: 0.8160 (OUTLIER) cc_final: 0.7435 (m-70) REVERT: G 106 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8308 (mtmt) REVERT: H 79 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8224 (mt-10) REVERT: H 89 SER cc_start: 0.9125 (m) cc_final: 0.8849 (p) REVERT: K 74 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7749 (mmm-85) REVERT: K 81 TYR cc_start: 0.9340 (m-10) cc_final: 0.9069 (m-10) REVERT: M 58 MET cc_start: 0.9122 (tmt) cc_final: 0.8912 (tmt) REVERT: M 530 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.8102 (t80) REVERT: S 59 ARG cc_start: 0.8388 (mtt90) cc_final: 0.8039 (mtm-85) REVERT: W 5 LYS cc_start: 0.8599 (mmmt) cc_final: 0.8242 (tptp) REVERT: W 72 MET cc_start: 0.8903 (ttm) cc_final: 0.8478 (mtt) REVERT: c 173 ASP cc_start: 0.8584 (t0) cc_final: 0.8263 (t0) REVERT: e 114 MET cc_start: 0.8459 (mmt) cc_final: 0.7718 (mtm) REVERT: g 109 LYS cc_start: 0.8339 (mttm) cc_final: 0.8005 (mmtp) REVERT: h 5 ASP cc_start: 0.8982 (t0) cc_final: 0.8639 (t0) REVERT: h 13 ASP cc_start: 0.9105 (t0) cc_final: 0.8813 (t0) REVERT: i 258 SER cc_start: 0.9558 (t) cc_final: 0.9336 (m) REVERT: i 343 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9032 (pp) REVERT: j 52 SER cc_start: 0.9235 (t) cc_final: 0.8956 (t) REVERT: l 145 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8592 (mm-30) REVERT: l 544 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8803 (mmm) REVERT: m 87 LYS cc_start: 0.8653 (ttmm) cc_final: 0.8136 (mtpt) REVERT: n 54 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7619 (pm20) REVERT: o 110 ASP cc_start: 0.8522 (m-30) cc_final: 0.8055 (m-30) REVERT: p 160 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7592 (tp30) REVERT: r 168 GLN cc_start: 0.9354 (OUTLIER) cc_final: 0.8677 (tt0) REVERT: r 437 MET cc_start: 0.9390 (mmt) cc_final: 0.9088 (mmt) REVERT: s 22 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8598 (tp) REVERT: s 277 TYR cc_start: 0.8928 (m-80) cc_final: 0.8644 (m-80) REVERT: v 101 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8395 (tp30) REVERT: w 120 ASP cc_start: 0.8681 (t0) cc_final: 0.8019 (t0) REVERT: w 145 ASP cc_start: 0.8397 (m-30) cc_final: 0.8064 (m-30) REVERT: w 227 MET cc_start: 0.8617 (mpp) cc_final: 0.8410 (mpp) REVERT: w 241 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.6360 (t80) outliers start: 125 outliers final: 88 residues processed: 1188 average time/residue: 0.7100 time to fit residues: 1437.9011 Evaluate side-chains 1190 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1089 time to evaluate : 6.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 369 VAL Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 451 ILE Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 89 LEU Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 80 ASP Chi-restraints excluded: chain e residue 96 SER Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 140 SER Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 45 THR Chi-restraints excluded: chain l residue 65 ASN Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 54 GLU Chi-restraints excluded: chain o residue 56 ARG Chi-restraints excluded: chain p residue 53 ASN Chi-restraints excluded: chain p residue 160 GLU Chi-restraints excluded: chain r residue 168 GLN Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 205 VAL Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 289 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 0.7980 chunk 743 optimal weight: 0.7980 chunk 678 optimal weight: 0.9980 chunk 723 optimal weight: 2.9990 chunk 435 optimal weight: 3.9990 chunk 314 optimal weight: 3.9990 chunk 567 optimal weight: 0.7980 chunk 221 optimal weight: 0.6980 chunk 653 optimal weight: 8.9990 chunk 683 optimal weight: 0.8980 chunk 720 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 247 GLN Z 33 GLN d 134 GLN e 148 GLN g 14 GLN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 366 ASN v 54 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 69848 Z= 0.153 Angle : 0.488 13.693 94403 Z= 0.242 Chirality : 0.039 0.248 10207 Planarity : 0.004 0.056 11765 Dihedral : 11.430 173.837 10656 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.57 % Favored : 96.38 % Rotamer: Outliers : 1.61 % Allowed : 16.68 % Favored : 81.71 % 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: 1.30 (0.10), residues: 8172 helix: 2.01 (0.08), residues: 4277 sheet: 0.09 (0.25), residues: 460 loop : -0.48 (0.11), residues: 3435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Q 202 HIS 0.006 0.001 HIS r 30 PHE 0.029 0.001 PHE i 292 TYR 0.021 0.001 TYR u 32 ARG 0.008 0.000 ARG v 21 *********************** 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 1222 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1107 time to evaluate : 5.953 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: A 327 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8980 (pt) REVERT: B 54 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8104 (t) REVERT: B 55 ASP cc_start: 0.8499 (m-30) cc_final: 0.7826 (m-30) REVERT: E 42 GLU cc_start: 0.8439 (tp30) cc_final: 0.8173 (tp30) REVERT: F 89 ARG cc_start: 0.8681 (ttp80) cc_final: 0.8447 (mtm110) REVERT: G 92 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8471 (mtpp) REVERT: G 103 HIS cc_start: 0.8149 (OUTLIER) cc_final: 0.7447 (m-70) REVERT: G 106 LYS cc_start: 0.8508 (mtmt) cc_final: 0.8258 (mtmt) REVERT: H 79 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8209 (mt-10) REVERT: H 89 SER cc_start: 0.9114 (m) cc_final: 0.8808 (p) REVERT: K 81 TYR cc_start: 0.9338 (m-10) cc_final: 0.9084 (m-10) REVERT: M 58 MET cc_start: 0.9128 (tmt) cc_final: 0.8903 (tmt) REVERT: M 107 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7720 (tp30) REVERT: M 530 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.8114 (t80) REVERT: S 59 ARG cc_start: 0.8396 (mtt90) cc_final: 0.8054 (mtm-85) REVERT: W 5 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8316 (tptp) REVERT: W 72 MET cc_start: 0.8892 (ttm) cc_final: 0.8485 (mtt) REVERT: Y 95 GLU cc_start: 0.8859 (tp30) cc_final: 0.8547 (tp30) REVERT: Z 86 TYR cc_start: 0.6778 (t80) cc_final: 0.6508 (t80) REVERT: b 111 LEU cc_start: 0.8688 (mt) cc_final: 0.8481 (mt) REVERT: c 173 ASP cc_start: 0.8581 (t0) cc_final: 0.8267 (t0) REVERT: e 114 MET cc_start: 0.8456 (mmt) cc_final: 0.7730 (mtm) REVERT: g 109 LYS cc_start: 0.8303 (mttm) cc_final: 0.7879 (mmtp) REVERT: h 5 ASP cc_start: 0.9018 (t0) cc_final: 0.8556 (t0) REVERT: h 13 ASP cc_start: 0.9107 (t0) cc_final: 0.8832 (t0) REVERT: i 40 MET cc_start: 0.9016 (tpp) cc_final: 0.8275 (tpp) REVERT: i 343 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9025 (pp) REVERT: j 52 SER cc_start: 0.9240 (t) cc_final: 0.8961 (t) REVERT: l 145 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8615 (mm-30) REVERT: l 426 ILE cc_start: 0.8372 (mt) cc_final: 0.8158 (tt) REVERT: l 544 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8789 (mmm) REVERT: m 87 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8147 (mtpt) REVERT: n 54 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7665 (pm20) REVERT: o 110 ASP cc_start: 0.8517 (m-30) cc_final: 0.8051 (m-30) REVERT: p 160 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7609 (tp30) REVERT: r 168 GLN cc_start: 0.9371 (OUTLIER) cc_final: 0.8719 (tt0) REVERT: s 22 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8631 (tp) REVERT: s 277 TYR cc_start: 0.8913 (m-80) cc_final: 0.8623 (m-80) REVERT: w 120 ASP cc_start: 0.8674 (t0) cc_final: 0.7956 (t0) REVERT: w 145 ASP cc_start: 0.8391 (m-30) cc_final: 0.8039 (m-30) REVERT: w 227 MET cc_start: 0.8651 (mpp) cc_final: 0.8427 (mpp) REVERT: w 241 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.6351 (t80) outliers start: 115 outliers final: 87 residues processed: 1175 average time/residue: 0.6656 time to fit residues: 1325.8015 Evaluate side-chains 1188 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1088 time to evaluate : 5.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 369 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 451 ILE Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 89 LEU Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 80 ASP Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain e residue 96 SER Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 140 SER Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 45 THR Chi-restraints excluded: chain l residue 65 ASN Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 54 GLU Chi-restraints excluded: chain o residue 56 ARG Chi-restraints excluded: chain p residue 160 GLU Chi-restraints excluded: chain r residue 168 GLN Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 205 VAL Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 289 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR 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: 9.9990 chunk 466 optimal weight: 3.9990 chunk 362 optimal weight: 1.9990 chunk 531 optimal weight: 6.9990 chunk 801 optimal weight: 5.9990 chunk 738 optimal weight: 0.9980 chunk 638 optimal weight: 5.9990 chunk 66 optimal weight: 0.1980 chunk 493 optimal weight: 0.7980 chunk 391 optimal weight: 0.0970 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 148 GLN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 366 ASN v 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 69848 Z= 0.153 Angle : 0.491 14.735 94403 Z= 0.242 Chirality : 0.039 0.256 10207 Planarity : 0.004 0.069 11765 Dihedral : 11.212 173.677 10656 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 1.48 % Allowed : 16.88 % Favored : 81.64 % 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: 1.31 (0.10), residues: 8172 helix: 2.02 (0.08), residues: 4271 sheet: 0.10 (0.25), residues: 460 loop : -0.47 (0.11), residues: 3441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP u 86 HIS 0.005 0.000 HIS r 30 PHE 0.028 0.001 PHE i 292 TYR 0.020 0.001 TYR r 406 ARG 0.009 0.000 ARG v 21 ********************** 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 1211 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1105 time to evaluate : 5.998 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7010 (tt0) REVERT: A 327 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8977 (pt) REVERT: B 54 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8104 (t) REVERT: B 55 ASP cc_start: 0.8479 (m-30) cc_final: 0.7818 (m-30) REVERT: E 42 GLU cc_start: 0.8440 (tp30) cc_final: 0.8172 (tp30) REVERT: F 31 GLN cc_start: 0.8225 (tp-100) cc_final: 0.7931 (tp40) REVERT: G 92 LYS cc_start: 0.8848 (ttmm) cc_final: 0.8453 (mtpp) REVERT: G 103 HIS cc_start: 0.8129 (OUTLIER) cc_final: 0.7233 (m-70) REVERT: G 106 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8315 (mtmt) REVERT: G 108 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7860 (mm) REVERT: H 79 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8184 (mt-10) REVERT: H 89 SER cc_start: 0.9130 (m) cc_final: 0.8789 (p) REVERT: I 23 LYS cc_start: 0.7578 (mttm) cc_final: 0.7366 (mttp) REVERT: K 81 TYR cc_start: 0.9331 (m-10) cc_final: 0.9072 (m-10) REVERT: M 58 MET cc_start: 0.9126 (tmt) cc_final: 0.8907 (tmt) REVERT: M 107 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7716 (tp30) REVERT: M 271 MET cc_start: 0.9082 (mmt) cc_final: 0.8807 (mmt) REVERT: M 530 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.8096 (t80) REVERT: S 59 ARG cc_start: 0.8347 (mtt90) cc_final: 0.8009 (mtm-85) REVERT: W 5 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8327 (tptp) REVERT: W 7 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8788 (tptp) REVERT: W 72 MET cc_start: 0.8885 (ttm) cc_final: 0.8498 (mtt) REVERT: Y 95 GLU cc_start: 0.8868 (tp30) cc_final: 0.8558 (tp30) REVERT: Z 86 TYR cc_start: 0.6784 (t80) cc_final: 0.6512 (t80) REVERT: b 111 LEU cc_start: 0.8684 (mt) cc_final: 0.8477 (mt) REVERT: c 173 ASP cc_start: 0.8543 (t0) cc_final: 0.8236 (t70) REVERT: e 114 MET cc_start: 0.8445 (mmt) cc_final: 0.7730 (mtm) REVERT: h 5 ASP cc_start: 0.9021 (t0) cc_final: 0.8571 (t0) REVERT: h 13 ASP cc_start: 0.9100 (t0) cc_final: 0.8848 (t0) REVERT: i 40 MET cc_start: 0.9030 (tpp) cc_final: 0.8284 (tpp) REVERT: i 282 MET cc_start: 0.8930 (mtt) cc_final: 0.8716 (mtm) REVERT: i 343 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9034 (pp) REVERT: j 52 SER cc_start: 0.9237 (t) cc_final: 0.8953 (t) REVERT: l 145 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8614 (mm-30) REVERT: l 426 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8145 (tt) REVERT: l 544 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8778 (mmm) REVERT: m 87 LYS cc_start: 0.8658 (ttmm) cc_final: 0.8143 (mtpt) REVERT: n 54 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7657 (pm20) REVERT: o 110 ASP cc_start: 0.8506 (m-30) cc_final: 0.8043 (m-30) REVERT: p 160 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: r 168 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.8708 (tt0) REVERT: s 22 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8622 (tp) REVERT: s 24 GLU cc_start: 0.8911 (tt0) cc_final: 0.8700 (tt0) REVERT: s 277 TYR cc_start: 0.8853 (m-80) cc_final: 0.8545 (m-80) REVERT: v 52 MET cc_start: 0.8316 (mmm) cc_final: 0.7917 (mmt) REVERT: w 120 ASP cc_start: 0.8677 (t0) cc_final: 0.7980 (t0) REVERT: w 145 ASP cc_start: 0.8378 (m-30) cc_final: 0.8034 (m-30) REVERT: w 227 MET cc_start: 0.8660 (mpp) cc_final: 0.8430 (mpp) REVERT: w 241 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.6344 (t80) outliers start: 106 outliers final: 88 residues processed: 1171 average time/residue: 0.6652 time to fit residues: 1323.8534 Evaluate side-chains 1198 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1094 time to evaluate : 5.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 369 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 89 LEU Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 80 ASP Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain e residue 96 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 140 SER Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 45 THR Chi-restraints excluded: chain l residue 65 ASN Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 54 GLU Chi-restraints excluded: chain o residue 56 ARG Chi-restraints excluded: chain p residue 160 GLU Chi-restraints excluded: chain r residue 168 GLN Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 205 VAL Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 289 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 507 optimal weight: 0.0070 chunk 680 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 588 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 639 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 656 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN F 25 GLN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 GLN e 148 GLN h 21 GLN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 366 ASN v 54 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.094367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.074205 restraints weight = 109521.765| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.95 r_work: 0.2669 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 69848 Z= 0.223 Angle : 0.513 14.541 94403 Z= 0.254 Chirality : 0.041 0.252 10207 Planarity : 0.004 0.066 11765 Dihedral : 11.189 174.648 10656 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.78 % Favored : 96.17 % Rotamer: Outliers : 1.82 % Allowed : 16.71 % Favored : 81.47 % 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: 1.24 (0.10), residues: 8172 helix: 1.94 (0.08), residues: 4277 sheet: 0.08 (0.25), residues: 459 loop : -0.49 (0.11), residues: 3436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP u 86 HIS 0.008 0.001 HIS r 30 PHE 0.030 0.001 PHE i 292 TYR 0.021 0.001 TYR l 587 ARG 0.009 0.000 ARG V 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19775.37 seconds wall clock time: 346 minutes 10.71 seconds (20770.71 seconds total)