Starting phenix.real_space_refine on Thu Feb 22 23:34:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jga_22316/02_2024/7jga_22316.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jga_22316/02_2024/7jga_22316.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jga_22316/02_2024/7jga_22316.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jga_22316/02_2024/7jga_22316.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jga_22316/02_2024/7jga_22316.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jga_22316/02_2024/7jga_22316.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= 0.009 sd= 0.248 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: 7 Type Number sf(0) Gaussians Br 7 7.06 5 P 12 5.49 5 Mg 4 5.21 5 S 103 5.16 5 C 22840 2.51 5 N 6208 2.21 5 O 6623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A ASP 273": "OD1" <-> "OD2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B ASP 123": "OD1" <-> "OD2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "B ASP 317": "OD1" <-> "OD2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B GLU 404": "OE1" <-> "OE2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 414": "OD1" <-> "OD2" Residue "B ASP 422": "OD1" <-> "OD2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B GLU 442": "OE1" <-> "OE2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B ASP 457": "OD1" <-> "OD2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B ASP 515": "OD1" <-> "OD2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ASP 70": "OD1" <-> "OD2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C ASP 119": "OD1" <-> "OD2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ASP 173": "OD1" <-> "OD2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ASP 241": "OD1" <-> "OD2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 310": "OE1" <-> "OE2" Residue "C ASP 336": "OD1" <-> "OD2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C GLU 388": "OE1" <-> "OE2" Residue "C GLU 404": "OE1" <-> "OE2" Residue "C ASP 412": "OD1" <-> "OD2" Residue "C GLU 442": "OE1" <-> "OE2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "C GLU 506": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D ASP 59": "OD1" <-> "OD2" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D ASP 145": "OD1" <-> "OD2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "D GLU 286": "OE1" <-> "OE2" Residue "D ARG 298": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ASP 357": "OD1" <-> "OD2" Residue "D ASP 398": "OD1" <-> "OD2" Residue "D GLU 409": "OE1" <-> "OE2" Residue "D GLU 446": "OE1" <-> "OE2" Residue "D ASP 448": "OD1" <-> "OD2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 292": "OE1" <-> "OE2" Residue "E ASP 317": "OD1" <-> "OD2" Residue "E GLU 332": "OE1" <-> "OE2" Residue "E ASP 384": "OD1" <-> "OD2" Residue "E GLU 393": "OE1" <-> "OE2" Residue "E GLU 396": "OE1" <-> "OE2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E ASP 398": "OD1" <-> "OD2" Residue "E GLU 434": "OE1" <-> "OE2" Residue "E GLU 437": "OE1" <-> "OE2" Residue "E GLU 446": "OE1" <-> "OE2" Residue "E GLU 469": "OE1" <-> "OE2" Residue "F ASP 21": "OD1" <-> "OD2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F ASP 59": "OD1" <-> "OD2" Residue "F GLU 78": "OE1" <-> "OE2" Residue "F ASP 108": "OD1" <-> "OD2" Residue "F ASP 129": "OD1" <-> "OD2" Residue "F ASP 145": "OD1" <-> "OD2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F ASP 206": "OD1" <-> "OD2" Residue "F ASP 317": "OD1" <-> "OD2" Residue "F ASP 363": "OD1" <-> "OD2" Residue "F GLU 364": "OE1" <-> "OE2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F GLU 409": "OE1" <-> "OE2" Residue "F GLU 420": "OE1" <-> "OE2" Residue "F GLU 434": "OE1" <-> "OE2" Residue "F GLU 446": "OE1" <-> "OE2" Residue "G GLU 26": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G ASP 64": "OD1" <-> "OD2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G ASP 85": "OD1" <-> "OD2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G ARG 151": "NH1" <-> "NH2" Residue "G GLU 152": "OE1" <-> "OE2" Residue "G GLU 189": "OE1" <-> "OE2" Residue "G ARG 201": "NH1" <-> "NH2" Residue "G GLU 207": "OE1" <-> "OE2" Residue "G GLU 209": "OE1" <-> "OE2" Residue "G GLU 284": "OE1" <-> "OE2" Residue "G GLU 292": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ASP 66": "OD1" <-> "OD2" Residue "H ARG 78": "NH1" <-> "NH2" Residue "H ARG 111": "NH1" <-> "NH2" Residue "a ARG 50": "NH1" <-> "NH2" Residue "a GLU 67": "OE1" <-> "OE2" Residue "a ARG 188": "NH1" <-> "NH2" Residue "a TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 222": "OD1" <-> "OD2" Residue "b PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 59": "OE1" <-> "OE2" Residue "b ARG 72": "NH1" <-> "NH2" Residue "b ARG 115": "NH1" <-> "NH2" Residue "b ARG 158": "NH1" <-> "NH2" Residue "d GLU 43": "OE1" <-> "OE2" Residue "d ASP 53": "OD1" <-> "OD2" Residue "d ASP 64": "OD1" <-> "OD2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "d GLU 89": "OE1" <-> "OE2" Residue "d GLU 96": "OE1" <-> "OE2" Residue "d ARG 173": "NH1" <-> "NH2" Residue "d ASP 188": "OD1" <-> "OD2" Residue "d GLU 205": "OE1" <-> "OE2" Residue "d GLU 225": "OE1" <-> "OE2" Residue "d GLU 238": "OE1" <-> "OE2" Residue "d ARG 239": "NH1" <-> "NH2" Residue "d ARG 260": "NH1" <-> "NH2" Residue "d ASP 269": "OD1" <-> "OD2" Residue "d GLU 272": "OE1" <-> "OE2" Residue "d GLU 306": "OE1" <-> "OE2" Residue "d ARG 353": "NH1" <-> "NH2" Residue "d ARG 372": "NH1" <-> "NH2" Residue "d ARG 399": "NH1" <-> "NH2" Residue "d ASP 425": "OD1" <-> "OD2" Residue "1 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 65": "OE1" <-> "OE2" Residue "2 ASP 32": "OD1" <-> "OD2" Residue "3 ASP 32": "OD1" <-> "OD2" Residue "3 GLU 65": "OE1" <-> "OE2" Residue "4 ARG 45": "NH1" <-> "NH2" Residue "5 GLU 65": "OE1" <-> "OE2" Residue "5 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 32": "OD1" <-> "OD2" Residue "6 GLU 65": "OE1" <-> "OE2" Residue "7 GLU 48": "OE1" <-> "OE2" Residue "7 PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 65": "OE1" <-> "OE2" Residue "9 ARG 45": "NH1" <-> "NH2" Residue "9 ARG 52": "NH1" <-> "NH2" Residue "9 TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35797 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3841 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 492} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3756 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 486} Chain breaks: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 64 Chain: "C" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3835 Classifications: {'peptide': 515} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 58 Chain: "D" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3486 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 64 Chain: "E" Number of atoms: 3516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3516 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 37 Chain: "F" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3489 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 55 Chain: "G" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2117 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 269} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "H" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 820 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 74 Chain: "a" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1594 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "b" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 949 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 3, 'TRANS': 137} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 66 Chain: "d" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 2968 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 10, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 23, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 180 Chain: "1" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} 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: "2" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} 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: "3" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 564 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "4" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} 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: "5" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 564 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "6" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 554 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "8" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} 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: "9" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.83, per 1000 atoms: 0.53 Number of scatterers: 35797 At special positions: 0 Unit cell: (126.69, 133.9, 243.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 7 34.99 S 103 16.00 P 12 15.00 Mg 4 11.99 O 6623 8.00 N 6208 7.00 C 22840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.59 Conformation dependent library (CDL) restraints added in 6.3 seconds 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8700 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 25 sheets defined 62.3% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 7 through 22 removed outlier: 3.695A pdb=" N ILE A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 177 through 189 removed outlier: 3.876A pdb=" N GLN A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 226 through 230 removed outlier: 5.937A pdb=" N MET A 229 " --> pdb=" O GLY A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 263 Proline residue: A 250 - end of helix removed outlier: 3.707A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 298 through 299 No H-bonds generated for 'chain 'A' and resid 298 through 299' Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.612A pdb=" N HIS A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.976A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 404 removed outlier: 5.204A pdb=" N SER A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.505A pdb=" N ALA A 408 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 432 removed outlier: 3.831A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 removed outlier: 3.963A pdb=" N VAL A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 4.157A pdb=" N SER A 458 " --> pdb=" O HIS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 479 removed outlier: 3.538A pdb=" N GLU A 473 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 removed outlier: 4.361A pdb=" N PHE A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 509 Processing helix chain 'B' and resid 9 through 22 removed outlier: 3.870A pdb=" N PHE B 22 " --> pdb=" O TYR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 212 through 226 Processing helix chain 'B' and resid 227 through 230 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.528A pdb=" N LYS B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Proline residue: B 250 - end of helix removed outlier: 3.622A pdb=" N HIS B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.810A pdb=" N ARG B 307 " --> pdb=" O TYR B 303 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 392 through 408 Processing helix chain 'B' and resid 414 through 432 removed outlier: 3.564A pdb=" N ALA B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 removed outlier: 4.200A pdb=" N VAL B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 478 removed outlier: 3.518A pdb=" N GLU B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 493 through 511 removed outlier: 3.882A pdb=" N VAL B 503 " --> pdb=" O LYS B 499 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.503A pdb=" N ARG C 142 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 227 through 230 Processing helix chain 'C' and resid 242 through 263 Proline residue: C 250 - end of helix removed outlier: 3.706A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 Processing helix chain 'C' and resid 293 through 297 removed outlier: 3.606A pdb=" N ALA C 296 " --> pdb=" O GLY C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 299 No H-bonds generated for 'chain 'C' and resid 298 through 299' Processing helix chain 'C' and resid 300 through 310 removed outlier: 3.830A pdb=" N HIS C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 307 " --> pdb=" O TYR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.626A pdb=" N GLY C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 removed outlier: 3.907A pdb=" N ASP C 336 " --> pdb=" O LYS C 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 339 through 349 removed outlier: 3.531A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 362 removed outlier: 3.540A pdb=" N GLN C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 382 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 392 through 408 Processing helix chain 'C' and resid 414 through 432 removed outlier: 3.630A pdb=" N ALA C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 removed outlier: 3.960A pdb=" N VAL C 446 " --> pdb=" O GLU C 442 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 458 removed outlier: 4.146A pdb=" N SER C 458 " --> pdb=" O HIS C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 479 removed outlier: 3.602A pdb=" N GLU C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 490 removed outlier: 4.316A pdb=" N PHE C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 removed outlier: 3.538A pdb=" N LYS C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 91 through 95 removed outlier: 3.666A pdb=" N VAL D 94 " --> pdb=" O GLY D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 130 Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 165 through 180 Processing helix chain 'D' and resid 193 through 207 Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 223 through 244 removed outlier: 3.675A pdb=" N ARG D 227 " --> pdb=" O PRO D 223 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 271 Processing helix chain 'D' and resid 282 through 292 Processing helix chain 'D' and resid 310 through 314 Processing helix chain 'D' and resid 317 through 325 Processing helix chain 'D' and resid 334 through 339 Processing helix chain 'D' and resid 362 through 389 removed outlier: 5.030A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 394 Processing helix chain 'D' and resid 395 through 412 removed outlier: 3.958A pdb=" N ARG D 404 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG D 407 " --> pdb=" O ASN D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 422 Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.910A pdb=" N LYS D 441 " --> pdb=" O GLU D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 455 Processing helix chain 'D' and resid 460 through 471 removed outlier: 3.707A pdb=" N SER D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.516A pdb=" N LYS E 95 " --> pdb=" O ASP E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 148 Processing helix chain 'E' and resid 165 through 177 removed outlier: 3.846A pdb=" N ASN E 175 " --> pdb=" O GLN E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 207 Processing helix chain 'E' and resid 208 through 211 removed outlier: 3.802A pdb=" N LYS E 211 " --> pdb=" O ASN E 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 208 through 211' Processing helix chain 'E' and resid 223 through 244 removed outlier: 5.539A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 271 removed outlier: 4.062A pdb=" N THR E 260 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 292 Processing helix chain 'E' and resid 311 through 314 Processing helix chain 'E' and resid 317 through 324 Processing helix chain 'E' and resid 334 through 340 Processing helix chain 'E' and resid 357 through 362 Processing helix chain 'E' and resid 362 through 390 removed outlier: 5.383A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE E 388 " --> pdb=" O ASP E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 412 removed outlier: 3.717A pdb=" N ARG E 404 " --> pdb=" O GLN E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 418 No H-bonds generated for 'chain 'E' and resid 416 through 418' Processing helix chain 'E' and resid 419 through 424 Processing helix chain 'E' and resid 431 through 445 Processing helix chain 'E' and resid 451 through 455 Processing helix chain 'E' and resid 460 through 471 Processing helix chain 'F' and resid 25 through 29 removed outlier: 4.044A pdb=" N VAL F 29 " --> pdb=" O ARG F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 Processing helix chain 'F' and resid 91 through 95 Processing helix chain 'F' and resid 111 through 115 removed outlier: 4.355A pdb=" N ASP F 114 " --> pdb=" O TYR F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 130 removed outlier: 3.528A pdb=" N LEU F 130 " --> pdb=" O PHE F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 148 Processing helix chain 'F' and resid 165 through 181 removed outlier: 4.090A pdb=" N ARG F 179 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 207 Processing helix chain 'F' and resid 208 through 211 removed outlier: 3.503A pdb=" N LYS F 211 " --> pdb=" O ASN F 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 208 through 211' Processing helix chain 'F' and resid 223 through 244 removed outlier: 4.765A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET F 237 " --> pdb=" O SER F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 268 removed outlier: 4.006A pdb=" N THR F 260 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY F 263 " --> pdb=" O PHE F 259 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 292 Processing helix chain 'F' and resid 293 through 295 No H-bonds generated for 'chain 'F' and resid 293 through 295' Processing helix chain 'F' and resid 311 through 314 Processing helix chain 'F' and resid 317 through 324 Processing helix chain 'F' and resid 325 through 327 No H-bonds generated for 'chain 'F' and resid 325 through 327' Processing helix chain 'F' and resid 334 through 340 Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 362 through 389 removed outlier: 3.825A pdb=" N VAL F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 413 removed outlier: 3.768A pdb=" N ARG F 407 " --> pdb=" O ASN F 403 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG F 410 " --> pdb=" O ARG F 406 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 418 No H-bonds generated for 'chain 'F' and resid 416 through 418' Processing helix chain 'F' and resid 419 through 424 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 451 through 456 removed outlier: 3.798A pdb=" N PHE F 455 " --> pdb=" O GLU F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 469 Processing helix chain 'G' and resid 5 through 61 removed outlier: 3.793A pdb=" N ALA G 34 " --> pdb=" O THR G 30 " (cutoff:3.500A) Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 90 through 111 removed outlier: 4.524A pdb=" N ALA G 94 " --> pdb=" O GLY G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 130 Processing helix chain 'G' and resid 146 through 163 removed outlier: 3.529A pdb=" N ALA G 150 " --> pdb=" O THR G 146 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 303 removed outlier: 3.521A pdb=" N ALA G 234 " --> pdb=" O THR G 230 " (cutoff:3.500A) Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 91 through 100 removed outlier: 3.535A pdb=" N ALA H 100 " --> pdb=" O LYS H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 117 Processing helix chain 'a' and resid 32 through 53 removed outlier: 4.008A pdb=" N THR a 38 " --> pdb=" O ALA a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 109 removed outlier: 4.404A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL a 108 " --> pdb=" O ASN a 104 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU a 109 " --> pdb=" O TRP a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 154 removed outlier: 3.893A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 157 through 165 Processing helix chain 'a' and resid 167 through 169 No H-bonds generated for 'chain 'a' and resid 167 through 169' Processing helix chain 'a' and resid 170 through 205 removed outlier: 3.703A pdb=" N ILE a 175 " --> pdb=" O ALA a 171 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL a 176 " --> pdb=" O PRO a 172 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 3.585A pdb=" N ARG a 188 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 246 removed outlier: 4.605A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.949A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 49 Processing helix chain 'b' and resid 49 through 161 removed outlier: 3.596A pdb=" N GLY b 143 " --> pdb=" O GLN b 139 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY b 150 " --> pdb=" O SER b 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 137 Processing helix chain 'd' and resid 139 through 157 Processing helix chain 'd' and resid 173 through 193 removed outlier: 3.596A pdb=" N SER d 189 " --> pdb=" O GLU d 185 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY d 193 " --> pdb=" O SER d 189 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 216 removed outlier: 3.617A pdb=" N ASN d 201 " --> pdb=" O ASP d 197 " (cutoff:3.500A) Processing helix chain 'd' and resid 216 through 224 Processing helix chain 'd' and resid 230 through 242 Processing helix chain 'd' and resid 246 through 259 removed outlier: 3.839A pdb=" N THR d 255 " --> pdb=" O ASP d 251 " (cutoff:3.500A) Processing helix chain 'd' and resid 263 through 286 removed outlier: 3.952A pdb=" N LEU d 267 " --> pdb=" O THR d 263 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 288 through 306 removed outlier: 3.564A pdb=" N GLU d 293 " --> pdb=" O VAL d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 314 Processing helix chain 'd' and resid 319 through 331 removed outlier: 3.848A pdb=" N ARG d 323 " --> pdb=" O PRO d 319 " (cutoff:3.500A) Processing helix chain 'd' and resid 338 through 351 Processing helix chain 'd' and resid 356 through 373 Processing helix chain 'd' and resid 386 through 402 Processing helix chain 'd' and resid 431 through 442 Processing helix chain '1' and resid 6 through 46 removed outlier: 3.935A pdb=" N THR 1 10 " --> pdb=" O ASN 1 6 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA 1 13 " --> pdb=" O ILE 1 9 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY 1 18 " --> pdb=" O LEU 1 14 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY 1 23 " --> pdb=" O LEU 1 19 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY 1 33 " --> pdb=" O GLY 1 29 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA 1 38 " --> pdb=" O ILE 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 47 through 52 removed outlier: 4.382A pdb=" N GLY 1 51 " --> pdb=" O GLU 1 48 " (cutoff:3.500A) Processing helix chain '1' and resid 53 through 80 Processing helix chain '2' and resid 6 through 46 Processing helix chain '2' and resid 49 through 82 removed outlier: 3.738A pdb=" N PHE 2 54 " --> pdb=" O GLN 2 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR 2 55 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) Proline residue: 2 56 - end of helix removed outlier: 3.600A pdb=" N LEU 2 63 " --> pdb=" O ILE 2 59 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA 2 67 " --> pdb=" O LEU 2 63 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE 2 70 " --> pdb=" O ALA 2 66 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 46 Processing helix chain '3' and resid 49 through 80 removed outlier: 3.675A pdb=" N PHE 3 54 " --> pdb=" O GLN 3 50 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N THR 3 55 " --> pdb=" O GLY 3 51 " (cutoff:3.500A) Proline residue: 3 56 - end of helix removed outlier: 4.243A pdb=" N ALA 3 67 " --> pdb=" O LEU 3 63 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR 3 68 " --> pdb=" O VAL 3 64 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE 3 70 " --> pdb=" O ALA 3 66 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU 3 77 " --> pdb=" O ALA 3 73 " (cutoff:3.500A) Processing helix chain '4' and resid 6 through 46 Processing helix chain '4' and resid 49 through 81 removed outlier: 4.215A pdb=" N THR 4 55 " --> pdb=" O GLY 4 51 " (cutoff:3.500A) Proline residue: 4 56 - end of helix Processing helix chain '5' and resid 6 through 46 removed outlier: 3.633A pdb=" N ALA 5 38 " --> pdb=" O ILE 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 81 removed outlier: 5.141A pdb=" N THR 5 55 " --> pdb=" O GLY 5 51 " (cutoff:3.500A) Proline residue: 5 56 - end of helix Processing helix chain '6' and resid 6 through 46 Processing helix chain '6' and resid 49 through 81 removed outlier: 3.565A pdb=" N PHE 6 54 " --> pdb=" O GLN 6 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR 6 55 " --> pdb=" O GLY 6 51 " (cutoff:3.500A) Proline residue: 6 56 - end of helix Processing helix chain '7' and resid 6 through 46 Processing helix chain '7' and resid 49 through 80 removed outlier: 4.291A pdb=" N THR 7 55 " --> pdb=" O GLY 7 51 " (cutoff:3.500A) Proline residue: 7 56 - end of helix Processing helix chain '8' and resid 6 through 45 Processing helix chain '8' and resid 46 through 48 No H-bonds generated for 'chain '8' and resid 46 through 48' Processing helix chain '8' and resid 49 through 81 removed outlier: 3.635A pdb=" N LEU 8 53 " --> pdb=" O ALA 8 49 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR 8 55 " --> pdb=" O GLY 8 51 " (cutoff:3.500A) Proline residue: 8 56 - end of helix removed outlier: 3.852A pdb=" N ILE 8 70 " --> pdb=" O ALA 8 66 " (cutoff:3.500A) Processing helix chain '9' and resid 6 through 46 removed outlier: 3.813A pdb=" N ARG 9 45 " --> pdb=" O SER 9 41 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN 9 46 " --> pdb=" O GLY 9 42 " (cutoff:3.500A) Processing helix chain '9' and resid 49 through 80 removed outlier: 4.319A pdb=" N THR 9 55 " --> pdb=" O GLY 9 51 " (cutoff:3.500A) Proline residue: 9 56 - end of helix removed outlier: 3.586A pdb=" N TYR 9 68 " --> pdb=" O VAL 9 64 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE 9 70 " --> pdb=" O ALA 9 66 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 5.025A pdb=" N LEU A 55 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG A 93 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU A 30 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL A 34 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 36 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 64 removed outlier: 5.025A pdb=" N LEU A 55 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG A 93 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU A 30 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 102 Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.715A pdb=" N VAL A 267 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU A 327 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE A 269 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE A 329 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE A 271 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLU A 331 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 69 removed outlier: 4.099A pdb=" N GLU B 54 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU B 55 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL B 34 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU B 69 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N THR E 80 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N GLU E 39 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR E 82 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N HIS E 37 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA E 84 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN E 34 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG E 63 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N HIS E 56 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU E 61 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLU E 23 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL E 12 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 102 Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.530A pdb=" N ILE B 330 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 149 removed outlier: 4.497A pdb=" N ILE B 162 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 351 through 352 Processing sheet with id=AB1, first strand: chain 'C' and resid 62 through 69 removed outlier: 4.091A pdb=" N GLU C 54 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU C 55 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N HIS C 43 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA C 37 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU F 78 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU F 39 " --> pdb=" O GLU F 78 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA F 35 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN F 34 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG F 63 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N HIS F 56 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU F 61 " --> pdb=" O HIS F 56 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLU F 23 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL F 12 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AB3, first strand: chain 'C' and resid 110 through 111 removed outlier: 3.729A pdb=" N ILE C 330 " --> pdb=" O ILE C 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 351 through 352 Processing sheet with id=AB5, first strand: chain 'C' and resid 534 through 540 removed outlier: 11.200A pdb=" N GLU C 534 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU C 536 " --> pdb=" O PRO G 205 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLN G 196 " --> pdb=" O ARG G 191 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ARG G 191 " --> pdb=" O GLN G 196 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA G 198 " --> pdb=" O GLU G 189 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU G 189 " --> pdb=" O ALA G 198 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA G 200 " --> pdb=" O PHE G 187 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N PHE G 187 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ARG G 202 " --> pdb=" O ILE G 185 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE G 185 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG G 76 " --> pdb=" O GLU G 182 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N PHE G 190 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA G 77 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N TYR G 117 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL G 79 " --> pdb=" O TYR G 117 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL G 119 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL G 81 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N VAL G 135 " --> pdb=" O PRO G 114 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU G 116 " --> pdb=" O VAL G 135 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N SER G 137 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL G 118 " --> pdb=" O SER G 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 16 removed outlier: 6.683A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU D 61 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N HIS D 56 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG D 63 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN D 34 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA D 35 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU D 39 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU D 78 " --> pdb=" O GLU D 39 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 87 through 90 removed outlier: 4.100A pdb=" N GLU D 116 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 98 through 99 removed outlier: 6.406A pdb=" N PHE D 99 " --> pdb=" O PHE D 217 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLN D 219 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER D 185 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL D 216 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE D 187 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLY D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY D 189 " --> pdb=" O GLY D 218 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE D 156 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS D 155 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR D 331 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA D 157 " --> pdb=" O THR D 331 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 87 through 90 removed outlier: 4.094A pdb=" N GLU E 116 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 100 removed outlier: 6.633A pdb=" N SER E 185 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL E 216 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE E 187 " --> pdb=" O VAL E 216 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLY E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY E 189 " --> pdb=" O GLY E 218 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N TYR E 309 " --> pdb=" O ILE E 253 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE E 156 " --> pdb=" O GLN E 306 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL E 308 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU E 158 " --> pdb=" O VAL E 308 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS E 155 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N THR E 331 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA E 157 " --> pdb=" O THR E 331 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 136 through 137 removed outlier: 4.272A pdb=" N TYR E 150 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 87 through 90 removed outlier: 4.076A pdb=" N GLU F 116 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.377A pdb=" N PHE F 99 " --> pdb=" O PHE F 217 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS F 155 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR F 331 " --> pdb=" O LYS F 155 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA F 157 " --> pdb=" O THR F 331 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 136 through 137 removed outlier: 4.249A pdb=" N TYR F 150 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 223 through 225 removed outlier: 3.860A pdb=" N GLN H 44 " --> pdb=" O GLU G 225 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL H 9 " --> pdb=" O VAL H 81 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 30 through 34 removed outlier: 3.769A pdb=" N PHE H 22 " --> pdb=" O GLU H 54 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA H 49 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN H 83 " --> pdb=" O ASP H 66 " (cutoff:3.500A) 2417 hydrogen bonds defined for protein. 6933 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: 14.92 Time building geometry restraints manager: 15.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 12116 1.36 - 1.51: 10684 1.51 - 1.65: 13428 1.65 - 1.80: 121 1.80 - 1.94: 73 Bond restraints: 36422 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.93e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.47e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.44e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.466 -0.057 1.00e-02 1.00e+04 3.21e+01 ... (remaining 36417 not shown) Histogram of bond angle deviations from ideal: 97.36 - 105.15: 709 105.15 - 112.94: 19887 112.94 - 120.73: 17026 120.73 - 128.52: 11669 128.52 - 136.31: 199 Bond angle restraints: 49490 Sorted by residual: angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.27 23.60 1.00e+00 1.00e+00 5.57e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 117.34 22.53 1.00e+00 1.00e+00 5.07e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 119.02 20.85 1.00e+00 1.00e+00 4.35e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 118.21 18.62 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 118.28 18.55 1.00e+00 1.00e+00 3.44e+02 ... (remaining 49485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.18: 20086 19.18 - 38.36: 1221 38.36 - 57.55: 275 57.55 - 76.73: 97 76.73 - 95.91: 67 Dihedral angle restraints: 21746 sinusoidal: 8169 harmonic: 13577 Sorted by residual: dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 -149.62 89.63 1 2.00e+01 2.50e-03 2.38e+01 dihedral pdb=" CA ALA F 276 " pdb=" C ALA F 276 " pdb=" N VAL F 277 " pdb=" CA VAL F 277 " ideal model delta harmonic sigma weight residual -180.00 -155.63 -24.37 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLN E 247 " pdb=" C GLN E 247 " pdb=" N ASP E 248 " pdb=" CA ASP E 248 " ideal model delta harmonic sigma weight residual 180.00 157.55 22.45 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 21743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 5445 0.086 - 0.171: 346 0.171 - 0.257: 9 0.257 - 0.343: 5 0.343 - 0.429: 5 Chirality restraints: 5810 Sorted by residual: chirality pdb=" C07 BQ1 6 601 " pdb=" C06 BQ1 6 601 " pdb=" C10 BQ1 6 601 " pdb=" C12 BQ1 6 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.83 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" C07 BQ1 4 601 " pdb=" C06 BQ1 4 601 " pdb=" C10 BQ1 4 601 " pdb=" C12 BQ1 4 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.82 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CA PRO b 51 " pdb=" N PRO b 51 " pdb=" C PRO b 51 " pdb=" CB PRO b 51 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 5807 not shown) Planarity restraints: 6389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 284 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" C ALA E 284 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA E 284 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP E 285 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 85 " 0.008 2.00e-02 2.50e+03 1.47e-02 4.33e+00 pdb=" CG TYR b 85 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR b 85 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR b 85 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR b 85 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR b 85 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR b 85 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR b 85 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG d 27 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C ARG d 27 " 0.034 2.00e-02 2.50e+03 pdb=" O ARG d 27 " -0.013 2.00e-02 2.50e+03 pdb=" N THR d 28 " -0.012 2.00e-02 2.50e+03 ... (remaining 6386 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 68 2.39 - 3.02: 22654 3.02 - 3.65: 54412 3.65 - 4.27: 84939 4.27 - 4.90: 142668 Nonbonded interactions: 304741 Sorted by model distance: nonbonded pdb=" O1B ATP A 600 " pdb="MG MG A 601 " model vdw 1.768 2.170 nonbonded pdb=" O2B ATP C 600 " pdb="MG MG C 601 " model vdw 1.836 2.170 nonbonded pdb=" OH TYR 7 68 " pdb=" OD1 ASN 8 71 " model vdw 1.879 2.440 nonbonded pdb=" O ALA H 29 " pdb=" NH2 ARG 3 45 " model vdw 1.907 2.520 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 1.956 2.170 ... (remaining 304736 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 '1' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '2' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '3' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 51 or (resid 52 and (n \ ame N or name CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '4' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '5' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 51 or (resid 52 and (n \ ame N or name CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '6' and (resid 5 through 47 or (resid 48 through 49 and (name N or name C \ A or name C or name O or name CB )) or resid 50 through 51 or (resid 52 and (nam \ e N or name CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '7' and (resid 5 through 47 or (resid 48 through 49 and (name N or name C \ A or name C or name O or name CB )) or resid 50 through 85)) selection = (chain '8' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '9' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) } ncs_group { reference = (chain 'A' and ((resid 9 through 17 and (name N or name CA or name C or name O o \ r name CB )) or resid 18 or (resid 19 through 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 or (resid 29 and (name N or name CA or nam \ e C or name O or name CB )) or resid 30 through 38 or (resid 39 and (name N or n \ ame CA or name C or name O or name CB )) or resid 40 through 44 or (resid 45 and \ (name N or name CA or name C or name O or name CB )) or resid 46 through 80 or \ (resid 81 and (name N or name CA or name C or name O or name CB )) or resid 82 t \ hrough 132 or (resid 133 and (name N or name CA or name C or name O or name CB ) \ ) or resid 134 through 190 or (resid 191 through 192 and (name N or name CA or n \ ame C or name O or name CB )) or resid 193 through 294 or (resid 295 through 296 \ and (name N or name CA or name C or name O or name CB )) or resid 297 through 3 \ 16 or (resid 317 through 318 and (name N or name CA or name C or name O or name \ CB )) or resid 319 through 355 or (resid 356 and (name N or name CA or name C or \ name O or name CB )) or resid 357 or (resid 358 and (name N or name CA or name \ C or name O or name CB )) or resid 359 through 401 or (resid 402 and (name N or \ name CA or name C or name O or name CB )) or resid 403 through 411 or (resid 412 \ and (name N or name CA or name C or name O or name CB )) or resid 413 through 4 \ 16 or (resid 417 through 419 and (name N or name CA or name C or name O or name \ CB )) or resid 420 through 456 or (resid 457 and (name N or name CA or name C or \ name O or name CB )) or resid 458 through 467 or (resid 468 and (name N or name \ CA or name C or name O or name CB )) or resid 469 through 475 or (resid 476 thr \ ough 477 and (name N or name CA or name C or name O or name CB )) or resid 478 t \ hrough 493 or (resid 494 through 499 and (name N or name CA or name C or name O \ or name CB )) or resid 500 through 505 or (resid 506 and (name N or name CA or n \ ame C or name O or name CB )) or resid 507 through 514 or (resid 515 and (name N \ or name CA or name C or name O or name CB )) or resid 518 through 520 or resid \ 600 through 601)) selection = (chain 'B' and (resid 9 through 18 or (resid 19 through 21 and (name N or name C \ A or name C or name O or name CB )) or resid 22 or resid 29 through 38 or (resid \ 39 and (name N or name CA or name C or name O or name CB )) or resid 40 through \ 80 or (resid 81 and (name N or name CA or name C or name O or name CB )) or res \ id 82 through 190 or (resid 191 through 192 and (name N or name CA or name C or \ name O or name CB )) or resid 193 through 316 or (resid 317 through 318 and (nam \ e N or name CA or name C or name O or name CB )) or resid 319 through 400 or (re \ sid 401 through 402 and (name N or name CA or name C or name O or name CB )) or \ resid 403 through 413 or (resid 414 through 419 and (name N or name CA or name C \ or name O or name CB )) or resid 420 through 456 or (resid 457 and (name N or n \ ame CA or name C or name O or name CB )) or resid 458 through 469 or (resid 470 \ and (name N or name CA or name C or name O or name CB )) or resid 471 through 49 \ 3 or (resid 494 through 499 and (name N or name CA or name C or name O or name C \ B )) or resid 500 through 514 or (resid 515 and (name N or name CA or name C or \ name O or name CB )) or resid 518 through 520 or resid 600 through 601)) selection = (chain 'C' and (resid 9 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 132 or (resid 133 and (name N or na \ me CA or name C or name O or name CB )) or resid 134 through 294 or (resid 295 t \ hrough 296 and (name N or name CA or name C or name O or name CB )) or resid 297 \ through 355 or (resid 356 and (name N or name CA or name C or name O or name CB \ )) or resid 357 or (resid 358 and (name N or name CA or name C or name O or nam \ e CB )) or resid 359 through 400 or (resid 401 through 402 and (name N or name C \ A or name C or name O or name CB )) or resid 403 through 411 or (resid 412 and ( \ name N or name CA or name C or name O or name CB )) or resid 413 or (resid 414 t \ hrough 419 and (name N or name CA or name C or name O or name CB )) or resid 420 \ through 461 or (resid 462 through 463 and (name N or name CA or name C or name \ O or name CB )) or resid 464 through 467 or (resid 468 and (name N or name CA or \ name C or name O or name CB )) or resid 469 or (resid 470 and (name N or name C \ A or name C or name O or name CB )) or resid 471 through 475 or (resid 476 throu \ gh 477 and (name N or name CA or name C or name O or name CB )) or resid 478 thr \ ough 494 or (resid 495 through 499 and (name N or name CA or name C or name O or \ name CB )) or resid 500 through 505 or (resid 506 and (name N or name CA or nam \ e C or name O or name CB )) or resid 507 through 515 or resid 537 through 538 or \ resid 540 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 through 104 or (resid 105 and (name N or na \ me CA or name C or name O or name CB )) or resid 106 through 137 or (resid 138 a \ nd (name N or name CA or name C or name O or name CB )) or resid 139 through 220 \ or (resid 221 through 222 and (name N or name CA or name C or name O or name CB \ )) or resid 223 through 253 or (resid 254 and (name N or name CA or name C or n \ ame O or name CB )) or resid 255 through 285 or (resid 286 and (name N or name C \ A or name C or name O or name CB )) or resid 287 through 288 or (resid 289 and ( \ name N or name CA or name C or name O or name CB )) or resid 290 through 291 or \ (resid 292 and (name N or name CA or name C or name O or name CB )) or resid 293 \ through 370 or (resid 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 395 or (resid 396 through 398 and (name N or name CA or \ name C or name O or name CB )) or resid 399 through 461 or (resid 462 through 4 \ 63 and (name N or name CA or name C or name O or name CB )) or resid 464 through \ 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) or r \ esid 467 through 471)) selection = (chain 'E' and (resid 8 through 103 or (resid 104 through 105 and (name N or nam \ e CA or name C or name O or name CB )) or resid 106 through 107 or (resid 108 an \ d (name N or name CA or name C or name O or name CB )) or resid 109 through 113 \ or (resid 114 and (name N or name CA or name C or name O or name CB )) or resid \ 115 through 134 or (resid 135 and (name N or name CA or name C or name O or name \ CB )) or resid 136 through 137 or (resid 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 198 or (resid 199 and (name N or nam \ e CA or name C or name O or name CB )) or resid 200 through 202 or (resid 203 an \ d (name N or name CA or name C or name O or name CB )) or resid 204 through 205 \ or (resid 206 through 207 and (name N or name CA or name C or name O or name CB \ )) or resid 208 through 220 or (resid 221 through 222 and (name N or name CA or \ name C or name O or name CB )) or resid 223 through 291 or (resid 292 and (name \ N or name CA or name C or name O or name CB )) or resid 293 through 369 or (resi \ d 370 through 371 and (name N or name CA or name C or name O or name CB )) or re \ sid 372 through 380 or (resid 381 and (name N or name CA or name C or name O or \ name CB )) or resid 382 through 383 or (resid 384 and (name N or name CA or name \ C or name O or name CB )) or resid 385 through 391 or (resid 392 through 393 an \ d (name N or name CA or name C or name O or name CB )) or resid 394 through 395 \ or (resid 396 through 398 and (name N or name CA or name C or name O or name CB \ )) or resid 399 through 402 or (resid 403 and (name N or name CA or name C or na \ me O or name CB )) or resid 404 through 432 or (resid 433 and (name N or name CA \ or name C or name O or name CB )) or resid 434 through 461 or (resid 462 throug \ h 463 and (name N or name CA or name C or name O or name CB )) or resid 464 thro \ ugh 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) o \ r resid 467 through 471)) selection = (chain 'F' and (resid 8 through 103 or (resid 104 through 105 and (name N or nam \ e CA or name C or name O or name CB )) or resid 106 or (resid 107 through 108 an \ d (name N or name CA or name C or name O or name CB )) or resid 109 through 113 \ or (resid 114 and (name N or name CA or name C or name O or name CB )) or resid \ 115 through 198 or (resid 199 and (name N or name CA or name C or name O or name \ CB )) or resid 200 through 202 or (resid 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 205 or (resid 206 through 207 and (n \ ame N or name CA or name C or name O or name CB )) or resid 208 through 253 or ( \ resid 254 and (name N or name CA or name C or name O or name CB )) or resid 255 \ through 285 or (resid 286 and (name N or name CA or name C or name O or name CB \ )) or resid 287 through 362 or (resid 363 through 364 and (name N or name CA or \ name C or name O or name CB )) or resid 365 through 369 or (resid 370 through 37 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 372 through \ 380 or (resid 381 and (name N or name CA or name C or name O or name CB )) or re \ sid 382 through 391 or (resid 392 through 393 and (name N or name CA or name C o \ r name O or name CB )) or resid 394 through 402 or (resid 403 and (name N or nam \ e CA or name C or name O or name CB )) or resid 404 through 424 or (resid 425 an \ d (name N or name CA or name C or name O or name CB )) or resid 426 through 471) \ ) } 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=1.00 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: 1.390 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: 0.020 Extract box with map and model: 8.790 Check model and map are aligned: 0.620 Set scattering table: 0.400 Process input model: 94.980 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.180 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 36422 Z= 0.492 Angle : 0.786 23.598 49490 Z= 0.498 Chirality : 0.047 0.429 5810 Planarity : 0.004 0.078 6389 Dihedral : 15.213 95.910 13046 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.05 % Favored : 97.80 % Rotamer: Outliers : 0.14 % Allowed : 4.86 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % 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: -1.98 (0.11), residues: 4774 helix: -1.14 (0.09), residues: 2551 sheet: -1.19 (0.21), residues: 514 loop : -1.34 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP a 212 HIS 0.010 0.001 HIS d 58 PHE 0.032 0.002 PHE a 99 TYR 0.024 0.002 TYR b 85 ARG 0.010 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 865 time to evaluate : 4.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8545 (mm110) cc_final: 0.8162 (mm-40) REVERT: A 71 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7597 (mt-10) REVERT: A 77 VAL cc_start: 0.8656 (p) cc_final: 0.8435 (m) REVERT: A 133 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6680 (mt-10) REVERT: A 160 THR cc_start: 0.8099 (p) cc_final: 0.7802 (t) REVERT: A 184 ASP cc_start: 0.6695 (m-30) cc_final: 0.6398 (m-30) REVERT: A 200 GLN cc_start: 0.8403 (mt0) cc_final: 0.8158 (mm110) REVERT: A 336 ASP cc_start: 0.7578 (t0) cc_final: 0.7303 (t0) REVERT: A 356 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7132 (mt-10) REVERT: A 372 VAL cc_start: 0.8204 (t) cc_final: 0.7854 (p) REVERT: A 384 LYS cc_start: 0.7848 (mmmt) cc_final: 0.7647 (tptp) REVERT: A 388 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7575 (mt-10) REVERT: A 429 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7447 (mm-30) REVERT: A 473 GLU cc_start: 0.8141 (tp30) cc_final: 0.7881 (tt0) REVERT: A 498 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7107 (mm-30) REVERT: B 19 VAL cc_start: 0.8176 (t) cc_final: 0.7907 (t) REVERT: B 194 LEU cc_start: 0.8340 (mt) cc_final: 0.8016 (mt) REVERT: B 348 ILE cc_start: 0.8132 (mt) cc_final: 0.7890 (mt) REVERT: B 349 THR cc_start: 0.8752 (p) cc_final: 0.8430 (p) REVERT: B 393 LEU cc_start: 0.6849 (tp) cc_final: 0.6585 (tp) REVERT: B 488 GLU cc_start: 0.7299 (tt0) cc_final: 0.6800 (pt0) REVERT: C 44 VAL cc_start: 0.8359 (t) cc_final: 0.8054 (m) REVERT: C 83 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7275 (mt-10) REVERT: C 300 ASP cc_start: 0.8271 (p0) cc_final: 0.7761 (p0) REVERT: C 335 ASN cc_start: 0.8837 (t0) cc_final: 0.8620 (t0) REVERT: C 365 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7608 (mtt-85) REVERT: C 399 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7474 (mm-40) REVERT: C 491 LYS cc_start: 0.8529 (mttp) cc_final: 0.8302 (mtmm) REVERT: D 67 MET cc_start: 0.8393 (mmp) cc_final: 0.8187 (mmt) REVERT: D 120 ILE cc_start: 0.8248 (pt) cc_final: 0.8045 (pt) REVERT: D 173 MET cc_start: 0.7771 (mmm) cc_final: 0.7226 (mmt) REVERT: D 179 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7476 (mtm180) REVERT: D 185 SER cc_start: 0.8700 (t) cc_final: 0.8304 (m) REVERT: D 222 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7602 (mt-10) REVERT: D 233 SER cc_start: 0.8112 (t) cc_final: 0.7482 (m) REVERT: D 237 MET cc_start: 0.7963 (mtt) cc_final: 0.7736 (mtp) REVERT: D 287 MET cc_start: 0.8326 (tpp) cc_final: 0.8067 (tpt) REVERT: D 292 GLU cc_start: 0.7495 (tp30) cc_final: 0.7263 (tp30) REVERT: D 305 MET cc_start: 0.8055 (mtp) cc_final: 0.7773 (mtp) REVERT: D 342 ILE cc_start: 0.7968 (mm) cc_final: 0.7737 (mt) REVERT: D 398 ASP cc_start: 0.6697 (m-30) cc_final: 0.6461 (m-30) REVERT: D 432 LEU cc_start: 0.7763 (tp) cc_final: 0.7531 (tp) REVERT: D 441 LYS cc_start: 0.7455 (mtpt) cc_final: 0.6620 (mttp) REVERT: D 447 PHE cc_start: 0.8234 (m-80) cc_final: 0.7810 (m-10) REVERT: D 456 PHE cc_start: 0.8227 (m-80) cc_final: 0.7945 (m-80) REVERT: E 279 TYR cc_start: 0.8378 (m-80) cc_final: 0.8120 (m-80) REVERT: E 315 TYR cc_start: 0.8439 (m-80) cc_final: 0.7753 (m-80) REVERT: E 332 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6875 (mt-10) REVERT: E 440 ASP cc_start: 0.7948 (t70) cc_final: 0.7696 (t70) REVERT: E 453 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8076 (mm-40) REVERT: E 457 LEU cc_start: 0.8722 (mt) cc_final: 0.8428 (mp) REVERT: F 66 SER cc_start: 0.8643 (m) cc_final: 0.8329 (p) REVERT: F 193 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7235 (mtt-85) REVERT: F 239 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6879 (mt-10) REVERT: F 458 ILE cc_start: 0.8405 (tp) cc_final: 0.8082 (tp) REVERT: G 26 GLU cc_start: 0.6717 (tt0) cc_final: 0.6385 (tt0) REVERT: G 41 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7074 (tm-30) REVERT: G 85 ASP cc_start: 0.7256 (t70) cc_final: 0.6314 (t0) REVERT: G 121 ARG cc_start: 0.7568 (ttm-80) cc_final: 0.7254 (mtp180) REVERT: G 136 GLU cc_start: 0.7736 (tp30) cc_final: 0.7479 (tp30) REVERT: G 162 MET cc_start: 0.7159 (mtp) cc_final: 0.6909 (mtp) REVERT: G 255 GLU cc_start: 0.7536 (tt0) cc_final: 0.7260 (tt0) REVERT: H 7 GLU cc_start: 0.6986 (tt0) cc_final: 0.6609 (mt-10) REVERT: a 100 ILE cc_start: 0.7257 (tp) cc_final: 0.6957 (mp) REVERT: a 163 VAL cc_start: 0.6323 (t) cc_final: 0.6013 (p) REVERT: d 132 ILE cc_start: 0.6366 (mt) cc_final: 0.6129 (mt) REVERT: d 298 ARG cc_start: 0.7275 (ttt90) cc_final: 0.6669 (ttm170) outliers start: 5 outliers final: 2 residues processed: 869 average time/residue: 0.5031 time to fit residues: 687.7600 Evaluate side-chains 602 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 599 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain d residue 253 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 401 optimal weight: 6.9990 chunk 360 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 243 optimal weight: 0.4980 chunk 192 optimal weight: 0.8980 chunk 373 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 chunk 226 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 chunk 432 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS B 143 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 435 GLN B 465 GLN C 112 ASN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN D 377 GLN D 421 GLN E 326 HIS F 326 HIS F 370 GLN F 400 GLN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN d 104 GLN d 116 GLN d 222 HIS d 266 ASN d 410 HIS 1 6 ASN 3 50 GLN ** 4 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 36422 Z= 0.240 Angle : 0.630 10.706 49490 Z= 0.325 Chirality : 0.044 0.221 5810 Planarity : 0.004 0.041 6389 Dihedral : 9.192 111.311 5439 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.68 % Favored : 98.18 % Rotamer: Outliers : 1.74 % Allowed : 10.58 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.12), residues: 4774 helix: 0.68 (0.10), residues: 2594 sheet: -0.88 (0.21), residues: 533 loop : -0.36 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 212 HIS 0.005 0.001 HIS D 97 PHE 0.026 0.002 PHE C 82 TYR 0.027 0.002 TYR a 145 ARG 0.007 0.000 ARG E 410 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 649 time to evaluate : 4.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7650 (mt-10) REVERT: A 160 THR cc_start: 0.8249 (p) cc_final: 0.7815 (t) REVERT: A 184 ASP cc_start: 0.6874 (m-30) cc_final: 0.6580 (m-30) REVERT: A 200 GLN cc_start: 0.8443 (mt0) cc_final: 0.8151 (mm-40) REVERT: A 310 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6565 (mm-30) REVERT: A 336 ASP cc_start: 0.7638 (t0) cc_final: 0.7370 (t0) REVERT: A 356 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6890 (mt-10) REVERT: A 365 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7749 (mtt90) REVERT: A 372 VAL cc_start: 0.8235 (t) cc_final: 0.7878 (p) REVERT: A 388 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7504 (mt-10) REVERT: A 429 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7404 (mm-30) REVERT: A 473 GLU cc_start: 0.7921 (tp30) cc_final: 0.7642 (tt0) REVERT: A 498 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7188 (mm-30) REVERT: B 132 LEU cc_start: 0.8355 (mt) cc_final: 0.8135 (mp) REVERT: B 194 LEU cc_start: 0.8318 (mt) cc_final: 0.8044 (mt) REVERT: B 229 MET cc_start: 0.8563 (mmm) cc_final: 0.8238 (mmt) REVERT: B 488 GLU cc_start: 0.7570 (tt0) cc_final: 0.7175 (pt0) REVERT: C 41 ILE cc_start: 0.8287 (mm) cc_final: 0.7988 (mt) REVERT: C 83 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7205 (mt-10) REVERT: C 197 ASP cc_start: 0.7495 (t0) cc_final: 0.7096 (m-30) REVERT: C 269 ILE cc_start: 0.7969 (mm) cc_final: 0.7562 (tt) REVERT: C 300 ASP cc_start: 0.8135 (p0) cc_final: 0.7404 (p0) REVERT: C 311 ARG cc_start: 0.8620 (mtm-85) cc_final: 0.8215 (ttp-110) REVERT: C 335 ASN cc_start: 0.8925 (t0) cc_final: 0.8550 (t0) REVERT: C 399 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7613 (mm-40) REVERT: C 491 LYS cc_start: 0.8533 (mttp) cc_final: 0.8330 (mtmm) REVERT: C 505 ASN cc_start: 0.7939 (m-40) cc_final: 0.7549 (m110) REVERT: D 67 MET cc_start: 0.8412 (mmp) cc_final: 0.8152 (mmt) REVERT: D 151 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8265 (t) REVERT: D 185 SER cc_start: 0.8645 (t) cc_final: 0.8317 (m) REVERT: D 222 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7538 (mt-10) REVERT: D 233 SER cc_start: 0.8068 (t) cc_final: 0.7845 (m) REVERT: D 292 GLU cc_start: 0.7495 (tp30) cc_final: 0.7020 (tp30) REVERT: D 314 ASP cc_start: 0.7893 (t0) cc_final: 0.7668 (t70) REVERT: D 342 ILE cc_start: 0.8088 (mm) cc_final: 0.7855 (mt) REVERT: D 447 PHE cc_start: 0.8334 (m-80) cc_final: 0.7964 (m-10) REVERT: E 279 TYR cc_start: 0.8539 (m-80) cc_final: 0.8184 (m-80) REVERT: E 315 TYR cc_start: 0.8556 (m-80) cc_final: 0.8047 (m-80) REVERT: E 322 THR cc_start: 0.8073 (m) cc_final: 0.7805 (p) REVERT: E 332 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7044 (mt-10) REVERT: E 440 ASP cc_start: 0.8025 (t70) cc_final: 0.7736 (t70) REVERT: E 453 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8048 (mm-40) REVERT: E 457 LEU cc_start: 0.8699 (mt) cc_final: 0.8496 (mp) REVERT: F 66 SER cc_start: 0.8748 (m) cc_final: 0.8451 (p) REVERT: F 239 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6882 (mt-10) REVERT: F 458 ILE cc_start: 0.8524 (tp) cc_final: 0.8187 (tp) REVERT: G 26 GLU cc_start: 0.6745 (tt0) cc_final: 0.6452 (tt0) REVERT: G 41 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7052 (tm-30) REVERT: G 85 ASP cc_start: 0.7284 (t70) cc_final: 0.6715 (t0) REVERT: G 136 GLU cc_start: 0.7782 (tp30) cc_final: 0.7464 (tp30) REVERT: G 162 MET cc_start: 0.7147 (mtp) cc_final: 0.6911 (mtp) REVERT: H 7 GLU cc_start: 0.7104 (tt0) cc_final: 0.6636 (mt-10) REVERT: a 188 ARG cc_start: 0.7383 (ttm-80) cc_final: 0.7169 (ttm-80) REVERT: d 132 ILE cc_start: 0.6401 (mt) cc_final: 0.6180 (mt) REVERT: d 298 ARG cc_start: 0.7277 (ttt90) cc_final: 0.6696 (ttm170) REVERT: d 440 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7998 (tm-30) outliers start: 61 outliers final: 37 residues processed: 676 average time/residue: 0.4793 time to fit residues: 533.5751 Evaluate side-chains 605 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 567 time to evaluate : 3.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 203 ILE Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 436 LEU Chi-restraints excluded: chain 6 residue 21 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 240 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 359 optimal weight: 10.0000 chunk 294 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 433 optimal weight: 2.9990 chunk 467 optimal weight: 9.9990 chunk 385 optimal weight: 0.0040 chunk 429 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 347 optimal weight: 6.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 219 GLN G 93 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 34 GLN d 141 GLN d 347 GLN 4 46 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 36422 Z= 0.242 Angle : 0.589 10.398 49490 Z= 0.300 Chirality : 0.043 0.236 5810 Planarity : 0.004 0.041 6389 Dihedral : 8.543 110.973 5435 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.74 % Favored : 98.14 % Rotamer: Outliers : 2.26 % Allowed : 12.93 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.12), residues: 4774 helix: 1.31 (0.10), residues: 2597 sheet: -0.70 (0.21), residues: 525 loop : -0.10 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 212 HIS 0.006 0.001 HIS a 158 PHE 0.028 0.001 PHE a 213 TYR 0.027 0.001 TYR a 145 ARG 0.006 0.000 ARG G 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 586 time to evaluate : 4.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7272 (pt0) cc_final: 0.7053 (pt0) REVERT: A 71 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7697 (mt-10) REVERT: A 160 THR cc_start: 0.8237 (p) cc_final: 0.7783 (t) REVERT: A 184 ASP cc_start: 0.6985 (m-30) cc_final: 0.6696 (m-30) REVERT: A 200 GLN cc_start: 0.8412 (mt0) cc_final: 0.8053 (mm-40) REVERT: A 336 ASP cc_start: 0.7680 (t0) cc_final: 0.7397 (t0) REVERT: A 356 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6901 (mt-10) REVERT: A 388 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7586 (mt-10) REVERT: A 429 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7390 (mm-30) REVERT: A 473 GLU cc_start: 0.7896 (tp30) cc_final: 0.7640 (tt0) REVERT: B 132 LEU cc_start: 0.8400 (mt) cc_final: 0.8183 (mp) REVERT: B 157 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7487 (t0) REVERT: B 194 LEU cc_start: 0.8289 (mt) cc_final: 0.8088 (mt) REVERT: B 269 ILE cc_start: 0.8049 (mm) cc_final: 0.7840 (mm) REVERT: B 488 GLU cc_start: 0.7603 (tt0) cc_final: 0.7291 (pt0) REVERT: C 132 LEU cc_start: 0.8920 (mt) cc_final: 0.8671 (mt) REVERT: C 229 MET cc_start: 0.8822 (mmm) cc_final: 0.8597 (tpt) REVERT: C 269 ILE cc_start: 0.7976 (mm) cc_final: 0.7620 (tt) REVERT: C 335 ASN cc_start: 0.8893 (t0) cc_final: 0.8465 (t0) REVERT: C 399 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7639 (mm-40) REVERT: D 67 MET cc_start: 0.8416 (mmp) cc_final: 0.8190 (mmt) REVERT: D 185 SER cc_start: 0.8618 (t) cc_final: 0.8282 (m) REVERT: D 292 GLU cc_start: 0.7472 (tp30) cc_final: 0.7075 (tp30) REVERT: D 314 ASP cc_start: 0.7785 (t0) cc_final: 0.7530 (t70) REVERT: D 416 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7905 (ptp) REVERT: D 447 PHE cc_start: 0.8347 (m-80) cc_final: 0.8005 (m-10) REVERT: E 315 TYR cc_start: 0.8604 (m-80) cc_final: 0.8171 (m-80) REVERT: E 332 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7076 (mt-10) REVERT: E 440 ASP cc_start: 0.8009 (t70) cc_final: 0.7721 (t70) REVERT: E 453 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8052 (mm-40) REVERT: F 66 SER cc_start: 0.8804 (m) cc_final: 0.8579 (p) REVERT: F 181 PHE cc_start: 0.7274 (t80) cc_final: 0.7042 (t80) REVERT: F 239 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6826 (mt-10) REVERT: F 254 ASP cc_start: 0.6951 (t0) cc_final: 0.6737 (t70) REVERT: F 305 MET cc_start: 0.7647 (tpp) cc_final: 0.7417 (ttt) REVERT: F 458 ILE cc_start: 0.8539 (tp) cc_final: 0.8220 (tp) REVERT: G 26 GLU cc_start: 0.6715 (tt0) cc_final: 0.6435 (tt0) REVERT: G 41 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7097 (tp30) REVERT: G 136 GLU cc_start: 0.7780 (tp30) cc_final: 0.7450 (tp30) REVERT: G 162 MET cc_start: 0.7158 (mtp) cc_final: 0.6932 (mtp) REVERT: H 7 GLU cc_start: 0.7251 (tt0) cc_final: 0.6460 (mm-30) REVERT: a 100 ILE cc_start: 0.7450 (tp) cc_final: 0.6914 (mp) REVERT: a 188 ARG cc_start: 0.7269 (ttm-80) cc_final: 0.7025 (ttm110) REVERT: d 440 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7913 (tm-30) REVERT: 7 72 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6722 (tt) outliers start: 79 outliers final: 49 residues processed: 630 average time/residue: 0.4700 time to fit residues: 489.5795 Evaluate side-chains 597 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 545 time to evaluate : 4.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 384 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 313 ASP Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 310 SER Chi-restraints excluded: chain d residue 436 LEU Chi-restraints excluded: chain 6 residue 21 MET Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 9 residue 20 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 427 optimal weight: 0.1980 chunk 325 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 chunk 434 optimal weight: 9.9990 chunk 460 optimal weight: 0.4980 chunk 227 optimal weight: 2.9990 chunk 411 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 453 GLN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN D 421 GLN E 55 GLN F 245 GLN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 36422 Z= 0.374 Angle : 0.622 10.324 49490 Z= 0.314 Chirality : 0.045 0.256 5810 Planarity : 0.004 0.044 6389 Dihedral : 8.328 112.327 5435 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.26 % Favored : 97.61 % Rotamer: Outliers : 2.95 % Allowed : 14.18 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.12), residues: 4774 helix: 1.50 (0.10), residues: 2582 sheet: -0.71 (0.21), residues: 550 loop : -0.10 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 247 HIS 0.005 0.001 HIS a 158 PHE 0.028 0.002 PHE 7 57 TYR 0.027 0.002 TYR a 145 ARG 0.005 0.001 ARG E 410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 579 time to evaluate : 4.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7274 (pt0) cc_final: 0.7041 (pt0) REVERT: A 71 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7721 (mt-10) REVERT: A 160 THR cc_start: 0.8239 (p) cc_final: 0.7787 (t) REVERT: A 200 GLN cc_start: 0.8491 (mt0) cc_final: 0.8072 (mm-40) REVERT: A 232 THR cc_start: 0.8098 (m) cc_final: 0.7869 (t) REVERT: A 336 ASP cc_start: 0.7736 (t0) cc_final: 0.7505 (t0) REVERT: A 356 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6877 (mt-10) REVERT: A 388 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7585 (mt-10) REVERT: A 429 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7312 (mm-30) REVERT: A 473 GLU cc_start: 0.7936 (tp30) cc_final: 0.7646 (tt0) REVERT: B 157 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7505 (t0) REVERT: B 194 LEU cc_start: 0.8339 (mt) cc_final: 0.8113 (mt) REVERT: B 269 ILE cc_start: 0.8169 (mm) cc_final: 0.7888 (mm) REVERT: B 488 GLU cc_start: 0.7691 (tt0) cc_final: 0.7385 (pt0) REVERT: C 229 MET cc_start: 0.8878 (mmm) cc_final: 0.8565 (tpt) REVERT: C 269 ILE cc_start: 0.8018 (mm) cc_final: 0.7701 (tt) REVERT: C 333 LYS cc_start: 0.8066 (mmtt) cc_final: 0.7688 (mtmt) REVERT: C 399 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7564 (mm-40) REVERT: D 67 MET cc_start: 0.8490 (mmp) cc_final: 0.8264 (mmt) REVERT: D 185 SER cc_start: 0.8617 (t) cc_final: 0.8266 (m) REVERT: D 272 ARG cc_start: 0.8217 (mtm180) cc_final: 0.7760 (mtt180) REVERT: D 279 TYR cc_start: 0.8734 (m-80) cc_final: 0.8509 (m-80) REVERT: D 292 GLU cc_start: 0.7502 (tp30) cc_final: 0.7082 (tp30) REVERT: D 314 ASP cc_start: 0.7859 (t0) cc_final: 0.7562 (t0) REVERT: D 447 PHE cc_start: 0.8420 (m-80) cc_final: 0.8106 (m-10) REVERT: D 452 GLU cc_start: 0.7778 (mp0) cc_final: 0.7565 (mt-10) REVERT: E 245 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8255 (mm110) REVERT: E 247 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7762 (mp10) REVERT: E 315 TYR cc_start: 0.8667 (m-80) cc_final: 0.8311 (m-80) REVERT: E 332 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7150 (mt-10) REVERT: E 440 ASP cc_start: 0.8023 (t70) cc_final: 0.7724 (t70) REVERT: E 453 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8040 (mm-40) REVERT: F 66 SER cc_start: 0.8812 (m) cc_final: 0.8538 (p) REVERT: F 239 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6884 (mt-10) REVERT: F 254 ASP cc_start: 0.7064 (t0) cc_final: 0.6789 (t70) REVERT: F 420 GLU cc_start: 0.7440 (tp30) cc_final: 0.7064 (tp30) REVERT: F 458 ILE cc_start: 0.8580 (tp) cc_final: 0.8265 (tp) REVERT: G 26 GLU cc_start: 0.6830 (tt0) cc_final: 0.6541 (tt0) REVERT: G 41 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7139 (tp30) REVERT: G 136 GLU cc_start: 0.7791 (tp30) cc_final: 0.7483 (tp30) REVERT: G 144 ARG cc_start: 0.7425 (tpp-160) cc_final: 0.6990 (tpt170) REVERT: G 162 MET cc_start: 0.7209 (mtp) cc_final: 0.6936 (mtp) REVERT: H 7 GLU cc_start: 0.7145 (tt0) cc_final: 0.6492 (mm-30) REVERT: a 100 ILE cc_start: 0.7466 (tp) cc_final: 0.6924 (mp) REVERT: d 440 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7877 (tm-30) REVERT: 7 72 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6723 (tt) REVERT: 8 21 MET cc_start: 0.6137 (mmm) cc_final: 0.5785 (mmm) outliers start: 103 outliers final: 68 residues processed: 636 average time/residue: 0.4844 time to fit residues: 512.1498 Evaluate side-chains 620 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 550 time to evaluate : 4.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 384 ASP Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 313 ASP Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 310 SER Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain d residue 436 LEU Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 9 residue 20 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 383 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 342 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 392 optimal weight: 3.9990 chunk 318 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 234 optimal weight: 0.8980 chunk 412 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 GLN C 143 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN D 365 HIS ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN 4 71 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 36422 Z= 0.242 Angle : 0.574 10.671 49490 Z= 0.288 Chirality : 0.043 0.278 5810 Planarity : 0.004 0.044 6389 Dihedral : 8.021 112.355 5435 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.12 % Favored : 97.76 % Rotamer: Outliers : 3.03 % Allowed : 15.61 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.21 (0.12), residues: 4774 helix: 1.71 (0.10), residues: 2579 sheet: -0.65 (0.21), residues: 548 loop : -0.02 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 212 HIS 0.005 0.001 HIS a 158 PHE 0.032 0.001 PHE 7 57 TYR 0.026 0.001 TYR a 145 ARG 0.006 0.000 ARG E 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 595 time to evaluate : 4.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7248 (pt0) cc_final: 0.7029 (pt0) REVERT: A 160 THR cc_start: 0.8234 (p) cc_final: 0.7787 (t) REVERT: A 184 ASP cc_start: 0.7055 (m-30) cc_final: 0.6825 (m-30) REVERT: A 200 GLN cc_start: 0.8484 (mt0) cc_final: 0.8031 (mm-40) REVERT: A 232 THR cc_start: 0.8040 (m) cc_final: 0.7819 (t) REVERT: A 269 ILE cc_start: 0.7834 (mm) cc_final: 0.7539 (mt) REVERT: A 310 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6617 (mm-30) REVERT: A 336 ASP cc_start: 0.7709 (t0) cc_final: 0.7434 (t0) REVERT: A 356 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6794 (mt-10) REVERT: A 388 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: A 429 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7316 (mm-30) REVERT: A 473 GLU cc_start: 0.7824 (tp30) cc_final: 0.7572 (tt0) REVERT: B 157 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7397 (t0) REVERT: B 488 GLU cc_start: 0.7725 (tt0) cc_final: 0.7411 (pt0) REVERT: C 229 MET cc_start: 0.8800 (mmm) cc_final: 0.8513 (tpt) REVERT: C 333 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7711 (mtmt) REVERT: C 399 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7565 (mm-40) REVERT: C 421 LEU cc_start: 0.7994 (tp) cc_final: 0.7690 (mp) REVERT: D 67 MET cc_start: 0.8445 (mmp) cc_final: 0.8224 (mmt) REVERT: D 185 SER cc_start: 0.8616 (t) cc_final: 0.8268 (m) REVERT: D 272 ARG cc_start: 0.8146 (mtt180) cc_final: 0.7735 (mtt180) REVERT: D 292 GLU cc_start: 0.7503 (tp30) cc_final: 0.7097 (tp30) REVERT: D 314 ASP cc_start: 0.7725 (t0) cc_final: 0.7431 (t0) REVERT: D 452 GLU cc_start: 0.7743 (mp0) cc_final: 0.7511 (mt-10) REVERT: E 45 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7856 (pp) REVERT: E 245 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8283 (mm110) REVERT: E 332 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7115 (mt-10) REVERT: E 440 ASP cc_start: 0.7864 (t70) cc_final: 0.7524 (t70) REVERT: E 453 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8169 (mm-40) REVERT: F 62 VAL cc_start: 0.8236 (m) cc_final: 0.8032 (p) REVERT: F 66 SER cc_start: 0.8808 (m) cc_final: 0.8390 (p) REVERT: F 254 ASP cc_start: 0.7052 (t0) cc_final: 0.6759 (t70) REVERT: F 305 MET cc_start: 0.7547 (tpp) cc_final: 0.7289 (tpp) REVERT: F 337 VAL cc_start: 0.7906 (t) cc_final: 0.7550 (p) REVERT: F 420 GLU cc_start: 0.7403 (tp30) cc_final: 0.7037 (tp30) REVERT: F 458 ILE cc_start: 0.8509 (tp) cc_final: 0.8158 (tp) REVERT: G 26 GLU cc_start: 0.6815 (tt0) cc_final: 0.6511 (tt0) REVERT: G 41 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7159 (tp30) REVERT: G 136 GLU cc_start: 0.7775 (tp30) cc_final: 0.7459 (tp30) REVERT: G 144 ARG cc_start: 0.7403 (tpp-160) cc_final: 0.6975 (mtp-110) REVERT: G 162 MET cc_start: 0.7219 (mtp) cc_final: 0.6946 (mtp) REVERT: H 7 GLU cc_start: 0.7129 (tt0) cc_final: 0.6484 (mm-30) REVERT: a 100 ILE cc_start: 0.7466 (tp) cc_final: 0.6938 (mp) REVERT: a 192 ASN cc_start: 0.5733 (OUTLIER) cc_final: 0.5373 (t0) REVERT: a 233 PHE cc_start: 0.7101 (t80) cc_final: 0.6570 (t80) REVERT: d 440 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7868 (tm-30) REVERT: 2 75 MET cc_start: 0.5417 (ppp) cc_final: 0.5005 (tmm) REVERT: 7 72 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6750 (tt) REVERT: 8 70 ILE cc_start: 0.6819 (pt) cc_final: 0.6619 (pt) outliers start: 106 outliers final: 68 residues processed: 652 average time/residue: 0.4547 time to fit residues: 495.6445 Evaluate side-chains 630 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 557 time to evaluate : 3.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 313 ASP Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 235 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 310 SER Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain d residue 436 LEU Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 9 residue 20 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 154 optimal weight: 0.1980 chunk 414 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 460 optimal weight: 2.9990 chunk 382 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 241 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS B 43 HIS C 89 GLN C 143 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN E 55 GLN ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 112 GLN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36422 Z= 0.217 Angle : 0.561 10.722 49490 Z= 0.282 Chirality : 0.042 0.291 5810 Planarity : 0.004 0.044 6389 Dihedral : 7.719 111.107 5435 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.24 % Favored : 97.63 % Rotamer: Outliers : 3.03 % Allowed : 16.44 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.12), residues: 4774 helix: 1.91 (0.10), residues: 2564 sheet: -0.59 (0.21), residues: 539 loop : 0.05 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 212 HIS 0.005 0.001 HIS d 273 PHE 0.032 0.001 PHE 7 57 TYR 0.024 0.001 TYR a 145 ARG 0.007 0.000 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 582 time to evaluate : 4.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7264 (pt0) cc_final: 0.7042 (pt0) REVERT: A 67 LEU cc_start: 0.8359 (tp) cc_final: 0.8114 (tp) REVERT: A 160 THR cc_start: 0.8240 (p) cc_final: 0.7792 (t) REVERT: A 184 ASP cc_start: 0.7081 (m-30) cc_final: 0.6830 (m-30) REVERT: A 200 GLN cc_start: 0.8471 (mt0) cc_final: 0.8001 (mm-40) REVERT: A 232 THR cc_start: 0.8034 (m) cc_final: 0.7806 (t) REVERT: A 269 ILE cc_start: 0.7818 (mm) cc_final: 0.7477 (mt) REVERT: A 310 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6585 (mm-30) REVERT: A 324 MET cc_start: 0.8325 (ttt) cc_final: 0.8051 (ttt) REVERT: A 336 ASP cc_start: 0.7694 (t0) cc_final: 0.7429 (t0) REVERT: A 356 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6815 (mt-10) REVERT: A 388 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7569 (mt-10) REVERT: A 429 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7302 (mm-30) REVERT: A 473 GLU cc_start: 0.7806 (tp30) cc_final: 0.7552 (tt0) REVERT: B 157 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7420 (t0) REVERT: B 466 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7712 (ttp80) REVERT: B 488 GLU cc_start: 0.7745 (tt0) cc_final: 0.7410 (pt0) REVERT: C 300 ASP cc_start: 0.8001 (p0) cc_final: 0.7350 (p0) REVERT: C 333 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7683 (mtmt) REVERT: C 399 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7604 (mm-40) REVERT: C 421 LEU cc_start: 0.7879 (tp) cc_final: 0.7591 (mp) REVERT: D 67 MET cc_start: 0.8447 (mmp) cc_final: 0.8234 (mmt) REVERT: D 179 ARG cc_start: 0.8158 (mtp180) cc_final: 0.7946 (mtp85) REVERT: D 185 SER cc_start: 0.8615 (t) cc_final: 0.8255 (m) REVERT: D 272 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7795 (mtt180) REVERT: D 292 GLU cc_start: 0.7508 (tp30) cc_final: 0.7107 (tp30) REVERT: D 314 ASP cc_start: 0.7693 (t0) cc_final: 0.7407 (t0) REVERT: D 452 GLU cc_start: 0.7742 (mp0) cc_final: 0.7275 (mt-10) REVERT: E 45 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7804 (pp) REVERT: E 219 GLN cc_start: 0.7711 (mm110) cc_final: 0.7297 (mm110) REVERT: E 332 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7166 (mt-10) REVERT: E 407 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7755 (mtt-85) REVERT: E 440 ASP cc_start: 0.7815 (t70) cc_final: 0.7493 (t70) REVERT: E 453 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8166 (mm-40) REVERT: F 66 SER cc_start: 0.8815 (m) cc_final: 0.8403 (p) REVERT: F 67 MET cc_start: 0.8323 (mmm) cc_final: 0.7036 (mmm) REVERT: F 254 ASP cc_start: 0.7081 (t0) cc_final: 0.6773 (t70) REVERT: F 337 VAL cc_start: 0.7913 (t) cc_final: 0.7570 (p) REVERT: F 420 GLU cc_start: 0.7417 (tp30) cc_final: 0.7080 (tp30) REVERT: F 458 ILE cc_start: 0.8491 (tp) cc_final: 0.8146 (tp) REVERT: G 26 GLU cc_start: 0.6755 (tt0) cc_final: 0.6462 (tt0) REVERT: G 85 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7812 (m-30) REVERT: G 136 GLU cc_start: 0.7834 (tp30) cc_final: 0.7511 (tp30) REVERT: G 144 ARG cc_start: 0.7437 (tpp-160) cc_final: 0.6918 (tpt170) REVERT: G 162 MET cc_start: 0.7215 (mtp) cc_final: 0.6988 (mtp) REVERT: G 206 MET cc_start: 0.8791 (mtp) cc_final: 0.8515 (mtm) REVERT: H 7 GLU cc_start: 0.7137 (tt0) cc_final: 0.6480 (mm-30) REVERT: a 100 ILE cc_start: 0.7434 (tp) cc_final: 0.6931 (mp) REVERT: a 192 ASN cc_start: 0.5757 (OUTLIER) cc_final: 0.5472 (t0) REVERT: a 233 PHE cc_start: 0.7066 (t80) cc_final: 0.6607 (t80) REVERT: d 241 LEU cc_start: 0.7727 (mt) cc_final: 0.7491 (mt) REVERT: d 440 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7871 (tm-30) REVERT: 2 75 MET cc_start: 0.5407 (ppp) cc_final: 0.4934 (tmm) REVERT: 7 72 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6758 (tt) outliers start: 106 outliers final: 72 residues processed: 632 average time/residue: 0.4719 time to fit residues: 494.0537 Evaluate side-chains 623 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 545 time to evaluate : 3.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 407 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 313 ASP Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 235 LEU Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 310 SER Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 7 residue 21 MET Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 9 residue 20 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 444 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 262 optimal weight: 3.9990 chunk 336 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 387 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 458 optimal weight: 7.9990 chunk 287 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 211 optimal weight: 0.2980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN E 55 GLN E 247 GLN ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN ** 4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 36422 Z= 0.331 Angle : 0.600 10.810 49490 Z= 0.301 Chirality : 0.044 0.302 5810 Planarity : 0.004 0.045 6389 Dihedral : 7.658 112.510 5435 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.39 % Favored : 97.49 % Rotamer: Outliers : 3.29 % Allowed : 16.59 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.34 (0.12), residues: 4774 helix: 1.86 (0.10), residues: 2568 sheet: -0.63 (0.21), residues: 550 loop : 0.00 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP a 212 HIS 0.005 0.001 HIS F 37 PHE 0.034 0.002 PHE 7 57 TYR 0.025 0.002 TYR a 145 ARG 0.007 0.000 ARG F 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 555 time to evaluate : 4.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7282 (pt0) cc_final: 0.7061 (pt0) REVERT: A 67 LEU cc_start: 0.8380 (tp) cc_final: 0.8129 (tp) REVERT: A 160 THR cc_start: 0.8252 (p) cc_final: 0.7804 (t) REVERT: A 184 ASP cc_start: 0.7060 (m-30) cc_final: 0.6839 (m-30) REVERT: A 200 GLN cc_start: 0.8497 (mt0) cc_final: 0.7977 (mm110) REVERT: A 232 THR cc_start: 0.8109 (m) cc_final: 0.7895 (t) REVERT: A 310 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6538 (mm-30) REVERT: A 336 ASP cc_start: 0.7706 (t0) cc_final: 0.7483 (t0) REVERT: A 388 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: A 429 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 473 GLU cc_start: 0.7873 (tp30) cc_final: 0.7601 (tt0) REVERT: B 157 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7536 (t0) REVERT: C 229 MET cc_start: 0.8988 (mmm) cc_final: 0.8627 (tpt) REVERT: C 399 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7567 (mm-40) REVERT: C 421 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7602 (mp) REVERT: C 429 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7038 (mm-30) REVERT: C 468 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: D 39 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7750 (mm-30) REVERT: D 67 MET cc_start: 0.8474 (mmp) cc_final: 0.8256 (mmt) REVERT: D 179 ARG cc_start: 0.8182 (mtp180) cc_final: 0.7961 (mtp85) REVERT: D 185 SER cc_start: 0.8635 (t) cc_final: 0.8268 (m) REVERT: D 292 GLU cc_start: 0.7451 (tp30) cc_final: 0.7057 (tp30) REVERT: D 314 ASP cc_start: 0.7772 (t0) cc_final: 0.7508 (t0) REVERT: D 446 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7247 (tt0) REVERT: D 452 GLU cc_start: 0.7821 (mp0) cc_final: 0.7317 (mt-10) REVERT: E 11 ARG cc_start: 0.7574 (mtm-85) cc_final: 0.6994 (mtm-85) REVERT: E 45 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7928 (pp) REVERT: E 245 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8292 (mm110) REVERT: E 332 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7205 (mt-10) REVERT: E 407 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7694 (mtt-85) REVERT: E 453 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8103 (mm-40) REVERT: F 66 SER cc_start: 0.8821 (m) cc_final: 0.8405 (p) REVERT: F 254 ASP cc_start: 0.7128 (t0) cc_final: 0.6793 (t70) REVERT: F 315 TYR cc_start: 0.8586 (m-80) cc_final: 0.8386 (m-10) REVERT: F 337 VAL cc_start: 0.7887 (t) cc_final: 0.7546 (p) REVERT: F 420 GLU cc_start: 0.7501 (tp30) cc_final: 0.7156 (tp30) REVERT: F 458 ILE cc_start: 0.8538 (tp) cc_final: 0.8198 (tp) REVERT: G 26 GLU cc_start: 0.6843 (tt0) cc_final: 0.6513 (tt0) REVERT: G 136 GLU cc_start: 0.7865 (tp30) cc_final: 0.7531 (tp30) REVERT: G 144 ARG cc_start: 0.7515 (tpp-160) cc_final: 0.7188 (ttm-80) REVERT: G 162 MET cc_start: 0.7246 (mtp) cc_final: 0.7030 (mtp) REVERT: H 7 GLU cc_start: 0.7122 (tt0) cc_final: 0.6475 (mm-30) REVERT: a 100 ILE cc_start: 0.7477 (tp) cc_final: 0.6962 (mp) REVERT: a 192 ASN cc_start: 0.5666 (OUTLIER) cc_final: 0.5372 (t0) REVERT: d 241 LEU cc_start: 0.7792 (mt) cc_final: 0.7537 (mt) REVERT: d 251 ASP cc_start: 0.7581 (t70) cc_final: 0.7369 (t0) REVERT: d 440 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7765 (tm-30) REVERT: 2 75 MET cc_start: 0.5427 (ppp) cc_final: 0.5163 (tmm) REVERT: 7 72 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6795 (tt) outliers start: 115 outliers final: 85 residues processed: 619 average time/residue: 0.4714 time to fit residues: 483.0037 Evaluate side-chains 630 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 537 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 247 GLN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 407 ARG Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 313 ASP Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 310 SER Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain d residue 436 LEU Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 7 residue 21 MET Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 9 residue 20 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 283 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 274 optimal weight: 0.0670 chunk 138 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 312 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 360 optimal weight: 5.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN E 55 GLN ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN ** 2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 46 GLN ** 4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 36422 Z= 0.210 Angle : 0.571 11.178 49490 Z= 0.285 Chirality : 0.042 0.323 5810 Planarity : 0.004 0.045 6389 Dihedral : 7.406 111.868 5435 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.24 % Favored : 97.63 % Rotamer: Outliers : 2.95 % Allowed : 17.30 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.51 (0.12), residues: 4774 helix: 2.02 (0.10), residues: 2563 sheet: -0.66 (0.22), residues: 519 loop : 0.05 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a 212 HIS 0.004 0.001 HIS d 273 PHE 0.036 0.001 PHE 7 57 TYR 0.023 0.001 TYR a 145 ARG 0.007 0.000 ARG E 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 572 time to evaluate : 4.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7230 (pt0) cc_final: 0.7017 (pt0) REVERT: A 67 LEU cc_start: 0.8327 (tp) cc_final: 0.8105 (tp) REVERT: A 160 THR cc_start: 0.8245 (p) cc_final: 0.7785 (t) REVERT: A 184 ASP cc_start: 0.7083 (m-30) cc_final: 0.6682 (m-30) REVERT: A 200 GLN cc_start: 0.8473 (mt0) cc_final: 0.7983 (mm-40) REVERT: A 232 THR cc_start: 0.8048 (m) cc_final: 0.7804 (t) REVERT: A 310 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6555 (mm-30) REVERT: A 336 ASP cc_start: 0.7689 (t0) cc_final: 0.7416 (t0) REVERT: A 388 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: A 429 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7316 (mm-30) REVERT: A 473 GLU cc_start: 0.7813 (tp30) cc_final: 0.7543 (tt0) REVERT: B 157 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7478 (t0) REVERT: B 279 ASP cc_start: 0.7145 (t0) cc_final: 0.6879 (t0) REVERT: B 461 VAL cc_start: 0.8833 (m) cc_final: 0.8615 (t) REVERT: B 466 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7732 (ttp80) REVERT: C 324 MET cc_start: 0.8060 (ttm) cc_final: 0.7824 (ttm) REVERT: C 399 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7608 (mm-40) REVERT: C 429 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7019 (mm-30) REVERT: C 468 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7591 (tt0) REVERT: D 39 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7607 (mm-30) REVERT: D 67 MET cc_start: 0.8462 (mmp) cc_final: 0.8234 (mmt) REVERT: D 173 MET cc_start: 0.8043 (mmm) cc_final: 0.7415 (mmt) REVERT: D 179 ARG cc_start: 0.8186 (mtp180) cc_final: 0.7920 (mtp85) REVERT: D 185 SER cc_start: 0.8633 (t) cc_final: 0.8261 (m) REVERT: D 221 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: D 292 GLU cc_start: 0.7443 (tp30) cc_final: 0.7061 (tp30) REVERT: D 314 ASP cc_start: 0.7695 (t0) cc_final: 0.7422 (t0) REVERT: D 446 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7246 (tt0) REVERT: D 452 GLU cc_start: 0.7752 (mp0) cc_final: 0.7335 (mt-10) REVERT: E 45 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7824 (pp) REVERT: E 71 ASP cc_start: 0.7270 (p0) cc_final: 0.7023 (p0) REVERT: E 219 GLN cc_start: 0.7740 (mm110) cc_final: 0.7354 (mm110) REVERT: E 247 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7478 (mt0) REVERT: E 332 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7188 (mt-10) REVERT: E 407 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7751 (mtt-85) REVERT: E 412 LEU cc_start: 0.7952 (mt) cc_final: 0.7690 (mm) REVERT: E 453 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8083 (mm-40) REVERT: E 457 LEU cc_start: 0.8593 (mt) cc_final: 0.8387 (mt) REVERT: F 36 LEU cc_start: 0.8116 (mt) cc_final: 0.7683 (mt) REVERT: F 66 SER cc_start: 0.8803 (m) cc_final: 0.8369 (p) REVERT: F 67 MET cc_start: 0.8295 (mmm) cc_final: 0.7007 (mmm) REVERT: F 173 MET cc_start: 0.7228 (tpp) cc_final: 0.6817 (mmt) REVERT: F 254 ASP cc_start: 0.7069 (t0) cc_final: 0.6714 (t70) REVERT: F 337 VAL cc_start: 0.7942 (t) cc_final: 0.7596 (p) REVERT: F 420 GLU cc_start: 0.7468 (tp30) cc_final: 0.7150 (tp30) REVERT: F 458 ILE cc_start: 0.8478 (tp) cc_final: 0.8124 (tp) REVERT: G 26 GLU cc_start: 0.6800 (tt0) cc_final: 0.6480 (tt0) REVERT: G 136 GLU cc_start: 0.7857 (tp30) cc_final: 0.7515 (tp30) REVERT: G 144 ARG cc_start: 0.7559 (tpp-160) cc_final: 0.7123 (mtp-110) REVERT: G 162 MET cc_start: 0.7180 (mtp) cc_final: 0.6958 (mtp) REVERT: G 206 MET cc_start: 0.8743 (mtp) cc_final: 0.8362 (mtm) REVERT: H 7 GLU cc_start: 0.7096 (tt0) cc_final: 0.6440 (mm-30) REVERT: a 192 ASN cc_start: 0.5690 (OUTLIER) cc_final: 0.5354 (t0) REVERT: a 233 PHE cc_start: 0.7200 (t80) cc_final: 0.6605 (t80) REVERT: d 241 LEU cc_start: 0.7757 (mt) cc_final: 0.7497 (mt) REVERT: d 440 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7720 (tm-30) REVERT: 2 75 MET cc_start: 0.5371 (ppp) cc_final: 0.5134 (tmm) REVERT: 7 72 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6798 (tt) outliers start: 103 outliers final: 74 residues processed: 629 average time/residue: 0.4693 time to fit residues: 488.6250 Evaluate side-chains 627 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 544 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 247 GLN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 407 ARG Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 313 ASP Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 310 SER Chi-restraints excluded: chain d residue 362 ILE Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 7 residue 21 MET Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 9 residue 20 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 417 optimal weight: 0.6980 chunk 439 optimal weight: 5.9990 chunk 401 optimal weight: 20.0000 chunk 427 optimal weight: 6.9990 chunk 257 optimal weight: 0.0980 chunk 186 optimal weight: 4.9990 chunk 335 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 386 optimal weight: 3.9990 chunk 404 optimal weight: 9.9990 chunk 426 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN C 143 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN E 55 GLN ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN d 273 HIS 4 71 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 36422 Z= 0.570 Angle : 0.708 11.113 49490 Z= 0.355 Chirality : 0.049 0.351 5810 Planarity : 0.005 0.047 6389 Dihedral : 7.620 114.921 5435 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.83 % Favored : 97.05 % Rotamer: Outliers : 3.00 % Allowed : 17.93 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.00 (0.12), residues: 4774 helix: 1.62 (0.10), residues: 2589 sheet: -0.88 (0.22), residues: 546 loop : -0.20 (0.16), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP a 212 HIS 0.008 0.002 HIS F 37 PHE 0.038 0.002 PHE 7 57 TYR 0.030 0.002 TYR B 436 ARG 0.006 0.001 ARG D 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 547 time to evaluate : 3.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7249 (pt0) cc_final: 0.7042 (pt0) REVERT: A 67 LEU cc_start: 0.8401 (tp) cc_final: 0.8122 (tp) REVERT: A 160 THR cc_start: 0.8252 (p) cc_final: 0.7826 (t) REVERT: A 200 GLN cc_start: 0.8599 (mt0) cc_final: 0.8055 (mm-40) REVERT: A 388 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: A 429 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7228 (mm-30) REVERT: A 473 GLU cc_start: 0.7942 (tp30) cc_final: 0.7610 (tt0) REVERT: B 279 ASP cc_start: 0.7221 (t0) cc_final: 0.6976 (t0) REVERT: B 466 ARG cc_start: 0.8024 (ttp80) cc_final: 0.7778 (ttp80) REVERT: C 269 ILE cc_start: 0.8165 (mm) cc_final: 0.7846 (tt) REVERT: C 348 ILE cc_start: 0.8560 (mt) cc_final: 0.8355 (mp) REVERT: C 399 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7507 (mm-40) REVERT: C 429 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7058 (mm-30) REVERT: C 468 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7540 (tt0) REVERT: D 39 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7551 (mm-30) REVERT: D 120 ILE cc_start: 0.8406 (pt) cc_final: 0.8143 (pt) REVERT: D 185 SER cc_start: 0.8669 (t) cc_final: 0.8269 (m) REVERT: D 279 TYR cc_start: 0.8721 (m-80) cc_final: 0.8414 (m-10) REVERT: D 292 GLU cc_start: 0.7506 (tp30) cc_final: 0.7123 (tp30) REVERT: D 446 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7419 (tt0) REVERT: D 447 PHE cc_start: 0.8473 (m-80) cc_final: 0.8255 (m-10) REVERT: E 45 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7953 (pp) REVERT: E 71 ASP cc_start: 0.7412 (p0) cc_final: 0.7125 (p0) REVERT: E 219 GLN cc_start: 0.7788 (mm110) cc_final: 0.7418 (mm-40) REVERT: E 247 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: E 332 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7271 (mt-10) REVERT: E 453 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8167 (mm-40) REVERT: F 66 SER cc_start: 0.8828 (m) cc_final: 0.8412 (p) REVERT: F 254 ASP cc_start: 0.7181 (t0) cc_final: 0.6819 (t70) REVERT: F 420 GLU cc_start: 0.7520 (tp30) cc_final: 0.7139 (tp30) REVERT: F 458 ILE cc_start: 0.8550 (tp) cc_final: 0.8248 (tp) REVERT: G 26 GLU cc_start: 0.6877 (tt0) cc_final: 0.6502 (tt0) REVERT: G 102 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7096 (tm-30) REVERT: G 136 GLU cc_start: 0.7900 (tp30) cc_final: 0.7550 (tp30) REVERT: G 144 ARG cc_start: 0.7561 (tpp-160) cc_final: 0.7205 (ttm-80) REVERT: G 162 MET cc_start: 0.7360 (mtp) cc_final: 0.7111 (mtp) REVERT: G 193 MET cc_start: 0.8944 (mmm) cc_final: 0.8735 (tpp) REVERT: G 230 THR cc_start: 0.8030 (m) cc_final: 0.7761 (t) REVERT: H 7 GLU cc_start: 0.7167 (tt0) cc_final: 0.6524 (mm-30) REVERT: a 192 ASN cc_start: 0.5967 (OUTLIER) cc_final: 0.5668 (t0) REVERT: d 241 LEU cc_start: 0.7813 (mt) cc_final: 0.7588 (mt) REVERT: d 440 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7692 (tm-30) REVERT: 2 70 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7565 (mm) REVERT: 2 75 MET cc_start: 0.5596 (ppp) cc_final: 0.5317 (tmm) REVERT: 7 72 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7050 (tt) outliers start: 105 outliers final: 86 residues processed: 617 average time/residue: 0.4853 time to fit residues: 500.2581 Evaluate side-chains 618 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 525 time to evaluate : 4.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 247 GLN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 313 ASP Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain b residue 30 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 112 ASP Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 310 SER Chi-restraints excluded: chain d residue 362 ILE Chi-restraints excluded: chain d residue 405 VAL Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 2 residue 70 ILE Chi-restraints excluded: chain 7 residue 21 MET Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 9 residue 20 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 280 optimal weight: 0.6980 chunk 452 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 214 optimal weight: 0.9990 chunk 314 optimal weight: 0.9990 chunk 474 optimal weight: 3.9990 chunk 436 optimal weight: 2.9990 chunk 377 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 291 optimal weight: 0.6980 chunk 231 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN C 143 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN E 247 GLN ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 36422 Z= 0.207 Angle : 0.585 11.200 49490 Z= 0.294 Chirality : 0.043 0.348 5810 Planarity : 0.004 0.045 6389 Dihedral : 7.280 114.653 5435 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.18 % Favored : 97.70 % Rotamer: Outliers : 2.34 % Allowed : 19.07 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.37 (0.12), residues: 4774 helix: 1.94 (0.10), residues: 2563 sheet: -0.76 (0.23), residues: 515 loop : -0.06 (0.16), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a 212 HIS 0.006 0.001 HIS d 273 PHE 0.036 0.001 PHE 7 57 TYR 0.023 0.001 TYR a 145 ARG 0.007 0.000 ARG F 406 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 574 time to evaluate : 4.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7230 (pt0) cc_final: 0.7025 (pt0) REVERT: A 67 LEU cc_start: 0.8337 (tp) cc_final: 0.8114 (tp) REVERT: A 160 THR cc_start: 0.8267 (p) cc_final: 0.7816 (t) REVERT: A 184 ASP cc_start: 0.7012 (m-30) cc_final: 0.6658 (m-30) REVERT: A 200 GLN cc_start: 0.8489 (mt0) cc_final: 0.7988 (mm110) REVERT: A 310 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6621 (mm-30) REVERT: A 388 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: A 429 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7275 (mm-30) REVERT: A 473 GLU cc_start: 0.7826 (tp30) cc_final: 0.7551 (tt0) REVERT: A 488 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7504 (mm-30) REVERT: B 39 ASP cc_start: 0.7025 (m-30) cc_final: 0.6822 (m-30) REVERT: B 279 ASP cc_start: 0.7132 (t0) cc_final: 0.6890 (t0) REVERT: B 461 VAL cc_start: 0.8833 (m) cc_final: 0.8576 (t) REVERT: B 466 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7756 (ttp80) REVERT: C 269 ILE cc_start: 0.8112 (mm) cc_final: 0.7848 (tt) REVERT: C 311 ARG cc_start: 0.8739 (ttp-110) cc_final: 0.8503 (mtm-85) REVERT: C 335 ASN cc_start: 0.8814 (t0) cc_final: 0.8591 (t0) REVERT: C 399 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7574 (mm-40) REVERT: C 429 GLU cc_start: 0.7411 (mm-30) cc_final: 0.6998 (mm-30) REVERT: C 468 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: D 39 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7527 (mm-30) REVERT: D 120 ILE cc_start: 0.8387 (pt) cc_final: 0.8120 (pt) REVERT: D 185 SER cc_start: 0.8663 (t) cc_final: 0.8273 (m) REVERT: D 292 GLU cc_start: 0.7423 (tp30) cc_final: 0.7040 (tp30) REVERT: D 447 PHE cc_start: 0.8415 (m-80) cc_final: 0.8178 (m-10) REVERT: D 452 GLU cc_start: 0.7778 (mp0) cc_final: 0.7383 (mt-10) REVERT: E 45 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7903 (pp) REVERT: E 71 ASP cc_start: 0.7317 (p0) cc_final: 0.7071 (p0) REVERT: E 219 GLN cc_start: 0.7763 (mm110) cc_final: 0.7357 (mm110) REVERT: E 247 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: E 292 GLU cc_start: 0.7831 (tp30) cc_final: 0.7385 (tp30) REVERT: E 332 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7193 (mt-10) REVERT: E 407 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7604 (mtt-85) REVERT: E 412 LEU cc_start: 0.7972 (mt) cc_final: 0.7683 (mm) REVERT: E 453 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8136 (mm-40) REVERT: F 36 LEU cc_start: 0.8098 (mt) cc_final: 0.7611 (mt) REVERT: F 66 SER cc_start: 0.8783 (m) cc_final: 0.8338 (p) REVERT: F 67 MET cc_start: 0.8215 (mmm) cc_final: 0.6913 (mmm) REVERT: F 152 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7819 (ttm170) REVERT: F 254 ASP cc_start: 0.7058 (t0) cc_final: 0.6707 (t70) REVERT: F 337 VAL cc_start: 0.7967 (t) cc_final: 0.7589 (p) REVERT: F 420 GLU cc_start: 0.7475 (tp30) cc_final: 0.7120 (tp30) REVERT: F 458 ILE cc_start: 0.8527 (tp) cc_final: 0.8205 (tp) REVERT: G 26 GLU cc_start: 0.6788 (tt0) cc_final: 0.6471 (tt0) REVERT: G 102 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7111 (tm-30) REVERT: G 118 VAL cc_start: 0.8288 (t) cc_final: 0.7886 (m) REVERT: G 136 GLU cc_start: 0.7859 (tp30) cc_final: 0.7495 (tp30) REVERT: G 144 ARG cc_start: 0.7573 (tpp-160) cc_final: 0.7229 (ttm-80) REVERT: G 162 MET cc_start: 0.7264 (mtp) cc_final: 0.7018 (mtp) REVERT: G 230 THR cc_start: 0.7963 (m) cc_final: 0.7706 (t) REVERT: H 7 GLU cc_start: 0.7109 (tt0) cc_final: 0.6467 (mm-30) REVERT: H 63 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7508 (mm) REVERT: a 192 ASN cc_start: 0.5925 (OUTLIER) cc_final: 0.5636 (t0) REVERT: a 233 PHE cc_start: 0.7118 (t80) cc_final: 0.6758 (t80) REVERT: d 241 LEU cc_start: 0.7834 (mt) cc_final: 0.7586 (mt) REVERT: d 401 TYR cc_start: 0.7260 (m-80) cc_final: 0.7047 (m-80) REVERT: d 440 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7733 (tm-30) REVERT: 2 70 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7531 (mm) REVERT: 2 75 MET cc_start: 0.5463 (ppp) cc_final: 0.5213 (tmm) REVERT: 6 75 MET cc_start: 0.5694 (tpt) cc_final: 0.5288 (tpt) REVERT: 7 72 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6916 (tt) outliers start: 82 outliers final: 69 residues processed: 622 average time/residue: 0.4786 time to fit residues: 488.1510 Evaluate side-chains 632 residues out of total 3763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 554 time to evaluate : 3.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 247 GLN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 407 ARG Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 313 ASP Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 112 ASP Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 362 ILE Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 2 residue 70 ILE Chi-restraints excluded: chain 7 residue 21 MET Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 9 residue 20 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 299 optimal weight: 0.6980 chunk 402 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 348 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 378 optimal weight: 2.9990 chunk 158 optimal weight: 0.5980 chunk 388 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN E 55 GLN ** E 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN ** 2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.148630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111314 restraints weight = 48664.321| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.83 r_work: 0.3182 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 36422 Z= 0.198 Angle : 0.580 10.836 49490 Z= 0.291 Chirality : 0.042 0.341 5810 Planarity : 0.004 0.047 6389 Dihedral : 7.106 110.880 5435 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.30 % Favored : 97.57 % Rotamer: Outliers : 2.23 % Allowed : 19.27 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.51 (0.12), residues: 4774 helix: 2.05 (0.10), residues: 2562 sheet: -0.67 (0.23), residues: 515 loop : 0.00 (0.16), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP a 212 HIS 0.007 0.001 HIS d 273 PHE 0.036 0.001 PHE 7 57 TYR 0.022 0.001 TYR a 145 ARG 0.007 0.000 ARG F 406 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9393.89 seconds wall clock time: 169 minutes 38.42 seconds (10178.42 seconds total)