Starting phenix.real_space_refine on Sat Feb 17 01:04:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4e_32302/02_2024/7w4e_32302_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4e_32302/02_2024/7w4e_32302.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4e_32302/02_2024/7w4e_32302_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4e_32302/02_2024/7w4e_32302_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4e_32302/02_2024/7w4e_32302_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4e_32302/02_2024/7w4e_32302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4e_32302/02_2024/7w4e_32302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4e_32302/02_2024/7w4e_32302_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4e_32302/02_2024/7w4e_32302_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 47 5.49 5 Mg 1 5.21 5 S 482 5.16 5 C 44171 2.51 5 N 11237 2.21 5 O 12230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 234": "OE1" <-> "OE2" Residue "J GLU 306": "OE1" <-> "OE2" Residue "J GLU 311": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L GLU 132": "OE1" <-> "OE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M GLU 217": "OE1" <-> "OE2" Residue "M GLU 269": "OE1" <-> "OE2" Residue "M GLU 410": "OE1" <-> "OE2" Residue "M GLU 535": "OE1" <-> "OE2" Residue "M GLU 647": "OE1" <-> "OE2" Residue "M GLU 660": "OE1" <-> "OE2" Residue "M GLU 670": "OE1" <-> "OE2" Residue "N GLU 50": "OE1" <-> "OE2" Residue "O GLU 72": "OE1" <-> "OE2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "O GLU 207": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "Q GLU 57": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 281": "OE1" <-> "OE2" Residue "Q GLU 336": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "T TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "W GLU 56": "OE1" <-> "OE2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W GLU 123": "OE1" <-> "OE2" Residue "X GLU 125": "OE1" <-> "OE2" Residue "X GLU 136": "OE1" <-> "OE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Z GLU 25": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 111": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 148": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "b GLU 8": "OE1" <-> "OE2" Residue "b GLU 17": "OE1" <-> "OE2" Residue "b GLU 27": "OE1" <-> "OE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "d GLU 166": "OE1" <-> "OE2" Residue "e GLU 130": "OE1" <-> "OE2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 55": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "i GLU 269": "OE1" <-> "OE2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 207": "OE1" <-> "OE2" Residue "l GLU 353": "OE1" <-> "OE2" Residue "l TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 397": "OE1" <-> "OE2" Residue "l GLU 559": "OE1" <-> "OE2" Residue "m GLU 81": "OE1" <-> "OE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "o GLU 22": "OE1" <-> "OE2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "p GLU 28": "OE1" <-> "OE2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p GLU 69": "OE1" <-> "OE2" Residue "p GLU 95": "OE1" <-> "OE2" Residue "p GLU 123": "OE1" <-> "OE2" Residue "p GLU 176": "OE1" <-> "OE2" Residue "r GLU 47": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 222": "OE1" <-> "OE2" Residue "r GLU 335": "OE1" <-> "OE2" Residue "s GLU 192": "OE1" <-> "OE2" Residue "s GLU 206": "OE1" <-> "OE2" Residue "s GLU 214": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "u GLU 17": "OE1" <-> "OE2" Residue "u GLU 153": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 33": "OE1" <-> "OE2" Residue "v GLU 45": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "v GLU 105": "OE1" <-> "OE2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "w GLU 79": "OE1" <-> "OE2" Residue "w GLU 171": "OE1" <-> "OE2" Residue "w GLU 213": "OE1" <-> "OE2" Residue "w GLU 254": "OE1" <-> "OE2" Residue "w GLU 267": "OE1" <-> "OE2" Residue "w GLU 303": "OE1" <-> "OE2" Residue "w GLU 333": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 68197 Number of models: 1 Model: "" Number of chains: 67 Chain: "A" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3327 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 967 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 676 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3459 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 566 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1156 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "X" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 703 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1005 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "h" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 851 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4816 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 28, 'TRANS': 577} Chain: "m" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1292 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "w" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'PEE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {' UQ': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 170 Unusual residues: {' UQ': 1, 'CDL': 1, 'NDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'PEE': 1, 'UQ1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 328 Unusual residues: {'CDL': 3, 'PEE': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 99 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "l" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 296 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "m" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 255 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "s" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "u" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS A 382 49.492 49.549 171.088 1.00 25.13 S ATOM 3057 SG CYS A 425 48.910 46.185 176.762 1.00 34.35 S ATOM 2735 SG CYS A 385 46.433 45.008 171.048 1.00 32.06 S ATOM 2696 SG CYS A 379 44.057 49.964 174.753 1.00 29.55 S ATOM 3958 SG CYS B 113 38.474 64.741 136.139 1.00 21.28 S ATOM 3977 SG CYS B 116 43.649 62.545 139.874 1.00 3.19 S ATOM 4000 SG CYS B 119 44.691 65.267 134.599 1.00 4.10 S ATOM 4329 SG CYS B 162 42.237 59.333 135.042 1.00 1.66 S ATOM 4027 SG CYS B 123 50.790 68.181 130.091 1.00 7.64 S ATOM 4253 SG CYS B 152 49.207 66.268 124.145 1.00 21.22 S ATOM 4300 SG CYS B 158 47.244 62.576 129.040 1.00 9.90 S ATOM 4279 SG CYS B 155 53.287 62.933 127.627 1.00 17.78 S ATOM 5721 SG CYS C 166 55.995 66.417 120.060 1.00 6.05 S ATOM 4993 SG CYS C 72 56.452 67.910 113.731 1.00 19.90 S ATOM 4987 SG CYS C 71 61.793 66.403 116.871 1.00 11.86 S ATOM 5491 SG CYS C 136 58.165 71.549 118.899 1.00 17.26 S ATOM 14931 SG CYS M 131 42.699 62.707 151.924 1.00 10.45 S ATOM 14910 SG CYS M 128 46.307 58.151 149.022 1.00 9.84 S ATOM 14971 SG CYS M 137 48.335 61.898 154.251 1.00 9.55 S ATOM 15303 SG CYS M 179 46.414 61.937 165.095 1.00 12.90 S ATOM 15657 SG CYS M 226 43.416 64.572 160.951 1.00 19.64 S ATOM 15327 SG CYS M 182 40.812 64.558 166.944 1.00 11.49 S ATOM 15280 SG CYS M 176 40.767 59.104 163.521 1.00 23.99 S ATOM 14528 SG CYS M 78 58.171 57.679 169.365 1.00 22.39 S ATOM 14629 SG CYS M 92 56.224 59.834 171.514 1.00 12.05 S ATOM 14417 SG CYS M 64 51.814 59.488 169.090 1.00 13.53 S ATOM 14503 SG CYS M 75 53.125 57.579 166.268 1.00 21.00 S ATOM 21466 SG CYS O 135 33.708 31.744 179.030 1.00 52.05 S ATOM 21500 SG CYS O 140 33.927 28.298 180.316 1.00 60.59 S ATOM 21780 SG CYS O 176 38.076 33.413 181.845 1.00 59.52 S ATOM 21803 SG CYS O 180 38.549 30.202 182.953 1.00 61.83 S ATOM 28542 SG CYS T 86 31.217 51.103 143.881 1.00 27.07 S ATOM 28720 SG CYS T 111 32.451 54.637 144.709 1.00 19.04 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.61 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.61 Time building chain proxies: 26.33, per 1000 atoms: 0.39 Number of scatterers: 68197 At special positions: 0 Unit cell: (215.188, 223.972, 228.363, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 482 16.00 P 47 15.00 Mg 1 11.99 O 12230 8.00 N 11237 7.00 C 44171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " distance=2.03 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.26 Conformation dependent library (CDL) restraints added in 9.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb=" SF4 C 301 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15532 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 348 helices and 30 sheets defined 52.5% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.68 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 95 through 102 removed outlier: 4.140A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.513A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.408A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.902A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 Proline residue: A 434 - end of helix removed outlier: 3.621A pdb=" N ARG A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.521A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 206 removed outlier: 5.548A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 111 through 122 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'E' and resid 25 through 50 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 67 Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.391A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 29 through 39 removed outlier: 4.002A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP F 35 " --> pdb=" O GLY F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 94 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 135 No H-bonds generated for 'chain 'G' and resid 132 through 135' Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.921A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 77 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 76 removed outlier: 4.084A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 3.621A pdb=" N MET J 92 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 222 removed outlier: 3.676A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 256 through 258 No H-bonds generated for 'chain 'J' and resid 256 through 258' Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 295 through 307 removed outlier: 4.007A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 322 Processing helix chain 'J' and resid 336 through 338 No H-bonds generated for 'chain 'J' and resid 336 through 338' Processing helix chain 'J' and resid 345 through 347 No H-bonds generated for 'chain 'J' and resid 345 through 347' Processing helix chain 'J' and resid 350 through 356 removed outlier: 5.580A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 361 No H-bonds generated for 'chain 'J' and resid 359 through 361' Processing helix chain 'J' and resid 366 through 368 No H-bonds generated for 'chain 'J' and resid 366 through 368' Processing helix chain 'K' and resid 76 through 80 Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.621A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 73 No H-bonds generated for 'chain 'L' and resid 70 through 73' Processing helix chain 'L' and resid 120 through 122 No H-bonds generated for 'chain 'L' and resid 120 through 122' Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.986A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 128 through 130 No H-bonds generated for 'chain 'M' and resid 128 through 130' Processing helix chain 'M' and resid 138 through 146 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.887A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 292 Processing helix chain 'M' and resid 294 through 298 Processing helix chain 'M' and resid 319 through 332 Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 378 through 380 No H-bonds generated for 'chain 'M' and resid 378 through 380' Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 390 through 395 removed outlier: 3.761A pdb=" N VAL M 394 " --> pdb=" O THR M 390 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU M 395 " --> pdb=" O ILE M 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 390 through 395' Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 456 Processing helix chain 'M' and resid 461 through 467 Processing helix chain 'M' and resid 478 through 481 Processing helix chain 'M' and resid 486 through 503 Processing helix chain 'M' and resid 522 through 528 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 589 through 591 No H-bonds generated for 'chain 'M' and resid 589 through 591' Processing helix chain 'M' and resid 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.692A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 removed outlier: 3.845A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 90 removed outlier: 4.156A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 198 through 208 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.724A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.833A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET P 173 " --> pdb=" O ILE P 170 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 41 through 47 removed outlier: 4.159A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 60 No H-bonds generated for 'chain 'Q' and resid 58 through 60' Processing helix chain 'Q' and resid 120 through 126 Processing helix chain 'Q' and resid 133 through 139 removed outlier: 3.892A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 3.948A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 262 removed outlier: 3.753A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG Q 254 " --> pdb=" O ASN Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.417A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 311 through 313 No H-bonds generated for 'chain 'Q' and resid 311 through 313' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 371 No H-bonds generated for 'chain 'Q' and resid 368 through 371' Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 438 removed outlier: 3.661A pdb=" N LEU Q 435 " --> pdb=" O HIS Q 431 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'S' and resid 2 through 31 Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix removed outlier: 3.689A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN S 31 " --> pdb=" O LYS S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 55 Processing helix chain 'S' and resid 66 through 69 removed outlier: 3.925A pdb=" N ILE S 69 " --> pdb=" O LEU S 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 66 through 69' Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'U' and resid 4 through 15 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 Processing helix chain 'U' and resid 79 through 82 No H-bonds generated for 'chain 'U' and resid 79 through 82' Processing helix chain 'V' and resid 3 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 32 through 99 Proline residue: W 73 - end of helix removed outlier: 4.182A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 138 Processing helix chain 'X' and resid 76 through 89 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 135 No H-bonds generated for 'chain 'X' and resid 132 through 135' Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 through 81 removed outlier: 3.767A pdb=" N LEU Y 81 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Y' and resid 94 through 97 No H-bonds generated for 'chain 'Y' and resid 94 through 97' Processing helix chain 'Z' and resid 28 through 38 Processing helix chain 'Z' and resid 46 through 54 removed outlier: 4.369A pdb=" N TRP Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ARG Z 52 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR Z 53 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 25 Processing helix chain 'b' and resid 70 through 73 No H-bonds generated for 'chain 'b' and resid 70 through 73' Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 110 through 112 No H-bonds generated for 'chain 'c' and resid 110 through 112' Processing helix chain 'c' and resid 129 through 149 Processing helix chain 'd' and resid 29 through 57 removed outlier: 4.788A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 143 removed outlier: 3.555A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA d 126 " --> pdb=" O ARG d 122 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LYS d 127 " --> pdb=" O GLN d 123 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU d 128 " --> pdb=" O ASN d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 174 Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 Processing helix chain 'e' and resid 115 through 131 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 removed outlier: 3.840A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 43 Processing helix chain 'h' and resid 49 through 55 removed outlier: 3.960A pdb=" N LYS h 54 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'h' and resid 96 through 99 No H-bonds generated for 'chain 'h' and resid 96 through 99' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.168A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.809A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 151 through 171 removed outlier: 4.073A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 192 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.612A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 252 Processing helix chain 'i' and resid 258 through 272 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.336A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 23 Processing helix chain 'j' and resid 56 through 80 removed outlier: 4.005A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU j 68 " --> pdb=" O LEU j 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.628A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN j 80 " --> pdb=" O PRO j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 20 Processing helix chain 'k' and resid 26 through 51 Processing helix chain 'k' and resid 55 through 85 Proline residue: k 60 - end of helix Processing helix chain 'k' and resid 90 through 92 No H-bonds generated for 'chain 'k' and resid 90 through 92' Processing helix chain 'l' and resid 3 through 23 removed outlier: 3.583A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.803A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 56 removed outlier: 4.186A pdb=" N VAL l 49 " --> pdb=" O THR l 45 " (cutoff:3.500A) Proline residue: l 50 - end of helix Processing helix chain 'l' and resid 84 through 107 Proline residue: l 91 - end of helix removed outlier: 3.838A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 132 Processing helix chain 'l' and resid 137 through 155 Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.887A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 204 Processing helix chain 'l' and resid 210 through 224 Processing helix chain 'l' and resid 227 through 229 No H-bonds generated for 'chain 'l' and resid 227 through 229' Processing helix chain 'l' and resid 231 through 238 removed outlier: 4.054A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 246 Processing helix chain 'l' and resid 252 through 262 removed outlier: 4.081A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.154A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 3.535A pdb=" N ILE l 293 " --> pdb=" O ALA l 289 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 Processing helix chain 'l' and resid 322 through 349 removed outlier: 4.169A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 380 Processing helix chain 'l' and resid 389 through 400 removed outlier: 4.747A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.920A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 471 removed outlier: 6.097A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 484 through 487 No H-bonds generated for 'chain 'l' and resid 484 through 487' Processing helix chain 'l' and resid 489 through 509 removed outlier: 3.782A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR l 509 " --> pdb=" O ASN l 505 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 526 through 533 Proline residue: l 530 - end of helix removed outlier: 4.209A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 Processing helix chain 'm' and resid 50 through 74 Processing helix chain 'm' and resid 87 through 109 Processing helix chain 'm' and resid 124 through 127 removed outlier: 3.838A pdb=" N ILE m 127 " --> pdb=" O ASP m 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 124 through 127' Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.152A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 4 through 34 removed outlier: 6.243A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.607A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 20 through 23 No H-bonds generated for 'chain 'o' and resid 20 through 23' Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.722A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 84 through 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 50 Processing helix chain 'p' and resid 57 through 74 Processing helix chain 'p' and resid 93 through 97 removed outlier: 4.391A pdb=" N CYS p 96 " --> pdb=" O ARG p 93 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 4.801A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 171 No H-bonds generated for 'chain 'p' and resid 168 through 171' Processing helix chain 'r' and resid 2 through 16 Proline residue: r 7 - end of helix Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.196A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 80 Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.716A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.631A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 140 through 170 removed outlier: 3.684A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE r 151 " --> pdb=" O TYR r 148 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.645A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.380A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 237 through 248 removed outlier: 4.609A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) Processing helix chain 'r' and resid 254 through 257 No H-bonds generated for 'chain 'r' and resid 254 through 257' Processing helix chain 'r' and resid 259 through 277 removed outlier: 3.784A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 removed outlier: 3.606A pdb=" N ILE r 286 " --> pdb=" O LEU r 282 " (cutoff:3.500A) Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.653A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 351 No H-bonds generated for 'chain 'r' and resid 348 through 351' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 414 removed outlier: 3.664A pdb=" N ILE r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET r 396 " --> pdb=" O ILE r 393 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR r 403 " --> pdb=" O MET r 400 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix Processing helix chain 'r' and resid 451 through 453 No H-bonds generated for 'chain 'r' and resid 451 through 453' Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.707A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 47 through 56 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.394A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 4.027A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 4.986A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.730A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 176 No H-bonds generated for 'chain 's' and resid 174 through 176' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 204 through 207 No H-bonds generated for 'chain 's' and resid 204 through 207' Processing helix chain 's' and resid 210 through 212 No H-bonds generated for 'chain 's' and resid 210 through 212' Processing helix chain 's' and resid 217 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 291 removed outlier: 3.832A pdb=" N MET s 286 " --> pdb=" O TYR s 282 " (cutoff:3.500A) Processing helix chain 's' and resid 293 through 311 Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 11 through 13 No H-bonds generated for 'chain 'u' and resid 11 through 13' Processing helix chain 'u' and resid 22 through 27 Processing helix chain 'u' and resid 29 through 35 Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 79 through 91 Processing helix chain 'u' and resid 102 through 115 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 82 through 123 Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 49 through 52 No H-bonds generated for 'chain 'w' and resid 49 through 52' Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 94 through 97 Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 166 through 175 removed outlier: 4.052A pdb=" N ARG w 175 " --> pdb=" O ALA w 172 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.272A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 252 removed outlier: 5.512A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix removed outlier: 4.051A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS w 252 " --> pdb=" O GLU w 248 " (cutoff:3.500A) Processing helix chain 'w' and resid 261 through 263 No H-bonds generated for 'chain 'w' and resid 261 through 263' Processing helix chain 'w' and resid 266 through 275 removed outlier: 3.642A pdb=" N TYR w 275 " --> pdb=" O GLU w 271 " (cutoff:3.500A) Processing helix chain 'w' and resid 283 through 285 No H-bonds generated for 'chain 'w' and resid 283 through 285' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 309 removed outlier: 5.306A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 239 through 244 removed outlier: 6.439A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 5.989A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.724A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 57 removed outlier: 3.635A pdb=" N GLU F 18 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.621A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 228 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'M' and resid 79 through 81 Processing sheet with id= M, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= N, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= O, first strand: chain 'M' and resid 246 through 251 removed outlier: 6.185A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL M 270 " --> pdb=" O ARG M 266 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'M' and resid 305 through 308 Processing sheet with id= Q, first strand: chain 'M' and resid 366 through 368 removed outlier: 8.445A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.119A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= T, first strand: chain 'N' and resid 60 through 63 removed outlier: 3.518A pdb=" N GLY N 40 " --> pdb=" O TYR N 48 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.716A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.868A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= X, first strand: chain 'Q' and resid 80 through 84 removed outlier: 6.489A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Q' and resid 394 through 402 removed outlier: 3.524A pdb=" N ARG Q 421 " --> pdb=" O VAL Q 412 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'T' and resid 77 through 79 Processing sheet with id= AA, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= AB, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.533A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.885A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'w' and resid 84 through 86 2941 hydrogen bonds defined for protein. 8205 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: 21.77 Time building geometry restraints manager: 22.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27751 1.40 - 1.62: 41179 1.62 - 1.84: 876 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 69886 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.262 0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.633 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.299 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.27e+02 ... (remaining 69881 not shown) Histogram of bond angle deviations from ideal: 73.59 - 85.99: 76 85.99 - 98.38: 7 98.38 - 110.78: 24182 110.78 - 123.18: 67192 123.18 - 135.58: 3017 Bond angle restraints: 94474 Sorted by residual: angle pdb=" C PRO h 94 " pdb=" N PRO h 95 " pdb=" CA PRO h 95 " ideal model delta sigma weight residual 119.66 127.55 -7.89 7.20e-01 1.93e+00 1.20e+02 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 124.18 -16.44 1.95e+00 2.62e-01 7.08e+01 angle pdb=" C ASP h 103 " pdb=" N PRO h 104 " pdb=" CA PRO h 104 " ideal model delta sigma weight residual 119.85 128.03 -8.18 1.01e+00 9.80e-01 6.56e+01 angle pdb=" C11 CDL l 701 " pdb=" CA5 CDL l 701 " pdb=" OA6 CDL l 701 " ideal model delta sigma weight residual 111.33 121.17 -9.84 1.32e+00 5.72e-01 5.54e+01 angle pdb=" C THR p 144 " pdb=" N PRO p 145 " pdb=" CA PRO p 145 " ideal model delta sigma weight residual 119.66 124.90 -5.24 7.20e-01 1.93e+00 5.29e+01 ... (remaining 94469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 40665 35.69 - 71.38: 1746 71.38 - 107.07: 136 107.07 - 142.76: 23 142.76 - 178.46: 11 Dihedral angle restraints: 42581 sinusoidal: 18486 harmonic: 24095 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual -102.41 76.05 -178.46 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -143.27 57.27 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 81.92 -141.92 1 2.00e+01 2.50e-03 4.29e+01 ... (remaining 42578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 9246 0.074 - 0.147: 900 0.147 - 0.221: 35 0.221 - 0.294: 7 0.294 - 0.368: 4 Chirality restraints: 10192 Sorted by residual: chirality pdb=" C3B NDP J 401 " pdb=" C2B NDP J 401 " pdb=" C4B NDP J 401 " pdb=" O3B NDP J 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.38 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA TYR h 92 " pdb=" N TYR h 92 " pdb=" C TYR h 92 " pdb=" CB TYR h 92 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA TYR Q 311 " pdb=" N TYR Q 311 " pdb=" C TYR Q 311 " pdb=" CB TYR Q 311 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 10189 not shown) Planarity restraints: 11768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ1 Q 501 " 0.382 2.00e-02 2.50e+03 3.49e-01 1.52e+03 pdb=" C11 UQ1 Q 501 " 0.016 2.00e-02 2.50e+03 pdb=" C7 UQ1 Q 501 " 0.390 2.00e-02 2.50e+03 pdb=" C8 UQ1 Q 501 " -0.413 2.00e-02 2.50e+03 pdb=" C9 UQ1 Q 501 " -0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ C 303 " -0.063 2.00e-02 2.50e+03 2.76e-01 9.51e+02 pdb=" C11 UQ C 303 " 0.089 2.00e-02 2.50e+03 pdb=" C7 UQ C 303 " -0.254 2.00e-02 2.50e+03 pdb=" C8 UQ C 303 " 0.487 2.00e-02 2.50e+03 pdb=" C9 UQ C 303 " -0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ C 303 " 0.265 2.00e-02 2.50e+03 2.66e-01 8.83e+02 pdb=" C18 UQ C 303 " -0.222 2.00e-02 2.50e+03 pdb=" C19 UQ C 303 " -0.369 2.00e-02 2.50e+03 pdb=" C20 UQ C 303 " 0.014 2.00e-02 2.50e+03 pdb=" C21 UQ C 303 " 0.312 2.00e-02 2.50e+03 ... (remaining 11765 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 7305 2.75 - 3.28: 65435 3.28 - 3.82: 116048 3.82 - 4.36: 143060 4.36 - 4.90: 242530 Nonbonded interactions: 574378 Sorted by model distance: nonbonded pdb=" NH1 ARG J 192 " pdb=" O ALA J 198 " model vdw 2.207 2.520 nonbonded pdb=" O ASP d 42 " pdb=" OG1 THR d 46 " model vdw 2.209 2.440 nonbonded pdb=" OD1 ASP B 165 " pdb=" NH2 ARG Q 368 " model vdw 2.221 2.520 nonbonded pdb=" O PRO A 325 " pdb=" OG1 THR A 347 " model vdw 2.223 2.440 nonbonded pdb=" O VAL V 141 " pdb=" OH TYR a 169 " model vdw 2.223 2.440 ... (remaining 574373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 69 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 156 or resid 201)) selection = (chain 'X' and (resid 69 through 149 or (resid 150 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 156 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.61 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 8.380 Check model and map are aligned: 0.750 Set scattering table: 0.480 Process input model: 151.560 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.317 69886 Z= 0.496 Angle : 0.833 17.560 94474 Z= 0.422 Chirality : 0.045 0.368 10192 Planarity : 0.009 0.349 11768 Dihedral : 18.864 178.455 27025 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.73 % Favored : 96.21 % Rotamer: Outliers : 0.29 % Allowed : 15.09 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.09), residues: 8173 helix: 1.67 (0.08), residues: 4303 sheet: 0.06 (0.25), residues: 447 loop : -0.50 (0.11), residues: 3423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.001 TRP w 353 HIS 0.010 0.001 HIS u 77 PHE 0.032 0.002 PHE i 292 TYR 0.028 0.002 TYR r 256 ARG 0.008 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1129 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1108 time to evaluate : 5.804 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 322 SER cc_start: 0.8585 (m) cc_final: 0.8255 (p) REVERT: B 68 ARG cc_start: 0.8629 (mtp85) cc_final: 0.8342 (mtt180) REVERT: C 44 GLU cc_start: 0.7402 (tt0) cc_final: 0.7164 (tm-30) REVERT: H 70 GLU cc_start: 0.7718 (tp30) cc_final: 0.7481 (tp30) REVERT: I 10 LEU cc_start: 0.8474 (mt) cc_final: 0.8260 (mm) REVERT: J 107 GLU cc_start: 0.7939 (tp30) cc_final: 0.7625 (tp30) REVERT: J 138 ASN cc_start: 0.8563 (m110) cc_final: 0.8090 (m110) REVERT: N 12 GLN cc_start: 0.7114 (tp40) cc_final: 0.6674 (tm-30) REVERT: N 50 GLU cc_start: 0.8515 (pt0) cc_final: 0.8217 (pt0) REVERT: P 85 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8299 (mt-10) REVERT: T 43 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8760 (tm130) REVERT: W 92 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7289 (mt-10) REVERT: W 98 MET cc_start: 0.8033 (mmm) cc_final: 0.7807 (mmm) REVERT: a 95 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7531 (mt-10) REVERT: b 93 LYS cc_start: 0.7998 (mttt) cc_final: 0.7728 (mtpp) REVERT: g 84 MET cc_start: 0.9033 (mmm) cc_final: 0.8777 (mmp) REVERT: g 109 LYS cc_start: 0.7671 (mtpt) cc_final: 0.7433 (ttpt) REVERT: h 13 ASP cc_start: 0.8610 (t0) cc_final: 0.8387 (t0) REVERT: h 59 GLU cc_start: 0.8390 (mp0) cc_final: 0.8144 (mp0) REVERT: i 313 MET cc_start: 0.9466 (ttm) cc_final: 0.9222 (mtt) REVERT: i 318 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7683 (mm-30) REVERT: k 37 MET cc_start: 0.9113 (tpt) cc_final: 0.8859 (mmm) REVERT: l 13 THR cc_start: 0.9290 (t) cc_final: 0.8929 (m) REVERT: l 503 GLU cc_start: 0.7937 (tp30) cc_final: 0.7684 (mm-30) REVERT: l 599 MET cc_start: 0.8588 (mmm) cc_final: 0.8272 (mmt) REVERT: m 87 LYS cc_start: 0.7537 (pttt) cc_final: 0.6961 (ptmm) REVERT: n 46 LYS cc_start: 0.8336 (tttt) cc_final: 0.8005 (tptm) REVERT: p 68 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7542 (mm-30) REVERT: r 3 LYS cc_start: 0.8708 (ptpt) cc_final: 0.8494 (ptmt) REVERT: r 269 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8913 (ptp) REVERT: r 294 MET cc_start: 0.9035 (mmm) cc_final: 0.8392 (mmp) REVERT: s 61 LEU cc_start: 0.8383 (mp) cc_final: 0.8047 (mt) REVERT: u 132 LYS cc_start: 0.7095 (ptpt) cc_final: 0.6889 (mttm) REVERT: v 70 LYS cc_start: 0.8529 (mttm) cc_final: 0.8121 (mttm) REVERT: v 81 LYS cc_start: 0.8673 (tppt) cc_final: 0.8418 (mptt) REVERT: w 37 GLN cc_start: 0.7197 (tp40) cc_final: 0.6916 (tm-30) outliers start: 21 outliers final: 8 residues processed: 1115 average time/residue: 1.5678 time to fit residues: 2247.5301 Evaluate side-chains 1041 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1032 time to evaluate : 5.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain o residue 7 LYS Chi-restraints excluded: chain r residue 269 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 679 optimal weight: 5.9990 chunk 610 optimal weight: 0.6980 chunk 338 optimal weight: 5.9990 chunk 208 optimal weight: 0.1980 chunk 411 optimal weight: 5.9990 chunk 325 optimal weight: 4.9990 chunk 630 optimal weight: 0.0270 chunk 244 optimal weight: 10.0000 chunk 383 optimal weight: 7.9990 chunk 469 optimal weight: 7.9990 chunk 731 optimal weight: 4.9990 overall best weight: 2.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 ASN M 514 ASN N 13 GLN O 69 ASN P 75 GLN P 77 GLN P 247 GLN U 11 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 ASN d 104 ASN e 140 ASN g 119 HIS h 25 GLN k 92 ASN l 23 ASN ** l 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 175 ASN n 11 HIS r 44 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 163 HIS v 65 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 69886 Z= 0.249 Angle : 0.562 10.493 94474 Z= 0.281 Chirality : 0.043 0.198 10192 Planarity : 0.005 0.058 11768 Dihedral : 15.206 178.093 10872 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.52 % Favored : 96.42 % Rotamer: Outliers : 2.78 % Allowed : 16.58 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.09), residues: 8173 helix: 1.66 (0.08), residues: 4289 sheet: 0.12 (0.25), residues: 437 loop : -0.54 (0.10), residues: 3447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS J 37 PHE 0.034 0.002 PHE i 292 TYR 0.022 0.001 TYR l 587 ARG 0.007 0.000 ARG u 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1263 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1064 time to evaluate : 5.790 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 SER cc_start: 0.8627 (m) cc_final: 0.8258 (p) REVERT: B 68 ARG cc_start: 0.8628 (mtp85) cc_final: 0.8395 (mtt180) REVERT: B 76 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.7571 (t80) REVERT: C 44 GLU cc_start: 0.7510 (tt0) cc_final: 0.7271 (tm-30) REVERT: F 73 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7511 (mp10) REVERT: G 82 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6551 (mtp85) REVERT: G 147 TYR cc_start: 0.7423 (t80) cc_final: 0.6854 (t80) REVERT: H 70 GLU cc_start: 0.7645 (tp30) cc_final: 0.7395 (tp30) REVERT: J 107 GLU cc_start: 0.7820 (tp30) cc_final: 0.7470 (tp30) REVERT: J 117 ARG cc_start: 0.8413 (ttt90) cc_final: 0.8199 (tpt-90) REVERT: J 138 ASN cc_start: 0.8513 (m110) cc_final: 0.8275 (m-40) REVERT: N 12 GLN cc_start: 0.7160 (tp40) cc_final: 0.6693 (tm-30) REVERT: N 50 GLU cc_start: 0.8507 (pt0) cc_final: 0.8248 (pt0) REVERT: S 28 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8402 (ttmt) REVERT: W 92 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7328 (mt-10) REVERT: W 121 MET cc_start: 0.8220 (tpp) cc_final: 0.7971 (tpp) REVERT: X 108 LEU cc_start: 0.7398 (mp) cc_final: 0.7174 (mp) REVERT: X 111 ASP cc_start: 0.8406 (p0) cc_final: 0.7609 (p0) REVERT: Z 14 MET cc_start: 0.2998 (tmm) cc_final: 0.2527 (tmm) REVERT: Z 25 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.7021 (mt-10) REVERT: Z 30 GLU cc_start: 0.7616 (tt0) cc_final: 0.7413 (tt0) REVERT: Z 33 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8131 (tp-100) REVERT: a 95 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7564 (mt-10) REVERT: a 103 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6654 (tp30) REVERT: a 106 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8626 (p) REVERT: b 93 LYS cc_start: 0.7984 (mttt) cc_final: 0.7707 (mtpp) REVERT: e 124 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.6803 (mtp85) REVERT: g 52 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8218 (mtp85) REVERT: g 84 MET cc_start: 0.9028 (mmm) cc_final: 0.8783 (mmp) REVERT: g 109 LYS cc_start: 0.7747 (mtpt) cc_final: 0.7512 (ttpt) REVERT: h 59 GLU cc_start: 0.8548 (mp0) cc_final: 0.8179 (mp0) REVERT: i 11 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8101 (mpp) REVERT: i 40 MET cc_start: 0.9131 (tpt) cc_final: 0.8777 (tpt) REVERT: i 89 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8626 (mtt) REVERT: i 313 MET cc_start: 0.9493 (ttm) cc_final: 0.9261 (mtt) REVERT: i 318 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7804 (mm-30) REVERT: j 85 LYS cc_start: 0.8697 (mmmt) cc_final: 0.8468 (mtmt) REVERT: k 37 MET cc_start: 0.9135 (tpt) cc_final: 0.8849 (mmm) REVERT: l 13 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.8996 (m) REVERT: l 525 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8924 (mtp) REVERT: l 599 MET cc_start: 0.8672 (mmm) cc_final: 0.8375 (mmt) REVERT: m 87 LYS cc_start: 0.7604 (pttt) cc_final: 0.7072 (ptmm) REVERT: n 46 LYS cc_start: 0.8341 (tttt) cc_final: 0.8010 (tptm) REVERT: o 7 LYS cc_start: 0.8847 (ptmt) cc_final: 0.8500 (ptmt) REVERT: r 3 LYS cc_start: 0.8721 (ptpt) cc_final: 0.8506 (ptmt) REVERT: r 103 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8827 (tt0) REVERT: r 294 MET cc_start: 0.9035 (mmm) cc_final: 0.8387 (mmp) REVERT: r 401 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8389 (tmm) REVERT: s 61 LEU cc_start: 0.8413 (mp) cc_final: 0.8089 (mt) REVERT: u 38 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.6687 (ttmm) REVERT: u 42 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: u 132 LYS cc_start: 0.7270 (ptpt) cc_final: 0.7052 (mttm) REVERT: u 157 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7603 (m-30) REVERT: v 81 LYS cc_start: 0.8729 (tppt) cc_final: 0.8457 (mptt) outliers start: 199 outliers final: 95 residues processed: 1169 average time/residue: 1.5445 time to fit residues: 2340.9848 Evaluate side-chains 1138 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1025 time to evaluate : 5.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain N residue 135 GLN Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 345 SER Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 57 LEU Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 123 GLU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain Z residue 25 GLU Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 11 MET Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 254 LEU Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain k residue 6 MET Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 349 SER Chi-restraints excluded: chain l residue 393 ASP Chi-restraints excluded: chain l residue 402 SER Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 543 SER Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 163 ILE Chi-restraints excluded: chain m residue 172 THR Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 33 GLU Chi-restraints excluded: chain p residue 144 THR Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 272 THR Chi-restraints excluded: chain r residue 401 MET Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain u residue 42 GLU Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 24 THR Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 248 GLU Chi-restraints excluded: chain w residue 285 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 406 optimal weight: 9.9990 chunk 226 optimal weight: 7.9990 chunk 608 optimal weight: 3.9990 chunk 497 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 732 optimal weight: 5.9990 chunk 791 optimal weight: 3.9990 chunk 652 optimal weight: 9.9990 chunk 726 optimal weight: 0.8980 chunk 249 optimal weight: 7.9990 chunk 587 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 HIS ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 HIS M 498 GLN N 13 GLN P 77 GLN P 247 GLN T 43 GLN U 11 ASN W 61 GLN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 140 ASN i 319 HIS j 10 ASN l 23 ASN l 175 ASN l 351 ASN p 12 HIS r 44 GLN r 304 GLN s 171 HIS v 65 GLN w 223 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 69886 Z= 0.406 Angle : 0.655 10.816 94474 Z= 0.331 Chirality : 0.047 0.225 10192 Planarity : 0.006 0.066 11768 Dihedral : 14.796 177.397 10858 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.43 % Favored : 95.51 % Rotamer: Outliers : 3.69 % Allowed : 17.19 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.09), residues: 8173 helix: 1.31 (0.08), residues: 4271 sheet: -0.07 (0.25), residues: 428 loop : -0.70 (0.10), residues: 3474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP l 144 HIS 0.012 0.002 HIS c 132 PHE 0.037 0.002 PHE i 292 TYR 0.028 0.002 TYR l 587 ARG 0.007 0.001 ARG Q 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1347 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1083 time to evaluate : 5.907 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 322 SER cc_start: 0.8700 (m) cc_final: 0.8321 (p) REVERT: A 338 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8430 (p0) REVERT: C 44 GLU cc_start: 0.7689 (tt0) cc_final: 0.7417 (tm-30) REVERT: C 49 LYS cc_start: 0.8707 (mmtm) cc_final: 0.8425 (mmmt) REVERT: E 87 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8597 (mtmp) REVERT: F 73 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7578 (mp10) REVERT: F 74 GLU cc_start: 0.8247 (pt0) cc_final: 0.8033 (pt0) REVERT: G 82 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6664 (mtp85) REVERT: G 123 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7814 (mt-10) REVERT: G 143 GLU cc_start: 0.8262 (mp0) cc_final: 0.8017 (mp0) REVERT: H 70 GLU cc_start: 0.7536 (tp30) cc_final: 0.7179 (tp30) REVERT: J 117 ARG cc_start: 0.8416 (ttt90) cc_final: 0.8122 (tpt-90) REVERT: J 138 ASN cc_start: 0.8554 (m110) cc_final: 0.8239 (m-40) REVERT: J 205 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7603 (m-30) REVERT: K 88 ASP cc_start: 0.7847 (m-30) cc_final: 0.7621 (m-30) REVERT: L 69 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7661 (mm-30) REVERT: M 658 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7440 (m-30) REVERT: N 13 GLN cc_start: 0.8048 (mt0) cc_final: 0.7799 (mt0) REVERT: N 21 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6034 (mpt180) REVERT: N 50 GLU cc_start: 0.8526 (pt0) cc_final: 0.8270 (pt0) REVERT: Q 60 HIS cc_start: 0.7523 (m90) cc_final: 0.7310 (m90) REVERT: S 28 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8541 (ttmt) REVERT: T 43 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8699 (tm-30) REVERT: U 30 ILE cc_start: 0.9130 (mt) cc_final: 0.8895 (mp) REVERT: W 92 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7582 (mt-10) REVERT: W 121 MET cc_start: 0.8194 (tpp) cc_final: 0.7882 (tpp) REVERT: X 108 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7710 (mp) REVERT: Y 41 GLU cc_start: 0.8085 (pt0) cc_final: 0.7408 (mm-30) REVERT: Y 65 MET cc_start: 0.9152 (tmm) cc_final: 0.8851 (ttt) REVERT: a 77 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.7834 (tp) REVERT: a 95 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7487 (mt-10) REVERT: a 103 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6636 (tp30) REVERT: b 93 LYS cc_start: 0.8127 (mttt) cc_final: 0.7796 (mtpp) REVERT: e 124 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.6910 (mtp85) REVERT: g 84 MET cc_start: 0.9017 (mmm) cc_final: 0.8777 (mmp) REVERT: h 43 CYS cc_start: 0.8027 (t) cc_final: 0.7771 (t) REVERT: h 59 GLU cc_start: 0.8754 (mp0) cc_final: 0.8368 (mp0) REVERT: i 11 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8143 (mpp) REVERT: i 89 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8720 (mtt) REVERT: i 318 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7840 (mm-30) REVERT: j 68 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7602 (mm-30) REVERT: j 85 LYS cc_start: 0.8661 (mmmt) cc_final: 0.8444 (mtmt) REVERT: k 37 MET cc_start: 0.9184 (tpt) cc_final: 0.8947 (mmm) REVERT: l 13 THR cc_start: 0.9336 (OUTLIER) cc_final: 0.8999 (m) REVERT: l 28 LYS cc_start: 0.8681 (mptp) cc_final: 0.8437 (mptp) REVERT: l 492 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8430 (mt) REVERT: m 87 LYS cc_start: 0.7737 (pttt) cc_final: 0.7363 (ptmm) REVERT: m 135 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.7036 (t80) REVERT: n 46 LYS cc_start: 0.8412 (tttt) cc_final: 0.8038 (tptm) REVERT: o 31 LYS cc_start: 0.8586 (tttp) cc_final: 0.8166 (ttmt) REVERT: o 112 LYS cc_start: 0.8078 (tttt) cc_final: 0.7538 (tttm) REVERT: o 114 LYS cc_start: 0.8457 (ttmt) cc_final: 0.7535 (ttpt) REVERT: r 3 LYS cc_start: 0.8813 (ptpt) cc_final: 0.8584 (ptmt) REVERT: r 294 MET cc_start: 0.9175 (mmm) cc_final: 0.8542 (mmp) REVERT: s 105 MET cc_start: 0.9173 (mmm) cc_final: 0.8812 (mtp) REVERT: u 11 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7870 (tp30) REVERT: u 12 ASP cc_start: 0.7611 (m-30) cc_final: 0.7151 (t0) REVERT: u 38 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7051 (ttmm) REVERT: u 42 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: u 73 GLN cc_start: 0.7515 (tp-100) cc_final: 0.6862 (mt0) REVERT: u 90 ASP cc_start: 0.8567 (t0) cc_final: 0.8244 (t0) REVERT: u 132 LYS cc_start: 0.7472 (ptpt) cc_final: 0.7268 (mttm) REVERT: u 157 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: v 81 LYS cc_start: 0.8785 (tppt) cc_final: 0.8501 (mptt) REVERT: v 83 GLU cc_start: 0.7964 (mp0) cc_final: 0.7762 (mp0) REVERT: v 93 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8118 (mm) REVERT: w 41 LEU cc_start: 0.9144 (tp) cc_final: 0.8915 (tp) REVERT: w 116 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8776 (ttpt) REVERT: w 124 ASN cc_start: 0.8016 (p0) cc_final: 0.7599 (p0) REVERT: w 351 TRP cc_start: 0.6913 (m100) cc_final: 0.6593 (m100) outliers start: 264 outliers final: 121 residues processed: 1238 average time/residue: 1.5397 time to fit residues: 2473.2416 Evaluate side-chains 1181 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1036 time to evaluate : 5.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain N residue 135 GLN Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 345 SER Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 123 GLU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 130 GLU Chi-restraints excluded: chain e residue 132 ASN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 11 MET Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 108 LEU Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 254 LEU Chi-restraints excluded: chain i residue 258 SER Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 107 THR Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 288 THR Chi-restraints excluded: chain l residue 351 ASN Chi-restraints excluded: chain l residue 393 ASP Chi-restraints excluded: chain l residue 402 SER Chi-restraints excluded: chain l residue 404 THR Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 492 ILE Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 543 SER Chi-restraints excluded: chain l residue 577 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 172 THR Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 33 GLU Chi-restraints excluded: chain o residue 46 GLU Chi-restraints excluded: chain p residue 144 THR Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 272 THR Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 85 MET Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 11 GLU Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain u residue 42 GLU Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 24 THR Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 93 LEU Chi-restraints excluded: chain w residue 116 LYS Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 248 GLU Chi-restraints excluded: chain w residue 265 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 4.9990 chunk 550 optimal weight: 5.9990 chunk 380 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 349 optimal weight: 0.6980 chunk 491 optimal weight: 0.8980 chunk 734 optimal weight: 0.8980 chunk 778 optimal weight: 2.9990 chunk 383 optimal weight: 5.9990 chunk 696 optimal weight: 3.9990 chunk 209 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 57 GLN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS E 70 ASN ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN I 51 ASN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 ASN M 498 GLN P 247 GLN Y 91 GLN Z 33 GLN e 140 ASN i 319 HIS j 10 ASN r 30 HIS r 44 GLN r 169 ASN r 304 GLN v 55 GLN v 65 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 69886 Z= 0.222 Angle : 0.546 10.586 94474 Z= 0.277 Chirality : 0.042 0.192 10192 Planarity : 0.005 0.061 11768 Dihedral : 14.273 177.467 10858 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.27 % Rotamer: Outliers : 3.32 % Allowed : 18.56 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.09), residues: 8173 helix: 1.48 (0.08), residues: 4289 sheet: -0.05 (0.25), residues: 434 loop : -0.67 (0.10), residues: 3450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP u 86 HIS 0.006 0.001 HIS J 37 PHE 0.033 0.001 PHE i 292 TYR 0.022 0.001 TYR l 587 ARG 0.006 0.000 ARG h 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 1060 time to evaluate : 5.949 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 322 SER cc_start: 0.8627 (m) cc_final: 0.8230 (p) REVERT: C 186 ARG cc_start: 0.8725 (mtm-85) cc_final: 0.8378 (ttm110) REVERT: E 74 THR cc_start: 0.8727 (t) cc_final: 0.8514 (p) REVERT: F 73 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7584 (mp10) REVERT: G 82 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6618 (mtp85) REVERT: G 123 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7702 (mt-10) REVERT: H 70 GLU cc_start: 0.7513 (tp30) cc_final: 0.7226 (tp30) REVERT: J 107 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.6850 (mm-30) REVERT: J 117 ARG cc_start: 0.8418 (ttt90) cc_final: 0.8206 (tpt-90) REVERT: J 138 ASN cc_start: 0.8555 (m110) cc_final: 0.8246 (m-40) REVERT: J 205 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: K 88 ASP cc_start: 0.7823 (m-30) cc_final: 0.7571 (m-30) REVERT: M 467 LYS cc_start: 0.8455 (tppp) cc_final: 0.7894 (tptt) REVERT: N 9 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6971 (mtm110) REVERT: N 13 GLN cc_start: 0.8008 (mt0) cc_final: 0.7780 (mt0) REVERT: N 21 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6058 (mpt180) REVERT: N 50 GLU cc_start: 0.8489 (pt0) cc_final: 0.8208 (pt0) REVERT: O 180 CYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8142 (m) REVERT: Q 349 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8243 (m110) REVERT: S 28 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8514 (ttmt) REVERT: T 43 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8729 (tm-30) REVERT: U 30 ILE cc_start: 0.9086 (mt) cc_final: 0.8838 (mp) REVERT: W 80 ASP cc_start: 0.7872 (m-30) cc_final: 0.7670 (m-30) REVERT: W 98 MET cc_start: 0.8141 (mmm) cc_final: 0.7577 (mmm) REVERT: X 108 LEU cc_start: 0.8036 (mp) cc_final: 0.7779 (mp) REVERT: Y 41 GLU cc_start: 0.8084 (pt0) cc_final: 0.7410 (mm-30) REVERT: Z 30 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: a 95 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7469 (mt-10) REVERT: a 103 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6657 (tp30) REVERT: b 93 LYS cc_start: 0.8044 (mttt) cc_final: 0.7736 (mtpp) REVERT: e 124 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.6816 (mtp85) REVERT: g 52 ARG cc_start: 0.8628 (mtp85) cc_final: 0.8332 (mtp85) REVERT: g 84 MET cc_start: 0.8948 (mmm) cc_final: 0.8746 (mmp) REVERT: g 109 LYS cc_start: 0.7914 (mtpt) cc_final: 0.7690 (ttpt) REVERT: h 43 CYS cc_start: 0.7995 (t) cc_final: 0.7710 (t) REVERT: h 59 GLU cc_start: 0.8648 (mp0) cc_final: 0.8354 (mp0) REVERT: i 11 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8157 (mpp) REVERT: i 89 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8689 (mtt) REVERT: i 318 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7900 (mm-30) REVERT: j 68 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7563 (mm-30) REVERT: j 85 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8369 (mtmt) REVERT: k 37 MET cc_start: 0.9141 (tpt) cc_final: 0.8877 (mmm) REVERT: l 13 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9001 (m) REVERT: l 28 LYS cc_start: 0.8707 (mptp) cc_final: 0.8484 (mptp) REVERT: l 300 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8502 (mptt) REVERT: l 554 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8692 (m-30) REVERT: m 87 LYS cc_start: 0.7663 (pttt) cc_final: 0.7285 (ptmm) REVERT: m 135 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.6679 (t80) REVERT: n 46 LYS cc_start: 0.8392 (tttt) cc_final: 0.8026 (tptm) REVERT: o 7 LYS cc_start: 0.8830 (ptmt) cc_final: 0.8419 (ptmt) REVERT: o 31 LYS cc_start: 0.8573 (tttp) cc_final: 0.8162 (ttmt) REVERT: o 112 LYS cc_start: 0.8065 (tttt) cc_final: 0.7791 (ttmt) REVERT: o 114 LYS cc_start: 0.8459 (ttmt) cc_final: 0.7527 (ttpt) REVERT: r 3 LYS cc_start: 0.8777 (ptpt) cc_final: 0.8544 (ptmt) REVERT: r 103 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8405 (tt0) REVERT: r 168 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8987 (tt0) REVERT: r 294 MET cc_start: 0.9087 (mmm) cc_final: 0.8424 (mmp) REVERT: s 105 MET cc_start: 0.9155 (mmm) cc_final: 0.8729 (mtp) REVERT: u 12 ASP cc_start: 0.7602 (m-30) cc_final: 0.7084 (t0) REVERT: u 38 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.6927 (ttmm) REVERT: u 42 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: u 73 GLN cc_start: 0.7440 (tp-100) cc_final: 0.6926 (mt0) REVERT: u 88 CYS cc_start: 0.7247 (t) cc_final: 0.6991 (t) REVERT: u 157 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: v 70 LYS cc_start: 0.8732 (mttm) cc_final: 0.8449 (mttm) REVERT: v 81 LYS cc_start: 0.8790 (tppt) cc_final: 0.8507 (mptt) REVERT: v 83 GLU cc_start: 0.8004 (mp0) cc_final: 0.7715 (mp0) REVERT: w 41 LEU cc_start: 0.9120 (tp) cc_final: 0.8912 (tp) REVERT: w 124 ASN cc_start: 0.8039 (p0) cc_final: 0.7647 (p0) outliers start: 237 outliers final: 118 residues processed: 1205 average time/residue: 1.5290 time to fit residues: 2394.4019 Evaluate side-chains 1170 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1028 time to evaluate : 7.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 198 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 454 ASP Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain O residue 180 CYS Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain Q residue 137 ASP Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 310 VAL Chi-restraints excluded: chain Q residue 345 SER Chi-restraints excluded: chain Q residue 349 ASN Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 123 GLU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain f residue 46 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 11 MET Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 182 SER Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 254 LEU Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 283 ILE Chi-restraints excluded: chain l residue 300 LYS Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 402 SER Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 172 THR Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 33 GLU Chi-restraints excluded: chain o residue 117 GLN Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 168 GLN Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 272 THR Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 85 MET Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain u residue 42 GLU Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 89 ILE Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 248 GLU Chi-restraints excluded: chain w residue 265 ASP Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 8.9990 chunk 441 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 579 optimal weight: 0.9990 chunk 321 optimal weight: 8.9990 chunk 664 optimal weight: 5.9990 chunk 537 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 397 optimal weight: 8.9990 chunk 698 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN I 51 ASN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN M 498 GLN P 247 GLN Y 91 GLN Z 33 GLN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 150 ASN i 319 HIS l 351 ASN o 52 ASN r 44 GLN u 65 GLN v 65 GLN w 223 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 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 : 0.006 0.070 69886 Z= 0.380 Angle : 0.629 10.837 94474 Z= 0.318 Chirality : 0.046 0.223 10192 Planarity : 0.005 0.068 11768 Dihedral : 14.244 176.670 10857 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.49 % Rotamer: Outliers : 3.86 % Allowed : 18.51 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.09), residues: 8173 helix: 1.27 (0.08), residues: 4293 sheet: -0.15 (0.25), residues: 428 loop : -0.77 (0.10), residues: 3452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP l 144 HIS 0.009 0.001 HIS T 95 PHE 0.038 0.002 PHE i 292 TYR 0.027 0.002 TYR l 587 ARG 0.006 0.001 ARG Q 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1036 time to evaluate : 5.921 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 322 SER cc_start: 0.8673 (m) cc_final: 0.8271 (p) REVERT: C 49 LYS cc_start: 0.8708 (mmtm) cc_final: 0.8411 (mmmt) REVERT: C 186 ARG cc_start: 0.8764 (mtm-85) cc_final: 0.8325 (ttm110) REVERT: C 188 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8516 (mtmm) REVERT: F 73 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7605 (mp10) REVERT: G 82 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6696 (mtp85) REVERT: G 123 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7738 (mt-10) REVERT: G 132 ASP cc_start: 0.7490 (t0) cc_final: 0.7176 (t70) REVERT: G 145 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8176 (t) REVERT: G 147 TYR cc_start: 0.7656 (t80) cc_final: 0.7261 (t80) REVERT: H 70 GLU cc_start: 0.7538 (tp30) cc_final: 0.7267 (tp30) REVERT: I 34 ARG cc_start: 0.9052 (mmm160) cc_final: 0.8732 (mmm160) REVERT: J 107 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.6862 (mm-30) REVERT: J 138 ASN cc_start: 0.8533 (m110) cc_final: 0.8185 (m-40) REVERT: J 205 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: K 88 ASP cc_start: 0.7836 (m-30) cc_final: 0.7535 (m-30) REVERT: L 69 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: M 467 LYS cc_start: 0.8507 (tppp) cc_final: 0.7930 (tptt) REVERT: M 658 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7247 (m-30) REVERT: N 9 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6921 (mtm110) REVERT: N 21 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6074 (mpt180) REVERT: N 50 GLU cc_start: 0.8521 (pt0) cc_final: 0.8265 (pt0) REVERT: O 180 CYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8221 (m) REVERT: S 28 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8568 (ttmt) REVERT: T 43 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8586 (tp40) REVERT: W 76 GLN cc_start: 0.8447 (tp-100) cc_final: 0.7853 (tp-100) REVERT: W 80 ASP cc_start: 0.7983 (m-30) cc_final: 0.7754 (m-30) REVERT: X 97 LYS cc_start: 0.7285 (tttt) cc_final: 0.7030 (mmtt) REVERT: X 111 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8003 (p0) REVERT: Y 41 GLU cc_start: 0.8166 (pt0) cc_final: 0.7481 (mm-30) REVERT: Z 30 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: a 77 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.7839 (tp) REVERT: a 103 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6644 (tp30) REVERT: e 124 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.6894 (mtp85) REVERT: g 19 GLU cc_start: 0.6771 (tp30) cc_final: 0.6443 (tp30) REVERT: g 109 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7754 (ttpt) REVERT: h 43 CYS cc_start: 0.8052 (t) cc_final: 0.7780 (t) REVERT: h 59 GLU cc_start: 0.8778 (mp0) cc_final: 0.8460 (mp0) REVERT: i 11 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8146 (mpp) REVERT: i 149 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8025 (tt) REVERT: i 318 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7892 (mm-30) REVERT: j 68 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7619 (mm-30) REVERT: j 83 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8345 (p0) REVERT: j 85 LYS cc_start: 0.8622 (mmmt) cc_final: 0.8404 (mtmt) REVERT: k 37 MET cc_start: 0.9175 (tpt) cc_final: 0.8909 (mmm) REVERT: l 13 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.9005 (m) REVERT: l 28 LYS cc_start: 0.8702 (mptp) cc_final: 0.8436 (mptp) REVERT: l 300 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8621 (mptt) REVERT: l 554 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8720 (m-30) REVERT: m 87 LYS cc_start: 0.7712 (pttt) cc_final: 0.7339 (ptmm) REVERT: m 135 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.6832 (t80) REVERT: n 46 LYS cc_start: 0.8489 (tttt) cc_final: 0.8106 (tptm) REVERT: o 31 LYS cc_start: 0.8609 (tttp) cc_final: 0.8205 (ttmt) REVERT: o 112 LYS cc_start: 0.8057 (tttt) cc_final: 0.7506 (tttm) REVERT: o 114 LYS cc_start: 0.8425 (ttmt) cc_final: 0.7544 (ttpt) REVERT: p 19 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8520 (tp) REVERT: r 103 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: r 168 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.9023 (tt0) REVERT: r 294 MET cc_start: 0.9147 (mmm) cc_final: 0.8495 (mmp) REVERT: s 70 MET cc_start: 0.9046 (mmm) cc_final: 0.8738 (mtt) REVERT: s 105 MET cc_start: 0.9124 (mmm) cc_final: 0.8774 (mtp) REVERT: s 204 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7589 (tp30) REVERT: u 11 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7747 (tp30) REVERT: u 12 ASP cc_start: 0.7711 (m-30) cc_final: 0.7195 (t0) REVERT: u 38 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7122 (ttmm) REVERT: u 42 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: u 73 GLN cc_start: 0.7516 (tp-100) cc_final: 0.6970 (mt0) REVERT: u 88 CYS cc_start: 0.7170 (t) cc_final: 0.6903 (t) REVERT: v 80 CYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7045 (p) REVERT: v 81 LYS cc_start: 0.8657 (tppt) cc_final: 0.8451 (mptt) REVERT: v 83 GLU cc_start: 0.8008 (mp0) cc_final: 0.7793 (mp0) REVERT: w 124 ASN cc_start: 0.7990 (p0) cc_final: 0.7576 (p0) REVERT: w 351 TRP cc_start: 0.6962 (m100) cc_final: 0.6472 (m100) REVERT: w 353 TRP cc_start: 0.8134 (OUTLIER) cc_final: 0.7128 (p90) outliers start: 276 outliers final: 147 residues processed: 1208 average time/residue: 1.5714 time to fit residues: 2458.1846 Evaluate side-chains 1199 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1018 time to evaluate : 5.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 198 THR Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain N residue 135 GLN Chi-restraints excluded: chain O residue 180 CYS Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 74 ASP Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 310 VAL Chi-restraints excluded: chain Q residue 345 SER Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 122 HIS Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 72 MET Chi-restraints excluded: chain W residue 123 GLU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 132 ASN Chi-restraints excluded: chain f residue 46 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 11 MET Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 108 LEU Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 254 LEU Chi-restraints excluded: chain i residue 258 SER Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 107 THR Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 283 ILE Chi-restraints excluded: chain l residue 300 LYS Chi-restraints excluded: chain l residue 351 ASN Chi-restraints excluded: chain l residue 402 SER Chi-restraints excluded: chain l residue 404 THR Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 543 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 172 THR Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 33 GLU Chi-restraints excluded: chain o residue 117 GLN Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 168 GLN Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 272 THR Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 85 MET Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 11 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain u residue 42 GLU Chi-restraints excluded: chain u residue 59 GLU Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 89 ILE Chi-restraints excluded: chain v residue 24 THR Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 248 GLU Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 265 ASP Chi-restraints excluded: chain w residue 352 ILE Chi-restraints excluded: chain w residue 353 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 6.9990 chunk 700 optimal weight: 6.9990 chunk 153 optimal weight: 0.0070 chunk 456 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 778 optimal weight: 6.9990 chunk 646 optimal weight: 0.8980 chunk 360 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 408 optimal weight: 7.9990 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN I 51 ASN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 ASN L 86 ASN M 498 GLN P 247 GLN Y 91 GLN Z 33 GLN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 107 GLN i 319 HIS l 194 ASN r 44 GLN s 317 GLN v 65 GLN w 223 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 69886 Z= 0.228 Angle : 0.549 10.607 94474 Z= 0.280 Chirality : 0.042 0.193 10192 Planarity : 0.005 0.062 11768 Dihedral : 13.856 177.559 10857 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 3.41 % Allowed : 19.36 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.09), residues: 8173 helix: 1.45 (0.08), residues: 4295 sheet: -0.13 (0.25), residues: 432 loop : -0.70 (0.10), residues: 3446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.006 0.001 HIS J 37 PHE 0.033 0.001 PHE i 292 TYR 0.022 0.001 TYR l 587 ARG 0.009 0.000 ARG p 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1292 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1048 time to evaluate : 6.020 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 322 SER cc_start: 0.8606 (m) cc_final: 0.8186 (p) REVERT: C 44 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: C 49 LYS cc_start: 0.8685 (mmtm) cc_final: 0.8398 (mmmt) REVERT: C 186 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8350 (ttm110) REVERT: E 87 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8773 (mtmt) REVERT: F 73 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7530 (mp10) REVERT: G 82 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6662 (mtp85) REVERT: G 123 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7713 (mt-10) REVERT: G 137 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7492 (pttm) REVERT: G 147 TYR cc_start: 0.7726 (t80) cc_final: 0.7404 (t80) REVERT: H 70 GLU cc_start: 0.7521 (tp30) cc_final: 0.7243 (tp30) REVERT: I 27 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8366 (ptt-90) REVERT: I 34 ARG cc_start: 0.9035 (mmm160) cc_final: 0.8820 (mmm160) REVERT: J 107 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.6817 (mm-30) REVERT: J 117 ARG cc_start: 0.8400 (ttt90) cc_final: 0.8183 (tpt-90) REVERT: J 138 ASN cc_start: 0.8531 (m110) cc_final: 0.8215 (m-40) REVERT: J 205 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: K 88 ASP cc_start: 0.7801 (m-30) cc_final: 0.7504 (m-30) REVERT: L 69 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7629 (mm-30) REVERT: M 467 LYS cc_start: 0.8512 (tppp) cc_final: 0.7958 (tptt) REVERT: M 658 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7271 (m-30) REVERT: N 9 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.6966 (mtm110) REVERT: N 21 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6179 (mpt180) REVERT: N 50 GLU cc_start: 0.8493 (pt0) cc_final: 0.8208 (pt0) REVERT: O 144 ASN cc_start: 0.8584 (t0) cc_final: 0.8320 (t0) REVERT: O 180 CYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8243 (m) REVERT: Q 349 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8248 (m110) REVERT: S 28 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8553 (ttmt) REVERT: T 43 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8615 (tp40) REVERT: W 80 ASP cc_start: 0.7879 (m-30) cc_final: 0.7620 (m-30) REVERT: X 97 LYS cc_start: 0.7235 (tttt) cc_final: 0.7006 (mmtt) REVERT: X 98 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7341 (tp) REVERT: X 111 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.7943 (p0) REVERT: Y 41 GLU cc_start: 0.8171 (pt0) cc_final: 0.7485 (mm-30) REVERT: Z 30 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: a 103 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6651 (tp30) REVERT: e 124 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.6798 (mtp85) REVERT: g 19 GLU cc_start: 0.6670 (tp30) cc_final: 0.6335 (tp30) REVERT: g 52 ARG cc_start: 0.8636 (mtp85) cc_final: 0.8360 (mtp85) REVERT: g 109 LYS cc_start: 0.7972 (mtpt) cc_final: 0.7751 (ttpt) REVERT: h 43 CYS cc_start: 0.8015 (t) cc_final: 0.7726 (t) REVERT: h 59 GLU cc_start: 0.8675 (mp0) cc_final: 0.8295 (mp0) REVERT: i 11 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8172 (mpp) REVERT: i 149 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8084 (tt) REVERT: i 318 GLU cc_start: 0.8228 (mm-30) cc_final: 0.8021 (mm-30) REVERT: j 68 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7514 (mm-30) REVERT: k 37 MET cc_start: 0.9141 (tpt) cc_final: 0.8855 (mmm) REVERT: l 13 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9004 (m) REVERT: l 20 MET cc_start: 0.8462 (mtt) cc_final: 0.8261 (mtt) REVERT: l 28 LYS cc_start: 0.8702 (mptp) cc_final: 0.8444 (mptp) REVERT: l 300 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8548 (mptt) REVERT: l 350 LEU cc_start: 0.9117 (mt) cc_final: 0.8862 (mt) REVERT: l 554 ASP cc_start: 0.9040 (m-30) cc_final: 0.8694 (m-30) REVERT: m 87 LYS cc_start: 0.7669 (pttt) cc_final: 0.7260 (ptmm) REVERT: m 135 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.6661 (t80) REVERT: o 7 LYS cc_start: 0.8789 (ptmt) cc_final: 0.8393 (ptmt) REVERT: o 31 LYS cc_start: 0.8627 (tttp) cc_final: 0.8216 (ttmt) REVERT: o 112 LYS cc_start: 0.8044 (tttt) cc_final: 0.7777 (ttmt) REVERT: r 103 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8780 (tp40) REVERT: r 152 TYR cc_start: 0.9331 (OUTLIER) cc_final: 0.7836 (t80) REVERT: r 168 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8988 (tt0) REVERT: r 294 MET cc_start: 0.9078 (mmm) cc_final: 0.8416 (mmp) REVERT: s 3 MET cc_start: 0.8741 (mmm) cc_final: 0.8473 (mmm) REVERT: s 61 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8211 (tp) REVERT: s 70 MET cc_start: 0.9023 (mmm) cc_final: 0.8754 (mtt) REVERT: s 105 MET cc_start: 0.9081 (mmm) cc_final: 0.8758 (mtp) REVERT: s 204 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7259 (tp30) REVERT: u 12 ASP cc_start: 0.7695 (m-30) cc_final: 0.7176 (t0) REVERT: u 38 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7087 (ttmm) REVERT: u 42 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: u 73 GLN cc_start: 0.7525 (tp-100) cc_final: 0.6933 (mt0) REVERT: u 88 CYS cc_start: 0.7186 (t) cc_final: 0.6947 (t) REVERT: u 90 ASP cc_start: 0.8588 (t0) cc_final: 0.8237 (t0) REVERT: u 109 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6871 (tm-30) REVERT: u 157 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7572 (m-30) REVERT: v 35 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7804 (mptm) REVERT: v 46 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.7915 (mtp) REVERT: v 80 CYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7015 (p) REVERT: v 81 LYS cc_start: 0.8618 (tppt) cc_final: 0.8322 (mmtt) REVERT: v 83 GLU cc_start: 0.7965 (mp0) cc_final: 0.7731 (mp0) REVERT: w 124 ASN cc_start: 0.7959 (p0) cc_final: 0.7557 (p0) REVERT: w 353 TRP cc_start: 0.8156 (OUTLIER) cc_final: 0.7202 (p90) outliers start: 244 outliers final: 127 residues processed: 1206 average time/residue: 1.5518 time to fit residues: 2426.9863 Evaluate side-chains 1176 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1013 time to evaluate : 5.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 198 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain N residue 135 GLN Chi-restraints excluded: chain O residue 180 CYS Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 74 ASP Chi-restraints excluded: chain Q residue 137 ASP Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 310 VAL Chi-restraints excluded: chain Q residue 345 SER Chi-restraints excluded: chain Q residue 349 ASN Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 72 MET Chi-restraints excluded: chain W residue 123 GLU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain f residue 46 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 11 MET Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 254 LEU Chi-restraints excluded: chain i residue 258 SER Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 283 ILE Chi-restraints excluded: chain l residue 300 LYS Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 172 THR Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 33 GLU Chi-restraints excluded: chain o residue 117 GLN Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 152 TYR Chi-restraints excluded: chain r residue 168 GLN Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 272 THR Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 85 MET Chi-restraints excluded: chain s residue 167 THR Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain u residue 42 GLU Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 89 ILE Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 24 THR Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain w residue 152 SER Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 248 GLU Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 265 ASP Chi-restraints excluded: chain w residue 352 ILE Chi-restraints excluded: chain w residue 353 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 9.9990 chunk 87 optimal weight: 0.0570 chunk 443 optimal weight: 1.9990 chunk 568 optimal weight: 0.9990 chunk 440 optimal weight: 0.8980 chunk 655 optimal weight: 6.9990 chunk 434 optimal weight: 8.9990 chunk 775 optimal weight: 10.0000 chunk 485 optimal weight: 10.0000 chunk 473 optimal weight: 9.9990 chunk 358 optimal weight: 6.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN E 70 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN I 51 ASN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 ASN L 86 ASN M 498 GLN P 247 GLN Y 91 GLN Z 33 GLN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 104 ASN h 21 GLN i 150 ASN i 319 HIS l 351 ASN r 44 GLN w 223 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 69886 Z= 0.248 Angle : 0.558 10.667 94474 Z= 0.283 Chirality : 0.042 0.201 10192 Planarity : 0.005 0.063 11768 Dihedral : 13.655 178.257 10857 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 3.48 % Allowed : 19.58 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.09), residues: 8173 helix: 1.44 (0.08), residues: 4307 sheet: -0.13 (0.25), residues: 433 loop : -0.68 (0.10), residues: 3433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.006 0.001 HIS J 37 PHE 0.035 0.001 PHE i 292 TYR 0.023 0.001 TYR l 587 ARG 0.008 0.000 ARG p 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1282 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1033 time to evaluate : 5.959 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 322 SER cc_start: 0.8593 (m) cc_final: 0.8178 (p) REVERT: C 44 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: C 49 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8336 (mmmt) REVERT: C 186 ARG cc_start: 0.8740 (mtm-85) cc_final: 0.8343 (ttm110) REVERT: F 73 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7540 (mp10) REVERT: G 82 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6612 (mtp85) REVERT: G 123 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7684 (mt-10) REVERT: G 137 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7506 (pttm) REVERT: G 147 TYR cc_start: 0.7758 (t80) cc_final: 0.7469 (t80) REVERT: H 70 GLU cc_start: 0.7573 (tp30) cc_final: 0.7323 (tp30) REVERT: H 77 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7295 (tp) REVERT: I 27 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8383 (ptt-90) REVERT: I 34 ARG cc_start: 0.9026 (mmm160) cc_final: 0.8795 (mmm160) REVERT: J 107 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6825 (mm-30) REVERT: J 117 ARG cc_start: 0.8402 (ttt90) cc_final: 0.8188 (tpt-90) REVERT: J 138 ASN cc_start: 0.8537 (m110) cc_final: 0.8216 (m-40) REVERT: J 205 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7543 (m-30) REVERT: K 88 ASP cc_start: 0.7792 (m-30) cc_final: 0.7494 (m-30) REVERT: L 69 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7663 (mm-30) REVERT: M 467 LYS cc_start: 0.8504 (tppp) cc_final: 0.7949 (tptt) REVERT: M 658 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7274 (m-30) REVERT: N 9 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.6961 (mtm110) REVERT: N 21 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6187 (mpt180) REVERT: N 50 GLU cc_start: 0.8498 (pt0) cc_final: 0.8208 (pt0) REVERT: O 144 ASN cc_start: 0.8570 (t0) cc_final: 0.8328 (t0) REVERT: O 180 CYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8232 (m) REVERT: Q 349 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8262 (m110) REVERT: T 43 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8630 (tp40) REVERT: W 80 ASP cc_start: 0.7823 (m-30) cc_final: 0.7582 (m-30) REVERT: X 97 LYS cc_start: 0.7278 (tttt) cc_final: 0.7064 (mmtt) REVERT: X 111 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.7961 (p0) REVERT: Y 41 GLU cc_start: 0.8148 (pt0) cc_final: 0.7490 (mm-30) REVERT: Z 30 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: a 103 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6651 (tp30) REVERT: c 91 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7337 (p0) REVERT: e 124 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.6795 (mtp85) REVERT: g 19 GLU cc_start: 0.6733 (tp30) cc_final: 0.6371 (tp30) REVERT: g 52 ARG cc_start: 0.8633 (mtp85) cc_final: 0.8356 (mtp85) REVERT: g 109 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7743 (ttpt) REVERT: h 43 CYS cc_start: 0.8027 (t) cc_final: 0.7746 (t) REVERT: h 59 GLU cc_start: 0.8689 (mp0) cc_final: 0.8307 (mp0) REVERT: i 11 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8180 (mpp) REVERT: i 149 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8033 (tt) REVERT: i 318 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7986 (mm-30) REVERT: k 37 MET cc_start: 0.9142 (tpt) cc_final: 0.8856 (mmm) REVERT: l 13 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.9017 (m) REVERT: l 20 MET cc_start: 0.8451 (mtt) cc_final: 0.8247 (mtt) REVERT: l 28 LYS cc_start: 0.8666 (mptp) cc_final: 0.8426 (mptp) REVERT: l 300 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8557 (mptt) REVERT: l 554 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8704 (m-30) REVERT: m 87 LYS cc_start: 0.7607 (pttt) cc_final: 0.7224 (ptmm) REVERT: m 135 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.6714 (t80) REVERT: o 7 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8401 (ptmt) REVERT: o 31 LYS cc_start: 0.8610 (tttp) cc_final: 0.8209 (ttmt) REVERT: o 112 LYS cc_start: 0.8046 (tttt) cc_final: 0.7507 (tttm) REVERT: o 124 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8736 (p) REVERT: r 103 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8798 (tt0) REVERT: r 168 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.9003 (tt0) REVERT: r 294 MET cc_start: 0.9078 (mmm) cc_final: 0.8401 (mmp) REVERT: s 61 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8329 (tp) REVERT: s 70 MET cc_start: 0.9018 (mmm) cc_final: 0.8765 (mtt) REVERT: s 105 MET cc_start: 0.9083 (mmm) cc_final: 0.8808 (mtp) REVERT: s 204 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7504 (tp30) REVERT: u 11 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7699 (tp30) REVERT: u 12 ASP cc_start: 0.7751 (m-30) cc_final: 0.7199 (t0) REVERT: u 38 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7087 (ttmm) REVERT: u 42 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: u 73 GLN cc_start: 0.7518 (tp-100) cc_final: 0.6887 (mt0) REVERT: u 88 CYS cc_start: 0.7202 (t) cc_final: 0.6970 (t) REVERT: u 89 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8541 (tt) REVERT: u 90 ASP cc_start: 0.8578 (t0) cc_final: 0.8193 (t0) REVERT: u 157 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7571 (m-30) REVERT: v 46 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7893 (mtp) REVERT: v 80 CYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6996 (p) REVERT: v 81 LYS cc_start: 0.8664 (tppt) cc_final: 0.8352 (mmtt) REVERT: v 83 GLU cc_start: 0.7960 (mp0) cc_final: 0.7688 (mp0) outliers start: 249 outliers final: 145 residues processed: 1197 average time/residue: 1.5352 time to fit residues: 2388.3580 Evaluate side-chains 1202 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1019 time to evaluate : 5.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 198 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain N residue 135 GLN Chi-restraints excluded: chain O residue 180 CYS Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 74 ASP Chi-restraints excluded: chain Q residue 137 ASP Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 310 VAL Chi-restraints excluded: chain Q residue 345 SER Chi-restraints excluded: chain Q residue 349 ASN Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 72 MET Chi-restraints excluded: chain W residue 123 GLU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 123 PHE Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain f residue 46 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain i residue 11 MET Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 108 LEU Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 254 LEU Chi-restraints excluded: chain i residue 258 SER Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain k residue 27 MET Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 283 ILE Chi-restraints excluded: chain l residue 288 THR Chi-restraints excluded: chain l residue 300 LYS Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 577 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 172 THR Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 33 GLU Chi-restraints excluded: chain o residue 7 LYS Chi-restraints excluded: chain o residue 46 GLU Chi-restraints excluded: chain o residue 117 GLN Chi-restraints excluded: chain o residue 124 THR Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 152 TYR Chi-restraints excluded: chain r residue 168 GLN Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 214 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 272 THR Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 85 MET Chi-restraints excluded: chain s residue 167 THR Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 11 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain u residue 42 GLU Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 89 ILE Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 24 THR Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain w residue 106 VAL Chi-restraints excluded: chain w residue 152 SER Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 248 GLU Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 265 ASP Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 480 optimal weight: 5.9990 chunk 309 optimal weight: 0.7980 chunk 463 optimal weight: 6.9990 chunk 233 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 493 optimal weight: 6.9990 chunk 528 optimal weight: 5.9990 chunk 383 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 609 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN E 70 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN I 51 ASN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN M 498 GLN O 89 GLN P 247 GLN Y 91 GLN Z 33 GLN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN l 274 GLN l 320 ASN r 44 GLN v 65 GLN w 223 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 69886 Z= 0.365 Angle : 0.623 10.963 94474 Z= 0.315 Chirality : 0.045 0.220 10192 Planarity : 0.005 0.067 11768 Dihedral : 13.750 178.719 10857 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.22 % Favored : 95.72 % Rotamer: Outliers : 3.46 % Allowed : 19.82 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.09), residues: 8173 helix: 1.28 (0.08), residues: 4282 sheet: -0.20 (0.24), residues: 430 loop : -0.77 (0.10), residues: 3461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP l 144 HIS 0.008 0.001 HIS J 37 PHE 0.038 0.002 PHE i 292 TYR 0.027 0.002 TYR l 587 ARG 0.006 0.001 ARG h 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1279 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1032 time to evaluate : 6.059 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 322 SER cc_start: 0.8625 (m) cc_final: 0.8210 (p) REVERT: C 44 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: C 49 LYS cc_start: 0.8709 (mmtm) cc_final: 0.8417 (mmmt) REVERT: C 186 ARG cc_start: 0.8767 (mtm-85) cc_final: 0.8348 (ttm110) REVERT: E 70 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8687 (p0) REVERT: F 73 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: G 82 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6732 (mtp85) REVERT: G 123 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7658 (mt-10) REVERT: G 137 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7537 (pttm) REVERT: G 147 TYR cc_start: 0.7798 (t80) cc_final: 0.7418 (t80) REVERT: H 70 GLU cc_start: 0.7582 (tp30) cc_final: 0.7321 (tp30) REVERT: H 77 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7528 (tp) REVERT: I 27 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8395 (ptt-90) REVERT: J 107 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.6846 (mm-30) REVERT: J 138 ASN cc_start: 0.8546 (m110) cc_final: 0.8190 (m-40) REVERT: J 205 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7590 (m-30) REVERT: K 88 ASP cc_start: 0.7778 (m-30) cc_final: 0.7461 (m-30) REVERT: L 69 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: M 467 LYS cc_start: 0.8487 (tppp) cc_final: 0.7926 (tptt) REVERT: M 658 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7261 (m-30) REVERT: N 9 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6971 (mtm110) REVERT: N 21 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6184 (mpt180) REVERT: N 50 GLU cc_start: 0.8517 (pt0) cc_final: 0.8257 (pt0) REVERT: O 44 THR cc_start: 0.8190 (m) cc_final: 0.7896 (t) REVERT: O 144 ASN cc_start: 0.8580 (t0) cc_final: 0.8300 (t0) REVERT: O 180 CYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8243 (m) REVERT: T 43 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8603 (tp40) REVERT: W 76 GLN cc_start: 0.8458 (tp-100) cc_final: 0.7859 (tp-100) REVERT: W 80 ASP cc_start: 0.7961 (m-30) cc_final: 0.7728 (m-30) REVERT: X 97 LYS cc_start: 0.7380 (tttt) cc_final: 0.7157 (mmtt) REVERT: X 111 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.7983 (p0) REVERT: Y 41 GLU cc_start: 0.8179 (pt0) cc_final: 0.7484 (mm-30) REVERT: Y 52 ARG cc_start: 0.6678 (mmm160) cc_final: 0.6238 (mmt-90) REVERT: Z 30 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: a 103 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6659 (tp30) REVERT: c 91 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7486 (p0) REVERT: e 124 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.6859 (mtp85) REVERT: g 19 GLU cc_start: 0.6776 (tp30) cc_final: 0.6419 (tp30) REVERT: g 109 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7826 (ttpt) REVERT: h 43 CYS cc_start: 0.7970 (t) cc_final: 0.7717 (t) REVERT: h 59 GLU cc_start: 0.8783 (mp0) cc_final: 0.8372 (mp0) REVERT: i 11 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8158 (mpp) REVERT: i 149 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8113 (tt) REVERT: i 318 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7912 (mm-30) REVERT: j 68 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: k 37 MET cc_start: 0.9163 (tpt) cc_final: 0.8888 (mmm) REVERT: l 13 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.9017 (m) REVERT: l 28 LYS cc_start: 0.8675 (mptp) cc_final: 0.8434 (mptp) REVERT: l 300 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8689 (mptt) REVERT: l 525 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8954 (mtp) REVERT: l 554 ASP cc_start: 0.9088 (OUTLIER) cc_final: 0.8731 (m-30) REVERT: m 87 LYS cc_start: 0.7652 (pttt) cc_final: 0.7179 (ptmm) REVERT: m 135 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.6817 (t80) REVERT: o 7 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8402 (ptmt) REVERT: o 31 LYS cc_start: 0.8711 (tttp) cc_final: 0.8315 (ttmt) REVERT: o 112 LYS cc_start: 0.8059 (tttt) cc_final: 0.7511 (tttm) REVERT: r 103 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: r 152 TYR cc_start: 0.9331 (OUTLIER) cc_final: 0.7831 (t80) REVERT: r 281 ASP cc_start: 0.8400 (t0) cc_final: 0.8144 (t0) REVERT: r 294 MET cc_start: 0.9123 (mmm) cc_final: 0.8547 (mmp) REVERT: s 61 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8358 (tp) REVERT: s 105 MET cc_start: 0.9083 (mmm) cc_final: 0.8830 (mtp) REVERT: s 204 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7578 (tp30) REVERT: u 11 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7765 (tp30) REVERT: u 38 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7184 (ttmm) REVERT: u 42 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: u 73 GLN cc_start: 0.7580 (tp-100) cc_final: 0.6945 (mt0) REVERT: u 88 CYS cc_start: 0.7245 (t) cc_final: 0.6996 (t) REVERT: u 89 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8571 (tt) REVERT: u 90 ASP cc_start: 0.8587 (t0) cc_final: 0.8214 (t0) REVERT: v 80 CYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7205 (p) REVERT: v 81 LYS cc_start: 0.8690 (tppt) cc_final: 0.8376 (mmtt) REVERT: v 83 GLU cc_start: 0.8012 (mp0) cc_final: 0.7720 (mp0) REVERT: v 103 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7287 (mt-10) REVERT: w 351 TRP cc_start: 0.6935 (m100) cc_final: 0.6405 (m100) REVERT: w 353 TRP cc_start: 0.8204 (OUTLIER) cc_final: 0.7158 (p90) outliers start: 247 outliers final: 157 residues processed: 1195 average time/residue: 1.5574 time to fit residues: 2426.5554 Evaluate side-chains 1207 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1012 time to evaluate : 5.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 198 THR Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain N residue 135 GLN Chi-restraints excluded: chain O residue 180 CYS Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 74 ASP Chi-restraints excluded: chain Q residue 137 ASP Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 310 VAL Chi-restraints excluded: chain Q residue 345 SER Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 122 HIS Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 72 MET Chi-restraints excluded: chain W residue 123 GLU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain f residue 46 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain i residue 11 MET Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 108 LEU Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 254 LEU Chi-restraints excluded: chain i residue 258 SER Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain k residue 27 MET Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 283 ILE Chi-restraints excluded: chain l residue 288 THR Chi-restraints excluded: chain l residue 300 LYS Chi-restraints excluded: chain l residue 402 SER Chi-restraints excluded: chain l residue 404 THR Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 577 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 172 THR Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 33 GLU Chi-restraints excluded: chain o residue 7 LYS Chi-restraints excluded: chain o residue 117 GLN Chi-restraints excluded: chain o residue 124 THR Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 152 TYR Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 214 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 272 THR Chi-restraints excluded: chain r residue 458 LEU Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 85 MET Chi-restraints excluded: chain s residue 167 THR Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 11 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 37 ASP Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain u residue 42 GLU Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 89 ILE Chi-restraints excluded: chain v residue 24 THR Chi-restraints excluded: chain v residue 35 LYS Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain w residue 106 VAL Chi-restraints excluded: chain w residue 152 SER Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 248 GLU Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 265 ASP Chi-restraints excluded: chain w residue 352 ILE Chi-restraints excluded: chain w residue 353 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 0.9990 chunk 743 optimal weight: 0.9990 chunk 678 optimal weight: 1.9990 chunk 723 optimal weight: 0.8980 chunk 435 optimal weight: 0.6980 chunk 314 optimal weight: 0.8980 chunk 567 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 chunk 653 optimal weight: 2.9990 chunk 683 optimal weight: 0.9990 chunk 720 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN E 70 ASN I 25 GLN I 51 ASN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 ASN L 86 ASN M 498 GLN O 69 ASN P 247 GLN Y 91 GLN h 21 GLN i 319 HIS l 320 ASN l 351 ASN n 11 HIS r 44 GLN r 192 ASN r 293 HIS v 55 GLN w 223 ASN w 323 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 69886 Z= 0.151 Angle : 0.518 10.698 94474 Z= 0.263 Chirality : 0.040 0.171 10192 Planarity : 0.004 0.058 11768 Dihedral : 13.099 179.821 10857 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.45 % Rotamer: Outliers : 1.87 % Allowed : 21.60 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.09), residues: 8173 helix: 1.60 (0.08), residues: 4296 sheet: -0.04 (0.25), residues: 430 loop : -0.62 (0.10), residues: 3447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP l 144 HIS 0.004 0.001 HIS J 37 PHE 0.030 0.001 PHE i 292 TYR 0.022 0.001 TYR l 422 ARG 0.008 0.000 ARG w 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1073 time to evaluate : 5.800 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 134 ASP cc_start: 0.6820 (OUTLIER) cc_final: 0.6620 (p0) REVERT: A 322 SER cc_start: 0.8447 (m) cc_final: 0.8036 (p) REVERT: B 43 MET cc_start: 0.8220 (mmm) cc_final: 0.7703 (mmt) REVERT: C 119 LYS cc_start: 0.9264 (tptm) cc_final: 0.9050 (tptp) REVERT: C 186 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8284 (ttm110) REVERT: G 82 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6622 (mtp85) REVERT: G 123 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7736 (mt-10) REVERT: G 143 GLU cc_start: 0.8140 (mp0) cc_final: 0.7898 (mp0) REVERT: G 147 TYR cc_start: 0.7465 (t80) cc_final: 0.7171 (t80) REVERT: H 66 LYS cc_start: 0.7894 (tppt) cc_final: 0.7554 (mmtt) REVERT: H 70 GLU cc_start: 0.7537 (tp30) cc_final: 0.7279 (tp30) REVERT: H 77 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6994 (tp) REVERT: I 27 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8147 (ptt-90) REVERT: I 41 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8210 (mt) REVERT: J 117 ARG cc_start: 0.8396 (ttt90) cc_final: 0.8184 (tpt-90) REVERT: J 138 ASN cc_start: 0.8537 (m110) cc_final: 0.8227 (m-40) REVERT: J 205 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7431 (m-30) REVERT: K 84 TYR cc_start: 0.8116 (m-80) cc_final: 0.7370 (m-10) REVERT: K 88 ASP cc_start: 0.7736 (m-30) cc_final: 0.7504 (m-30) REVERT: N 9 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6938 (mtm110) REVERT: N 50 GLU cc_start: 0.8429 (pt0) cc_final: 0.8206 (pt0) REVERT: O 144 ASN cc_start: 0.8530 (t0) cc_final: 0.8279 (t0) REVERT: O 180 CYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8247 (m) REVERT: O 239 LYS cc_start: 0.5641 (OUTLIER) cc_final: 0.5189 (mttp) REVERT: T 43 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8660 (tp40) REVERT: U 68 SER cc_start: 0.7553 (p) cc_final: 0.7289 (m) REVERT: W 80 ASP cc_start: 0.7776 (m-30) cc_final: 0.7528 (m-30) REVERT: X 97 LYS cc_start: 0.7251 (tttt) cc_final: 0.7020 (mmtp) REVERT: X 111 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7871 (p0) REVERT: X 125 GLU cc_start: 0.8416 (tp30) cc_final: 0.8213 (tp30) REVERT: Y 41 GLU cc_start: 0.8146 (pt0) cc_final: 0.7476 (mm-30) REVERT: Z 30 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: Z 72 LYS cc_start: 0.8347 (tptt) cc_final: 0.7563 (ttmt) REVERT: a 103 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6690 (tp30) REVERT: b 27 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8440 (mt-10) REVERT: c 53 LYS cc_start: 0.8819 (tttp) cc_final: 0.8486 (tttt) REVERT: d 15 ARG cc_start: 0.7281 (tpp80) cc_final: 0.6614 (tpt170) REVERT: e 87 MET cc_start: 0.9171 (tmm) cc_final: 0.8871 (tmt) REVERT: g 19 GLU cc_start: 0.6684 (tp30) cc_final: 0.6323 (tp30) REVERT: g 52 ARG cc_start: 0.8627 (mtp85) cc_final: 0.8324 (mtp85) REVERT: h 43 CYS cc_start: 0.8003 (t) cc_final: 0.7722 (t) REVERT: h 59 GLU cc_start: 0.8636 (mp0) cc_final: 0.8266 (mp0) REVERT: i 11 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8184 (mpp) REVERT: i 149 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8023 (tt) REVERT: i 282 MET cc_start: 0.8871 (mtp) cc_final: 0.8639 (mtp) REVERT: k 37 MET cc_start: 0.9076 (tpt) cc_final: 0.8797 (mmm) REVERT: l 13 THR cc_start: 0.9310 (OUTLIER) cc_final: 0.9032 (m) REVERT: l 28 LYS cc_start: 0.8661 (mptp) cc_final: 0.8428 (mptp) REVERT: l 300 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8535 (mptt) REVERT: l 554 ASP cc_start: 0.9013 (m-30) cc_final: 0.8672 (m-30) REVERT: m 87 LYS cc_start: 0.7582 (pttt) cc_final: 0.7202 (ptmm) REVERT: n 46 LYS cc_start: 0.8364 (tttt) cc_final: 0.7886 (tptm) REVERT: o 7 LYS cc_start: 0.8707 (ptmt) cc_final: 0.8355 (ptmt) REVERT: o 31 LYS cc_start: 0.8720 (tttp) cc_final: 0.8278 (ttmt) REVERT: o 112 LYS cc_start: 0.8030 (tttt) cc_final: 0.7776 (ttmt) REVERT: r 103 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8684 (tp40) REVERT: r 152 TYR cc_start: 0.9301 (OUTLIER) cc_final: 0.7818 (t80) REVERT: r 281 ASP cc_start: 0.8221 (t0) cc_final: 0.7973 (t0) REVERT: r 294 MET cc_start: 0.8906 (mmm) cc_final: 0.8245 (mmp) REVERT: s 105 MET cc_start: 0.8954 (mmm) cc_final: 0.8733 (mtp) REVERT: u 11 GLU cc_start: 0.8059 (tp30) cc_final: 0.7729 (tp30) REVERT: u 23 SER cc_start: 0.8527 (p) cc_final: 0.8222 (m) REVERT: u 73 GLN cc_start: 0.7474 (tp-100) cc_final: 0.6929 (mt0) REVERT: u 89 ILE cc_start: 0.8887 (mm) cc_final: 0.8518 (tt) REVERT: u 90 ASP cc_start: 0.8569 (t0) cc_final: 0.8201 (t0) REVERT: u 157 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7559 (m-30) REVERT: v 46 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.7928 (mtp) REVERT: v 80 CYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6829 (p) REVERT: v 81 LYS cc_start: 0.8539 (tppt) cc_final: 0.8282 (mmtt) REVERT: v 83 GLU cc_start: 0.7905 (mp0) cc_final: 0.7628 (mp0) REVERT: v 103 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7267 (mt-10) outliers start: 134 outliers final: 69 residues processed: 1163 average time/residue: 1.5617 time to fit residues: 2358.9108 Evaluate side-chains 1101 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1011 time to evaluate : 6.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 180 CYS Chi-restraints excluded: chain O residue 239 LYS Chi-restraints excluded: chain Q residue 137 ASP Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 310 VAL Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 72 MET Chi-restraints excluded: chain W residue 123 GLU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain i residue 11 MET Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 283 ILE Chi-restraints excluded: chain l residue 288 THR Chi-restraints excluded: chain l residue 300 LYS Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 172 THR Chi-restraints excluded: chain n residue 33 GLU Chi-restraints excluded: chain o residue 117 GLN Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 152 TYR Chi-restraints excluded: chain r residue 214 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 85 MET Chi-restraints excluded: chain s residue 167 THR Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 265 ASP Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 474 optimal weight: 4.9990 chunk 764 optimal weight: 2.9990 chunk 466 optimal weight: 7.9990 chunk 362 optimal weight: 0.2980 chunk 531 optimal weight: 1.9990 chunk 801 optimal weight: 0.6980 chunk 738 optimal weight: 4.9990 chunk 638 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 493 optimal weight: 5.9990 chunk 391 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN I 51 ASN ** K 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN M 453 GLN M 498 GLN M 514 ASN O 69 ASN ** O 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 247 GLN c 115 ASN h 21 GLN l 320 ASN l 351 ASN n 11 HIS r 44 GLN r 169 ASN r 192 ASN r 304 GLN u 65 GLN w 223 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 69886 Z= 0.189 Angle : 0.539 11.899 94474 Z= 0.271 Chirality : 0.041 0.321 10192 Planarity : 0.005 0.058 11768 Dihedral : 12.934 179.267 10856 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.30 % Rotamer: Outliers : 1.71 % Allowed : 22.07 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.09), residues: 8173 helix: 1.62 (0.08), residues: 4302 sheet: -0.02 (0.25), residues: 432 loop : -0.59 (0.10), residues: 3439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP u 86 HIS 0.005 0.001 HIS J 37 PHE 0.034 0.001 PHE i 292 TYR 0.024 0.001 TYR S 60 ARG 0.007 0.000 ARG h 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1147 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1025 time to evaluate : 5.950 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 322 SER cc_start: 0.8470 (m) cc_final: 0.8060 (p) REVERT: C 119 LYS cc_start: 0.9281 (tptm) cc_final: 0.9061 (tptp) REVERT: C 186 ARG cc_start: 0.8697 (mtm-85) cc_final: 0.8412 (ttm170) REVERT: G 82 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6626 (mtp85) REVERT: G 123 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7689 (mt-10) REVERT: G 143 GLU cc_start: 0.8109 (mp0) cc_final: 0.7804 (mp0) REVERT: G 147 TYR cc_start: 0.7477 (t80) cc_final: 0.7108 (t80) REVERT: H 70 GLU cc_start: 0.7529 (tp30) cc_final: 0.7256 (tp30) REVERT: I 27 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8225 (ptt-90) REVERT: I 41 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8214 (mt) REVERT: J 117 ARG cc_start: 0.8395 (ttt90) cc_final: 0.8184 (tpt-90) REVERT: J 138 ASN cc_start: 0.8543 (m110) cc_final: 0.8226 (m-40) REVERT: J 205 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7494 (m-30) REVERT: K 84 TYR cc_start: 0.8002 (m-80) cc_final: 0.7255 (m-10) REVERT: K 88 ASP cc_start: 0.7780 (m-30) cc_final: 0.7512 (m-30) REVERT: N 9 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6943 (mtm110) REVERT: N 21 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6177 (mpt180) REVERT: N 50 GLU cc_start: 0.8476 (pt0) cc_final: 0.8187 (pt0) REVERT: O 144 ASN cc_start: 0.8533 (t0) cc_final: 0.8275 (t0) REVERT: O 180 CYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8246 (m) REVERT: O 239 LYS cc_start: 0.5639 (OUTLIER) cc_final: 0.5196 (mttp) REVERT: T 43 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8673 (tp40) REVERT: U 68 SER cc_start: 0.7568 (p) cc_final: 0.7358 (m) REVERT: W 80 ASP cc_start: 0.7763 (m-30) cc_final: 0.7515 (m-30) REVERT: X 97 LYS cc_start: 0.7335 (tttt) cc_final: 0.7019 (mmtt) REVERT: X 111 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.7910 (p0) REVERT: Y 41 GLU cc_start: 0.8147 (pt0) cc_final: 0.7479 (mm-30) REVERT: Z 30 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: Z 72 LYS cc_start: 0.8376 (tptt) cc_final: 0.7572 (ttmt) REVERT: a 103 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6671 (tp30) REVERT: b 27 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8452 (mt-10) REVERT: c 33 THR cc_start: 0.5937 (OUTLIER) cc_final: 0.5712 (p) REVERT: c 127 ASN cc_start: 0.8448 (p0) cc_final: 0.8044 (p0) REVERT: d 15 ARG cc_start: 0.7244 (tpp80) cc_final: 0.6624 (tpt170) REVERT: e 87 MET cc_start: 0.9198 (tmm) cc_final: 0.8891 (tmt) REVERT: g 19 GLU cc_start: 0.6695 (tp30) cc_final: 0.6324 (tp30) REVERT: g 52 ARG cc_start: 0.8564 (mtp85) cc_final: 0.8333 (mtp85) REVERT: h 43 CYS cc_start: 0.7933 (t) cc_final: 0.7663 (t) REVERT: h 59 GLU cc_start: 0.8678 (mp0) cc_final: 0.8290 (mp0) REVERT: i 11 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8236 (mpp) REVERT: i 149 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7997 (tt) REVERT: k 37 MET cc_start: 0.9091 (tpt) cc_final: 0.8848 (mmm) REVERT: l 13 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9026 (m) REVERT: l 28 LYS cc_start: 0.8652 (mptp) cc_final: 0.8415 (mptp) REVERT: l 300 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8538 (mptt) REVERT: l 554 ASP cc_start: 0.9021 (m-30) cc_final: 0.8667 (m-30) REVERT: m 87 LYS cc_start: 0.7601 (pttt) cc_final: 0.7219 (ptmm) REVERT: n 46 LYS cc_start: 0.8362 (tttt) cc_final: 0.7875 (tptm) REVERT: o 7 LYS cc_start: 0.8729 (ptmt) cc_final: 0.8372 (ptmt) REVERT: o 31 LYS cc_start: 0.8732 (tttp) cc_final: 0.8291 (ttmt) REVERT: o 112 LYS cc_start: 0.8056 (tttt) cc_final: 0.7784 (ttmt) REVERT: r 103 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8744 (tt0) REVERT: r 281 ASP cc_start: 0.8249 (t0) cc_final: 0.8011 (t0) REVERT: r 294 MET cc_start: 0.8941 (mmm) cc_final: 0.8254 (mmp) REVERT: s 61 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8181 (tt) REVERT: s 105 MET cc_start: 0.9052 (mmm) cc_final: 0.8786 (mtp) REVERT: u 11 GLU cc_start: 0.8099 (tp30) cc_final: 0.7782 (tp30) REVERT: u 23 SER cc_start: 0.8576 (p) cc_final: 0.8255 (m) REVERT: u 42 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: u 73 GLN cc_start: 0.7551 (tp-100) cc_final: 0.6912 (mt0) REVERT: u 89 ILE cc_start: 0.8899 (mm) cc_final: 0.8576 (tt) REVERT: u 90 ASP cc_start: 0.8574 (t0) cc_final: 0.8164 (t0) REVERT: u 157 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7616 (m-30) REVERT: v 80 CYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7068 (p) REVERT: v 81 LYS cc_start: 0.8556 (tppt) cc_final: 0.8308 (mmtt) REVERT: v 83 GLU cc_start: 0.7959 (mp0) cc_final: 0.7681 (mp0) REVERT: v 103 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7265 (mt-10) outliers start: 122 outliers final: 79 residues processed: 1110 average time/residue: 1.5752 time to fit residues: 2262.8067 Evaluate side-chains 1109 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1009 time to evaluate : 5.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 473 MET Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 180 CYS Chi-restraints excluded: chain O residue 239 LYS Chi-restraints excluded: chain Q residue 137 ASP Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 310 VAL Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 72 MET Chi-restraints excluded: chain W residue 123 GLU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain i residue 11 MET Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 283 ILE Chi-restraints excluded: chain l residue 288 THR Chi-restraints excluded: chain l residue 300 LYS Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 543 SER Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 172 THR Chi-restraints excluded: chain n residue 33 GLU Chi-restraints excluded: chain o residue 117 GLN Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 152 TYR Chi-restraints excluded: chain r residue 214 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 85 MET Chi-restraints excluded: chain s residue 167 THR Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain u residue 42 GLU Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 35 LYS Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 265 ASP Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 507 optimal weight: 1.9990 chunk 680 optimal weight: 0.0170 chunk 195 optimal weight: 0.7980 chunk 588 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 639 optimal weight: 0.1980 chunk 267 optimal weight: 0.9990 chunk 656 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 117 optimal weight: 0.3980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN ** K 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 ASN L 86 ASN M 498 GLN O 69 ASN ** O 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 247 GLN Y 91 GLN h 21 GLN l 320 ASN l 351 ASN n 11 HIS r 44 GLN r 192 ASN w 223 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.120307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.098979 restraints weight = 94900.788| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.32 r_work: 0.2929 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.295 69886 Z= 0.201 Angle : 0.626 59.194 94474 Z= 0.324 Chirality : 0.041 0.552 10192 Planarity : 0.005 0.237 11768 Dihedral : 12.931 179.249 10856 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 1.83 % Allowed : 22.10 % Favored : 76.07 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.09), residues: 8173 helix: 1.63 (0.08), residues: 4301 sheet: -0.01 (0.25), residues: 432 loop : -0.58 (0.10), residues: 3440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP u 86 HIS 0.006 0.001 HIS J 37 PHE 0.034 0.001 PHE i 292 TYR 0.021 0.001 TYR S 60 ARG 0.006 0.000 ARG w 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30494.04 seconds wall clock time: 527 minutes 27.93 seconds (31647.93 seconds total)