Starting phenix.real_space_refine on Fri Mar 15 03:12:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4c_32300/03_2024/7w4c_32300_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4c_32300/03_2024/7w4c_32300.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4c_32300/03_2024/7w4c_32300_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4c_32300/03_2024/7w4c_32300_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4c_32300/03_2024/7w4c_32300_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4c_32300/03_2024/7w4c_32300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4c_32300/03_2024/7w4c_32300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4c_32300/03_2024/7w4c_32300_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4c_32300/03_2024/7w4c_32300_updated.pdb" } resolution = 2.7 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 44181 2.51 5 N 11241 2.21 5 O 12235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "J PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 234": "OE1" <-> "OE2" Residue "J GLU 320": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M GLU 211": "OE1" <-> "OE2" Residue "M GLU 283": "OE1" <-> "OE2" Residue "M GLU 396": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "M GLU 618": "OE1" <-> "OE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "O GLU 72": "OE1" <-> "OE2" Residue "O GLU 173": "OE1" <-> "OE2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P GLU 194": "OE1" <-> "OE2" Residue "P GLU 209": "OE1" <-> "OE2" Residue "P GLU 225": "OE1" <-> "OE2" Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q GLU 212": "OE1" <-> "OE2" Residue "Q GLU 370": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T GLU 64": "OE1" <-> "OE2" Residue "T GLU 105": "OE1" <-> "OE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "V GLU 82": "OE1" <-> "OE2" Residue "V GLU 138": "OE1" <-> "OE2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W GLU 108": "OE1" <-> "OE2" Residue "X GLU 123": "OE1" <-> "OE2" Residue "X GLU 125": "OE1" <-> "OE2" Residue "X GLU 129": "OE1" <-> "OE2" Residue "X GLU 136": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "a GLU 130": "OE1" <-> "OE2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a GLU 148": "OE1" <-> "OE2" Residue "b GLU 17": "OE1" <-> "OE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 47": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "d GLU 101": "OE1" <-> "OE2" Residue "d GLU 172": "OE1" <-> "OE2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "h GLU 24": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 269": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "j GLU 38": "OE1" <-> "OE2" Residue "j GLU 68": "OE1" <-> "OE2" Residue "j GLU 105": "OE1" <-> "OE2" Residue "j GLU 115": "OE1" <-> "OE2" Residue "k GLU 70": "OE1" <-> "OE2" Residue "l GLU 60": "OE1" <-> "OE2" Residue "l GLU 353": "OE1" <-> "OE2" Residue "l GLU 445": "OE1" <-> "OE2" Residue "m PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 81": "OE1" <-> "OE2" Residue "m GLU 138": "OE1" <-> "OE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "p GLU 54": "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 335": "OE1" <-> "OE2" Residue "r GLU 378": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s GLU 143": "OE1" <-> "OE2" Residue "s GLU 192": "OE1" <-> "OE2" Residue "s GLU 204": "OE1" <-> "OE2" Residue "s GLU 214": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "s GLU 253": "OE1" <-> "OE2" Residue "u GLU 11": "OE1" <-> "OE2" Residue "u GLU 17": "OE1" <-> "OE2" Residue "u GLU 80": "OE1" <-> "OE2" Residue "u GLU 149": "OE1" <-> "OE2" Residue "u GLU 155": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "v PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "v GLU 105": "OE1" <-> "OE2" Residue "w GLU 55": "OE1" <-> "OE2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "w GLU 115": "OE1" <-> "OE2" Residue "w GLU 171": "OE1" <-> "OE2" Residue "w GLU 185": "OE1" <-> "OE2" Residue "w GLU 248": "OE1" <-> "OE2" Residue "w GLU 251": "OE1" <-> "OE2" Residue "w GLU 264": "OE1" <-> "OE2" Residue "w GLU 274": "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-5265/modules/chem_data/mon_lib" Total number of atoms: 68216 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 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: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1657 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 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: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1161 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "X" Number of atoms: 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: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1307 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 135} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "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: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 863 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "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: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1058 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "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: 3624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3624 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "s" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2507 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 163 Unusual residues: {' UQ': 1, 'PEE': 1, 'PLX': 1, 'SF4': 1, 'UQ1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 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: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "J" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 133 Unusual residues: {' UQ': 1, 'NDP': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "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: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'UQ1': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 339 Unusual residues: {'CDL': 3, 'PEE': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 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: "i" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "j" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 336 Unusual residues: {'CDL': 2, 'PEE': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "n" 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: "r" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 130 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2718 SG CYS A 382 48.895 49.361 169.582 1.00 26.99 S ATOM 3060 SG CYS A 425 48.325 46.083 175.301 1.00 31.53 S ATOM 2738 SG CYS A 385 45.905 44.866 169.477 1.00 26.34 S ATOM 2699 SG CYS A 379 43.452 49.735 173.326 1.00 27.18 S ATOM 3961 SG CYS B 113 38.096 64.803 134.757 1.00 14.91 S ATOM 3980 SG CYS B 116 43.250 62.683 138.567 1.00 14.20 S ATOM 4003 SG CYS B 119 44.338 65.635 133.104 1.00 16.46 S ATOM 4332 SG CYS B 162 41.885 59.679 133.678 1.00 10.23 S ATOM 4030 SG CYS B 123 50.515 68.626 128.806 1.00 6.11 S ATOM 4256 SG CYS B 152 48.947 66.858 122.861 1.00 9.72 S ATOM 4303 SG CYS B 158 47.062 63.019 127.711 1.00 12.91 S ATOM 4282 SG CYS B 155 53.129 63.465 126.296 1.00 13.41 S ATOM 5724 SG CYS C 166 55.725 67.177 118.735 1.00 13.68 S ATOM 4996 SG CYS C 72 56.183 68.565 112.466 1.00 8.68 S ATOM 4990 SG CYS C 71 61.542 67.079 115.494 1.00 12.61 S ATOM 5494 SG CYS C 136 57.960 72.233 117.699 1.00 11.01 S ATOM 14949 SG CYS M 131 42.229 62.818 150.526 1.00 13.22 S ATOM 14928 SG CYS M 128 45.966 58.248 147.588 1.00 19.96 S ATOM 14989 SG CYS M 137 47.966 61.836 152.715 1.00 14.43 S ATOM 15321 SG CYS M 179 45.841 61.727 163.657 1.00 20.24 S ATOM 15675 SG CYS M 226 42.801 64.457 159.523 1.00 15.15 S ATOM 15345 SG CYS M 182 40.156 64.294 165.555 1.00 21.68 S ATOM 15298 SG CYS M 176 40.167 58.963 162.061 1.00 19.71 S ATOM 14546 SG CYS M 78 57.556 57.567 167.871 1.00 18.85 S ATOM 14647 SG CYS M 92 55.597 59.652 170.156 1.00 29.00 S ATOM 14435 SG CYS M 64 51.256 59.424 167.817 1.00 21.40 S ATOM 14521 SG CYS M 75 52.607 57.544 164.866 1.00 22.61 S ATOM 21484 SG CYS O 135 33.301 31.249 177.398 1.00 49.74 S ATOM 21518 SG CYS O 140 33.307 27.788 178.527 1.00 61.79 S ATOM 21798 SG CYS O 176 37.582 33.022 180.008 1.00 58.23 S ATOM 21821 SG CYS O 180 38.183 29.874 181.105 1.00 58.05 S ATOM 28546 SG CYS T 86 30.858 51.057 142.254 1.00 33.50 S ATOM 28724 SG CYS T 111 31.960 54.760 143.156 1.00 25.67 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.67 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.67 Time building chain proxies: 25.95, per 1000 atoms: 0.38 Number of scatterers: 68216 At special positions: 0 Unit cell: (216.286, 225.069, 226.167, 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 12235 8.00 N 11241 7.00 C 44181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " distance=2.03 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.04 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.03 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: 20.18 Conformation dependent library (CDL) restraints added in 8.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " 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="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " 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=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " 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: 357 helices and 28 sheets defined 52.6% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.74 Creating SS restraints... 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: 4.179A 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 178 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: 3.609A 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 344 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.444A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.973A 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: 3.520A 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: 3.584A 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: 5.616A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.889A 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 80 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 removed outlier: 3.516A pdb=" N ARG C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 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 70 removed outlier: 4.067A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.438A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 39 removed outlier: 4.912A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 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 137 removed outlier: 6.675A pdb=" N LYS G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 4.014A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 78 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 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 75 removed outlier: 4.115A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 3.554A pdb=" N MET J 92 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 120 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 223 removed outlier: 3.675A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.416A 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) removed outlier: 4.964A pdb=" N PHE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 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: 4.021A 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 348 No H-bonds generated for 'chain 'J' and resid 345 through 348' Processing helix chain 'J' and resid 350 through 356 removed outlier: 5.720A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 4.722A 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 77 through 80 Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.561A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.827A 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 131 through 141 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.969A 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: 3.796A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 244 No H-bonds generated for 'chain 'M' and resid 242 through 244' 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 382 through 385 Processing helix chain 'M' and resid 392 through 395 Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 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 557 through 559 No H-bonds generated for 'chain 'M' and resid 557 through 559' Processing helix chain 'M' and resid 589 through 591 No H-bonds generated for 'chain 'M' and resid 589 through 591' Processing helix chain 'M' and resid 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 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: 3.705A 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: 3.925A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 90 removed outlier: 4.422A 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 104 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: 4.743A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.757A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET P 173 " --> pdb=" O ILE P 170 " (cutoff:3.500A) removed outlier: 4.060A 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: 3.984A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.729A 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: 3.886A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (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: 4.010A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 262 removed outlier: 3.887A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.874A 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: 4.714A 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: 3.751A pdb=" N LEU Q 435 " --> pdb=" O HIS Q 431 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.748A 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 29 Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 42 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'U' and resid 4 through 15 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 Processing helix chain 'U' and resid 79 through 82 No H-bonds generated for 'chain 'U' and resid 79 through 82' Processing helix chain 'V' and resid 3 through 10 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 80 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: 3.986A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 137 Processing helix chain 'X' and resid 76 through 89 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 135 No H-bonds generated for 'chain 'X' and resid 132 through 135' Processing helix chain 'X' and resid 141 through 151 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 through 81 removed outlier: 3.852A pdb=" N LEU Y 81 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 97 No H-bonds generated for 'chain 'Y' and resid 94 through 97' Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 38 Processing helix chain 'Z' and resid 46 through 54 removed outlier: 4.595A pdb=" N TRP Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ARG Z 52 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.324A 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 88 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 'b' and resid 90 through 92 No H-bonds generated for 'chain 'b' and resid 90 through 92' 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 83 through 85 No H-bonds generated for 'chain 'c' and resid 83 through 85' 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: 4.838A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 124 removed outlier: 3.922A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 174 Processing helix chain 'e' and resid 66 through 69 No H-bonds generated for 'chain 'e' and resid 66 through 69' Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 99 through 107 Processing helix chain 'e' and resid 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 19 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 removed outlier: 3.822A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 44 Processing helix chain 'h' and resid 49 through 55 removed outlier: 4.013A pdb=" N LYS h 54 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'h' and resid 96 through 98 No H-bonds generated for 'chain 'h' and resid 96 through 98' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.102A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.835A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 171 removed outlier: 4.052A 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 230 No H-bonds generated for 'chain 'i' and resid 227 through 230' Processing helix chain 'i' and resid 233 through 235 No H-bonds generated for 'chain 'i' and resid 233 through 235' Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 272 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.344A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 23 Processing helix chain 'j' and resid 56 through 80 removed outlier: 3.910A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU j 68 " --> pdb=" O LEU j 64 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.623A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN j 80 " --> pdb=" O PRO j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 20 Processing helix chain 'k' and resid 26 through 51 Processing helix chain 'k' and resid 55 through 85 removed outlier: 4.030A pdb=" N MET k 58 " --> pdb=" O LEU k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix Processing helix chain 'k' and resid 90 through 92 No H-bonds generated for 'chain 'k' and resid 90 through 92' Processing helix chain 'l' and resid 3 through 23 removed outlier: 3.685A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.823A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.261A 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: 3.807A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 133 Processing helix chain 'l' and resid 137 through 155 Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.987A 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: 4.052A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.295A 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: 4.605A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.173A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 3.707A pdb=" N ILE l 293 " --> pdb=" O ALA l 289 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 319 Processing helix chain 'l' and resid 322 through 349 removed outlier: 4.136A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 4.062A 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 401 removed outlier: 4.849A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET l 401 " --> pdb=" O GLU l 397 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.976A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 469 removed outlier: 6.018A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 484 through 487 No H-bonds generated for 'chain 'l' and resid 484 through 487' Processing helix chain 'l' and resid 489 through 509 removed outlier: 4.051A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.471A 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: 4.369A 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 138 through 147 removed outlier: 4.276A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR m 147 " --> pdb=" O ILE m 143 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 4 through 14 removed outlier: 6.409A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 34 removed outlier: 3.796A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 20 through 22 No H-bonds generated for 'chain 'o' and resid 20 through 22' Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.828A 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 117 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 51 removed outlier: 4.440A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 74 Processing helix chain 'p' and resid 95 through 97 No H-bonds generated for 'chain 'p' and resid 95 through 97' 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: 4.677A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 4.774A 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: 4.327A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.779A 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: 3.574A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.985A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.611A 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 169 removed outlier: 3.807A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE r 151 " --> pdb=" O TYR r 148 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 4.708A 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: 4.624A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.178A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 237 through 249 removed outlier: 4.804A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 254 through 257 No H-bonds generated for 'chain 'r' and resid 254 through 257' Processing helix chain 'r' and resid 259 through 277 removed outlier: 3.704A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.656A 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: 4.191A pdb=" N MET r 396 " --> pdb=" O ILE r 393 " (cutoff:3.500A) removed outlier: 4.046A 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 454 Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.766A 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: 4.400A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 3.946A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.080A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.579A 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: 3.557A 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 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 81 through 123 Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 50 through 52 No H-bonds generated for 'chain 'w' and resid 50 through 52' Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 95 through 97 No H-bonds generated for 'chain 'w' and resid 95 through 97' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 166 through 175 removed outlier: 3.879A pdb=" N ARG w 175 " --> pdb=" O ALA w 172 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.302A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.547A 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: 5.006A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix removed outlier: 3.509A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) removed outlier: 3.964A 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 274 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: 5.198A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 333 Processing helix chain 'w' and resid 341 through 343 No H-bonds generated for 'chain 'w' and resid 341 through 343' Processing helix chain 'w' and resid 345 through 347 No H-bonds generated for 'chain 'w' and resid 345 through 347' Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 240 through 244 removed outlier: 6.923A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.003A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.178A 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: 6.571A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.202A 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 58 removed outlier: 3.695A 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: 6.554A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 228 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 removed outlier: 6.292A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL M 270 " --> pdb=" O ARG M 266 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 305 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 365 through 368 removed outlier: 4.610A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.226A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= S, first strand: chain 'N' and resid 60 through 63 removed outlier: 3.649A pdb=" N GLY N 40 " --> pdb=" O TYR N 48 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.509A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.802A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU P 83 " --> pdb=" O SER P 79 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 6.416A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 removed outlier: 3.580A pdb=" N ARG Q 421 " --> pdb=" O VAL Q 412 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= Z, first strand: chain 'l' and resid 61 through 67 removed outlier: 3.734A pdb=" N MET l 61 " --> pdb=" O MET l 82 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.659A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'w' and resid 84 through 86 2933 hydrogen bonds defined for protein. 8181 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: 20.10 Time building geometry restraints manager: 22.52 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: 27742 1.40 - 1.62: 41205 1.62 - 1.84: 876 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 69903 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.264 0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.288 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.631 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.298 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.297 0.227 2.00e-02 2.50e+03 1.28e+02 ... (remaining 69898 not shown) Histogram of bond angle deviations from ideal: 73.59 - 85.99: 76 85.99 - 98.39: 1 98.39 - 110.78: 23897 110.78 - 123.18: 67492 123.18 - 135.57: 3029 Bond angle restraints: 94495 Sorted by residual: angle pdb=" N ILE c 105 " pdb=" CA ILE c 105 " pdb=" C ILE c 105 " ideal model delta sigma weight residual 110.72 123.37 -12.65 1.01e+00 9.80e-01 1.57e+02 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 124.06 -16.32 1.95e+00 2.62e-01 6.97e+01 angle pdb=" C11 CDL l 702 " pdb=" CA5 CDL l 702 " pdb=" OA6 CDL l 702 " ideal model delta sigma weight residual 111.33 120.83 -9.50 1.32e+00 5.72e-01 5.16e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 117.43 -13.59 1.91e+00 2.73e-01 5.03e+01 angle pdb=" O1X NDP J 401 " pdb=" P2B NDP J 401 " pdb=" O3X NDP J 401 " ideal model delta sigma weight residual 117.46 109.27 8.19 1.17e+00 7.36e-01 4.93e+01 ... (remaining 94490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 40391 35.71 - 71.42: 1892 71.42 - 107.13: 127 107.13 - 142.84: 18 142.84 - 178.54: 14 Dihedral angle restraints: 42442 sinusoidal: 18348 harmonic: 24094 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 76.14 -178.54 1 2.00e+01 2.50e-03 4.80e+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 -60.00 101.90 -161.90 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" CA LEU I 106 " pdb=" C LEU I 106 " pdb=" N SER I 107 " pdb=" CA SER I 107 " ideal model delta harmonic sigma weight residual 180.00 150.50 29.50 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 42439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 9554 0.084 - 0.168: 638 0.168 - 0.252: 19 0.252 - 0.336: 2 0.336 - 0.420: 2 Chirality restraints: 10215 Sorted by residual: chirality pdb=" CA ILE c 105 " pdb=" N ILE c 105 " pdb=" C ILE c 105 " pdb=" CB ILE c 105 " both_signs ideal model delta sigma weight residual False 2.43 2.01 0.42 2.00e-01 2.50e+01 4.41e+00 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 3.38e+00 chirality pdb=" C3D NDP J 401 " pdb=" C2D NDP J 401 " pdb=" C4D NDP J 401 " pdb=" O3D NDP J 401 " both_signs ideal model delta sigma weight residual False -2.71 -2.42 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 10212 not shown) Planarity restraints: 11770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ C 305 " 0.395 2.00e-02 2.50e+03 3.53e-01 1.56e+03 pdb=" C18 UQ C 305 " -0.395 2.00e-02 2.50e+03 pdb=" C19 UQ C 305 " -0.395 2.00e-02 2.50e+03 pdb=" C20 UQ C 305 " -0.000 2.00e-02 2.50e+03 pdb=" C21 UQ C 305 " 0.396 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ1 C 304 " 0.341 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C11 UQ1 C 304 " 0.007 2.00e-02 2.50e+03 pdb=" C7 UQ1 C 304 " 0.315 2.00e-02 2.50e+03 pdb=" C8 UQ1 C 304 " -0.298 2.00e-02 2.50e+03 pdb=" C9 UQ1 C 304 " -0.365 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ C 305 " -0.066 2.00e-02 2.50e+03 2.72e-01 9.26e+02 pdb=" C11 UQ C 305 " 0.093 2.00e-02 2.50e+03 pdb=" C7 UQ C 305 " -0.252 2.00e-02 2.50e+03 pdb=" C8 UQ C 305 " 0.479 2.00e-02 2.50e+03 pdb=" C9 UQ C 305 " -0.254 2.00e-02 2.50e+03 ... (remaining 11767 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3618 2.73 - 3.27: 66844 3.27 - 3.82: 116701 3.82 - 4.36: 147176 4.36 - 4.90: 244569 Nonbonded interactions: 578908 Sorted by model distance: nonbonded pdb=" N GLU c 46 " pdb=" OE1 GLU c 46 " model vdw 2.188 2.520 nonbonded pdb=" O ASP Y 76 " pdb=" OH TYR l 385 " model vdw 2.197 2.440 nonbonded pdb=" O PRO A 325 " pdb=" OG1 THR A 347 " model vdw 2.198 2.440 nonbonded pdb=" O ASP d 42 " pdb=" OG1 THR d 46 " model vdw 2.204 2.440 nonbonded pdb=" NZ LYS E 29 " pdb=" O35 8Q1 G 201 " model vdw 2.204 2.520 ... (remaining 578903 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=0.67 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: 0.970 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: 0.040 Extract box with map and model: 8.020 Check model and map are aligned: 0.740 Set scattering table: 0.450 Process input model: 150.850 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.316 69903 Z= 0.493 Angle : 0.822 17.785 94495 Z= 0.412 Chirality : 0.042 0.420 10215 Planarity : 0.009 0.353 11770 Dihedral : 18.953 178.545 26883 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.39 % Favored : 96.51 % Rotamer: Outliers : 1.33 % Allowed : 19.33 % Favored : 79.35 % 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: 0.86 (0.09), residues: 8173 helix: 1.53 (0.08), residues: 4309 sheet: 0.17 (0.25), residues: 407 loop : -0.56 (0.10), residues: 3457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP w 353 HIS 0.007 0.001 HIS J 37 PHE 0.032 0.001 PHE i 292 TYR 0.024 0.001 TYR r 406 ARG 0.015 0.000 ARG F 26 *********************** 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 1202 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1107 time to evaluate : 5.898 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: L 86 ASN cc_start: 0.9175 (OUTLIER) cc_final: 0.8623 (m-40) REVERT: M 558 GLN cc_start: 0.7747 (mp10) cc_final: 0.7512 (mm-40) REVERT: N 21 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.7208 (tpp80) REVERT: O 224 SER cc_start: 0.8908 (t) cc_final: 0.8686 (t) REVERT: Q 57 GLU cc_start: 0.7664 (tt0) cc_final: 0.7428 (tm-30) REVERT: V 107 SER cc_start: 0.8548 (t) cc_final: 0.8184 (m) REVERT: W 52 LYS cc_start: 0.8948 (ttmm) cc_final: 0.8634 (mmtt) REVERT: Z 75 PHE cc_start: 0.8652 (t80) cc_final: 0.8424 (t80) REVERT: c 103 GLU cc_start: 0.8525 (pt0) cc_final: 0.8264 (pt0) REVERT: d 35 LYS cc_start: 0.8277 (mtmm) cc_final: 0.8044 (mtpm) REVERT: g 97 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8271 (ttmt) REVERT: i 291 TYR cc_start: 0.9203 (t80) cc_final: 0.8972 (t80) REVERT: j 1 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6438 (tmt) REVERT: j 87 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8858 (tmm) REVERT: k 70 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7969 (mt-10) REVERT: m 102 CYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6450 (m) REVERT: s 227 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8664 (tp30) REVERT: v 35 LYS cc_start: 0.7964 (mmmt) cc_final: 0.7689 (mppt) outliers start: 95 outliers final: 68 residues processed: 1184 average time/residue: 1.6154 time to fit residues: 2454.9141 Evaluate side-chains 1136 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1063 time to evaluate : 5.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 295 ASP Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 672 SER Chi-restraints excluded: chain M residue 677 GLN Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 57 SER Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 87 MET Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 185 SER Chi-restraints excluded: chain l residue 272 LEU Chi-restraints excluded: chain l residue 359 MET Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 102 CYS Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 304 GLN Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 178 SER Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain w residue 41 LEU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 203 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 679 optimal weight: 6.9990 chunk 610 optimal weight: 2.9990 chunk 338 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 411 optimal weight: 7.9990 chunk 325 optimal weight: 6.9990 chunk 630 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 383 optimal weight: 0.9980 chunk 469 optimal weight: 7.9990 chunk 731 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN F 93 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN I 25 GLN K 90 ASN M 304 GLN T 43 GLN U 11 ASN U 71 GLN V 134 GLN W 24 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN Y 91 GLN a 189 ASN f 61 GLN i 322 GLN l 109 HIS p 124 GLN w 219 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.0533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 69903 Z= 0.275 Angle : 0.586 11.937 94495 Z= 0.297 Chirality : 0.044 0.224 10215 Planarity : 0.005 0.055 11770 Dihedral : 15.355 176.334 10819 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.00 % Favored : 95.93 % Rotamer: Outliers : 3.17 % Allowed : 17.03 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.09), residues: 8173 helix: 1.48 (0.08), residues: 4325 sheet: 0.18 (0.25), residues: 396 loop : -0.56 (0.10), residues: 3452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.008 0.001 HIS J 37 PHE 0.036 0.002 PHE i 292 TYR 0.023 0.002 TYR l 587 ARG 0.011 0.000 ARG P 44 *********************** 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 1313 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1086 time to evaluate : 5.812 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: E 27 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7210 (mt-10) REVERT: G 139 MET cc_start: 0.7818 (mmp) cc_final: 0.7247 (mpm) REVERT: J 85 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8736 (ptt180) REVERT: L 73 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7678 (mtmt) REVERT: M 535 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6216 (pp20) REVERT: O 64 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7463 (tp30) REVERT: O 167 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7870 (mttp) REVERT: P 85 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8194 (mp0) REVERT: Q 57 GLU cc_start: 0.7678 (tt0) cc_final: 0.7423 (tm-30) REVERT: X 137 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.7843 (mtmt) REVERT: d 171 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6171 (tttm) REVERT: e 116 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7315 (mm-30) REVERT: h 42 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8333 (mt-10) REVERT: i 149 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8075 (tp) REVERT: i 291 TYR cc_start: 0.9307 (t80) cc_final: 0.9076 (t80) REVERT: j 44 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7295 (mpt) REVERT: k 97 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.6905 (mm-40) REVERT: l 373 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8956 (tt) REVERT: l 525 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.8271 (mpp) REVERT: p 62 GLN cc_start: 0.7739 (tm-30) cc_final: 0.6997 (tm-30) REVERT: p 127 ARG cc_start: 0.8090 (ttp80) cc_final: 0.7580 (ttp-110) REVERT: s 206 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: s 222 MET cc_start: 0.9422 (mtp) cc_final: 0.9218 (mtm) REVERT: s 233 MET cc_start: 0.9328 (tmm) cc_final: 0.9113 (tmm) REVERT: u 132 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8231 (mtpp) outliers start: 227 outliers final: 108 residues processed: 1208 average time/residue: 1.6159 time to fit residues: 2499.9734 Evaluate side-chains 1181 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1056 time to evaluate : 5.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 470 LYS Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain M residue 579 MET Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain M residue 677 GLN Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 167 LYS Chi-restraints excluded: chain O residue 220 SER Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 122 HIS Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 79 GLN Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 79 LYS Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain W residue 120 MET Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain d residue 171 LYS Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 73 MET Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 272 LEU Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 461 SER Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 514 LYS Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain m residue 50 SER Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 304 GLN Chi-restraints excluded: chain r residue 387 SER Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 98 MET Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain s residue 206 GLU Chi-restraints excluded: chain u residue 73 GLN Chi-restraints excluded: chain u residue 132 LYS Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 218 ILE 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: 10.0000 chunk 608 optimal weight: 0.7980 chunk 497 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 chunk 732 optimal weight: 0.6980 chunk 791 optimal weight: 9.9990 chunk 652 optimal weight: 9.9990 chunk 726 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 587 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN F 93 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN I 25 GLN K 90 ASN M 304 GLN T 43 GLN U 11 ASN U 71 GLN V 134 GLN W 24 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN Y 91 GLN Z 33 GLN a 189 ASN d 131 GLN i 322 GLN k 92 ASN l 109 HIS p 62 GLN p 124 GLN r 188 ASN u 64 ASN v 54 GLN v 65 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 69903 Z= 0.293 Angle : 0.586 11.140 94495 Z= 0.298 Chirality : 0.044 0.220 10215 Planarity : 0.005 0.058 11770 Dihedral : 14.691 177.983 10752 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.82 % Favored : 96.11 % Rotamer: Outliers : 3.61 % Allowed : 17.14 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.09), residues: 8173 helix: 1.45 (0.08), residues: 4317 sheet: 0.21 (0.25), residues: 399 loop : -0.58 (0.10), residues: 3457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.016 0.001 HIS J 323 PHE 0.034 0.002 PHE i 292 TYR 0.023 0.002 TYR l 587 ARG 0.015 0.000 ARG P 44 *********************** 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 1341 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1083 time to evaluate : 5.945 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 184 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7230 (ttmm) REVERT: E 27 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7189 (mt-10) REVERT: G 103 HIS cc_start: 0.7699 (t-90) cc_final: 0.7491 (t-90) REVERT: J 85 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8727 (ptt180) REVERT: K 80 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7249 (mm-30) REVERT: L 73 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7639 (mtmt) REVERT: M 535 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.6202 (pp20) REVERT: N 12 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: N 21 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7331 (tpp80) REVERT: O 61 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8429 (ptpt) REVERT: O 64 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7508 (tp30) REVERT: O 167 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7897 (mttp) REVERT: P 85 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8206 (mp0) REVERT: Q 57 GLU cc_start: 0.7676 (tt0) cc_final: 0.7419 (tm-30) REVERT: X 74 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8422 (tp) REVERT: X 137 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.7454 (mtmt) REVERT: Z 14 MET cc_start: 0.5783 (OUTLIER) cc_final: 0.5371 (pp-130) REVERT: a 98 LEU cc_start: 0.9350 (tp) cc_final: 0.9143 (tm) REVERT: d 171 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6233 (tttm) REVERT: e 83 ASP cc_start: 0.9163 (OUTLIER) cc_final: 0.8845 (t0) REVERT: e 116 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7355 (mm-30) REVERT: h 24 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.6675 (tm-30) REVERT: h 42 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: i 149 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8070 (tp) REVERT: i 291 TYR cc_start: 0.9327 (t80) cc_final: 0.9092 (t80) REVERT: j 1 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6457 (tmt) REVERT: j 44 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7294 (mpt) REVERT: k 97 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.6952 (mm-40) REVERT: l 150 MET cc_start: 0.9136 (mmm) cc_final: 0.8715 (mmm) REVERT: l 197 ASP cc_start: 0.8696 (p0) cc_final: 0.8455 (p0) REVERT: l 373 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8958 (tt) REVERT: l 525 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8254 (mpp) REVERT: o 26 SER cc_start: 0.8748 (p) cc_final: 0.8488 (t) REVERT: p 62 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: p 127 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7553 (ttp-110) REVERT: r 114 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: s 222 MET cc_start: 0.9447 (mtp) cc_final: 0.9238 (mtm) REVERT: s 243 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8744 (mt) REVERT: u 12 ASP cc_start: 0.7747 (t0) cc_final: 0.7339 (t0) REVERT: u 88 CYS cc_start: 0.7544 (t) cc_final: 0.7033 (t) REVERT: u 121 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8056 (m-30) REVERT: u 132 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8298 (mtpp) REVERT: v 54 GLN cc_start: 0.8513 (pt0) cc_final: 0.8209 (pm20) outliers start: 258 outliers final: 132 residues processed: 1209 average time/residue: 1.6093 time to fit residues: 2514.8060 Evaluate side-chains 1218 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1057 time to evaluate : 5.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain M residue 579 MET Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain M residue 677 GLN Chi-restraints excluded: chain M residue 715 THR Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain O residue 61 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 167 LYS Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 220 SER Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 192 LEU 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 S residue 59 ARG Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 79 LYS Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain W residue 120 MET Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 52 ARG Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 171 LYS Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 136 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain g residue 109 LYS Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 272 LEU Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 359 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 461 SER Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 514 LYS Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain p residue 62 GLN Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 304 GLN Chi-restraints excluded: chain r residue 387 SER Chi-restraints excluded: chain r residue 440 HIS Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 98 MET Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 206 GLU Chi-restraints excluded: chain s residue 243 LEU Chi-restraints excluded: chain u residue 73 GLN Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain u residue 121 ASP Chi-restraints excluded: chain u residue 132 LYS Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 218 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 2.9990 chunk 550 optimal weight: 7.9990 chunk 380 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 349 optimal weight: 7.9990 chunk 491 optimal weight: 6.9990 chunk 734 optimal weight: 5.9990 chunk 778 optimal weight: 0.0060 chunk 383 optimal weight: 4.9990 chunk 696 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN B 180 HIS E 45 ASN F 93 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN I 25 GLN K 90 ASN M 304 GLN M 498 GLN M 669 ASN P 77 GLN P 247 GLN T 43 GLN T 122 HIS U 11 ASN U 71 GLN V 134 GLN W 24 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN Y 91 GLN a 189 ASN i 322 GLN l 109 HIS m 175 ASN p 124 GLN u 64 ASN u 95 GLN v 65 GLN w 219 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 69903 Z= 0.368 Angle : 0.626 12.232 94495 Z= 0.319 Chirality : 0.046 0.281 10215 Planarity : 0.005 0.061 11770 Dihedral : 14.455 175.305 10751 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.05 % Favored : 95.88 % Rotamer: Outliers : 4.11 % Allowed : 16.86 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.65 (0.09), residues: 8173 helix: 1.32 (0.08), residues: 4320 sheet: 0.29 (0.26), residues: 379 loop : -0.65 (0.10), residues: 3474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP u 86 HIS 0.014 0.001 HIS J 323 PHE 0.033 0.002 PHE i 292 TYR 0.025 0.002 TYR l 587 ARG 0.015 0.001 ARG P 44 *********************** 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 1378 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1084 time to evaluate : 5.843 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 184 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7272 (ttmm) REVERT: E 27 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7217 (mt-10) REVERT: G 103 HIS cc_start: 0.7732 (t-90) cc_final: 0.7489 (t-90) REVERT: G 115 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8123 (tm130) REVERT: J 85 ARG cc_start: 0.9315 (OUTLIER) cc_final: 0.8764 (ptt180) REVERT: K 80 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7270 (mm-30) REVERT: L 73 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7554 (mtmt) REVERT: M 535 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6216 (pp20) REVERT: N 12 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: N 21 ARG cc_start: 0.7634 (ttm-80) cc_final: 0.7339 (tpp80) REVERT: O 61 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8457 (ptpt) REVERT: O 64 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7544 (tp30) REVERT: O 159 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7124 (mptt) REVERT: O 167 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7874 (mttp) REVERT: O 212 LYS cc_start: 0.7833 (mmmm) cc_final: 0.7333 (tppt) REVERT: P 144 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9187 (mttt) REVERT: V 106 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5233 (mtt-85) REVERT: X 137 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8123 (mmmt) REVERT: a 72 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7961 (ttm170) REVERT: a 98 LEU cc_start: 0.9360 (tp) cc_final: 0.9132 (tm) REVERT: d 16 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8291 (ptm160) REVERT: d 171 LYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6112 (tttm) REVERT: e 83 ASP cc_start: 0.9195 (OUTLIER) cc_final: 0.8920 (t0) REVERT: e 116 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7414 (mm-30) REVERT: e 124 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7758 (mpt-90) REVERT: h 24 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.6711 (tm-30) REVERT: h 42 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8256 (mt-10) REVERT: i 69 MET cc_start: 0.9323 (mtp) cc_final: 0.9107 (mtp) REVERT: i 149 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8114 (tp) REVERT: i 291 TYR cc_start: 0.9347 (t80) cc_final: 0.9126 (t80) REVERT: j 1 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6468 (tmt) REVERT: j 44 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7315 (mpt) REVERT: k 97 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.6972 (mm-40) REVERT: l 197 ASP cc_start: 0.8724 (p0) cc_final: 0.8478 (p0) REVERT: l 373 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8973 (tt) REVERT: l 525 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.8261 (mpp) REVERT: m 1 MET cc_start: 0.1741 (OUTLIER) cc_final: 0.1105 (mtm) REVERT: p 55 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.6973 (mtpt) REVERT: p 127 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7575 (ttp-110) REVERT: p 141 GLN cc_start: 0.7923 (tt0) cc_final: 0.7715 (mt0) REVERT: r 114 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7907 (tm-30) REVERT: r 186 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8774 (tp) REVERT: s 133 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9001 (mm) REVERT: s 143 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: s 222 MET cc_start: 0.9463 (mtp) cc_final: 0.9240 (mtm) REVERT: s 233 MET cc_start: 0.9372 (tmm) cc_final: 0.9154 (tmm) REVERT: s 243 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8782 (mt) REVERT: u 88 CYS cc_start: 0.7623 (t) cc_final: 0.7161 (t) REVERT: u 132 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8298 (mtpp) REVERT: v 22 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7957 (ttp) REVERT: v 35 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7798 (mppt) REVERT: v 54 GLN cc_start: 0.8564 (pt0) cc_final: 0.8249 (pm20) REVERT: w 253 CYS cc_start: 0.5045 (OUTLIER) cc_final: 0.4592 (t) REVERT: w 254 GLU cc_start: 0.5704 (OUTLIER) cc_final: 0.5295 (pm20) outliers start: 294 outliers final: 146 residues processed: 1248 average time/residue: 1.6166 time to fit residues: 2589.6924 Evaluate side-chains 1245 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1060 time to evaluate : 5.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain M residue 579 MET Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain M residue 677 GLN Chi-restraints excluded: chain M residue 715 THR Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain O residue 61 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 167 LYS Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 220 SER Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 192 LEU 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 S residue 59 ARG Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 122 HIS Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 79 GLN Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain W residue 120 MET Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 52 ARG Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain d residue 16 ARG Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 171 LYS Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain g residue 109 LYS Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 207 ILE Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 272 LEU Chi-restraints excluded: chain l residue 359 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 461 SER Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 514 LYS Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 120 LYS Chi-restraints excluded: chain p residue 55 LYS Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 285 LEU Chi-restraints excluded: chain r residue 304 GLN Chi-restraints excluded: chain r residue 387 SER Chi-restraints excluded: chain r residue 440 HIS Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 98 MET Chi-restraints excluded: chain s residue 133 LEU Chi-restraints excluded: chain s residue 143 GLU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 206 GLU Chi-restraints excluded: chain s residue 243 LEU Chi-restraints excluded: chain u residue 73 GLN Chi-restraints excluded: chain u residue 132 LYS Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 22 MET Chi-restraints excluded: chain v residue 45 GLU Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 218 ILE Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 254 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 5.9990 chunk 441 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 579 optimal weight: 4.9990 chunk 321 optimal weight: 10.0000 chunk 664 optimal weight: 8.9990 chunk 537 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 397 optimal weight: 8.9990 chunk 698 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS E 45 ASN F 93 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN I 25 GLN K 90 ASN M 304 GLN T 43 GLN T 122 HIS U 11 ASN U 71 GLN V 134 GLN W 24 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN Y 91 GLN a 189 ASN d 23 GLN e 86 ASN h 82 GLN i 91 ASN i 322 GLN l 34 ASN l 109 HIS p 124 GLN s 304 HIS u 64 ASN v 65 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 69903 Z= 0.467 Angle : 0.682 13.258 94495 Z= 0.347 Chirality : 0.049 0.248 10215 Planarity : 0.006 0.066 11770 Dihedral : 14.504 175.812 10749 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 4.11 % Allowed : 17.28 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.40 (0.09), residues: 8173 helix: 1.10 (0.08), residues: 4333 sheet: 0.28 (0.26), residues: 392 loop : -0.76 (0.10), residues: 3448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP u 86 HIS 0.027 0.002 HIS T 122 PHE 0.032 0.002 PHE i 292 TYR 0.027 0.002 TYR l 587 ARG 0.013 0.001 ARG P 44 *********************** 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 1353 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1059 time to evaluate : 5.875 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 184 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.6525 (ttmm) REVERT: G 103 HIS cc_start: 0.7799 (t-90) cc_final: 0.7553 (t-90) REVERT: G 115 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8170 (tm130) REVERT: J 85 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.8776 (ptt180) REVERT: K 80 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7260 (mm-30) REVERT: L 73 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7412 (mtmt) REVERT: M 535 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6297 (pp20) REVERT: N 12 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7450 (mp10) REVERT: N 21 ARG cc_start: 0.7689 (ttm-80) cc_final: 0.7369 (tpp80) REVERT: O 61 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8411 (ptpt) REVERT: O 64 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7623 (tp30) REVERT: O 167 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7874 (mttp) REVERT: O 212 LYS cc_start: 0.7951 (mmmm) cc_final: 0.7431 (tppt) REVERT: P 144 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9201 (mttt) REVERT: V 106 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5221 (mtt-85) REVERT: X 137 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8121 (mmmt) REVERT: a 72 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7975 (ttm170) REVERT: a 98 LEU cc_start: 0.9342 (tp) cc_final: 0.9103 (tm) REVERT: b 21 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7863 (mtp180) REVERT: b 112 GLU cc_start: 0.8216 (mp0) cc_final: 0.7898 (mp0) REVERT: d 171 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6107 (tttm) REVERT: e 83 ASP cc_start: 0.9216 (OUTLIER) cc_final: 0.8967 (t0) REVERT: e 116 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7483 (mm-30) REVERT: e 124 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7698 (mpt-90) REVERT: h 24 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: h 42 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8242 (mt-10) REVERT: i 149 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8179 (tp) REVERT: i 269 GLU cc_start: 0.8752 (tp30) cc_final: 0.8368 (tp30) REVERT: i 291 TYR cc_start: 0.9361 (t80) cc_final: 0.9107 (t80) REVERT: j 1 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6492 (tmt) REVERT: j 44 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7330 (mpt) REVERT: k 97 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7005 (mm-40) REVERT: l 150 MET cc_start: 0.9085 (mmm) cc_final: 0.8801 (mmm) REVERT: l 197 ASP cc_start: 0.8762 (p0) cc_final: 0.8527 (p0) REVERT: l 373 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8984 (tp) REVERT: l 525 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8254 (mpp) REVERT: l 562 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8858 (tt) REVERT: o 26 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.8307 (m) REVERT: p 55 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6982 (mtpt) REVERT: p 127 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7603 (ttp-110) REVERT: p 141 GLN cc_start: 0.8107 (tt0) cc_final: 0.7674 (mt0) REVERT: p 176 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7001 (mt-10) REVERT: r 114 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7907 (tm-30) REVERT: s 143 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: s 222 MET cc_start: 0.9476 (mtp) cc_final: 0.9254 (mtm) REVERT: s 233 MET cc_start: 0.9373 (tmm) cc_final: 0.9152 (tmm) REVERT: s 243 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8793 (mt) REVERT: u 73 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.8047 (mt0) REVERT: u 88 CYS cc_start: 0.7703 (t) cc_final: 0.7270 (t) REVERT: u 132 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8331 (mtpp) REVERT: u 155 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7277 (pm20) REVERT: v 22 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8006 (ttp) REVERT: v 35 LYS cc_start: 0.8159 (mmmt) cc_final: 0.7934 (mppt) REVERT: v 38 GLU cc_start: 0.7549 (pm20) cc_final: 0.7156 (tt0) REVERT: w 253 CYS cc_start: 0.4622 (OUTLIER) cc_final: 0.4319 (t) REVERT: w 254 GLU cc_start: 0.5765 (OUTLIER) cc_final: 0.5554 (pm20) outliers start: 294 outliers final: 156 residues processed: 1217 average time/residue: 1.6357 time to fit residues: 2551.2077 Evaluate side-chains 1232 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1036 time to evaluate : 5.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain M residue 579 MET Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain M residue 677 GLN Chi-restraints excluded: chain M residue 715 THR Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain O residue 61 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 167 LYS Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 220 SER Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 192 LEU 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 S residue 59 ARG Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 79 GLN Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain W residue 120 MET Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 52 ARG Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain b residue 21 ARG Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain d residue 16 ARG Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 171 LYS Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 136 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain i residue 11 MET Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 207 ILE Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain j residue 109 LYS Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 73 THR Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 272 LEU Chi-restraints excluded: chain l residue 359 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 514 LYS Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain o residue 26 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 120 LYS Chi-restraints excluded: chain o residue 121 LEU Chi-restraints excluded: chain p residue 55 LYS Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 49 SER Chi-restraints excluded: chain r residue 108 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 285 LEU Chi-restraints excluded: chain r residue 304 GLN Chi-restraints excluded: chain r residue 387 SER Chi-restraints excluded: chain r residue 444 LEU Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 143 GLU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 206 GLU Chi-restraints excluded: chain s residue 243 LEU Chi-restraints excluded: chain u residue 73 GLN Chi-restraints excluded: chain u residue 89 ILE Chi-restraints excluded: chain u residue 132 LYS Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 22 MET Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 45 GLU Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 218 ILE Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 254 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 1.9990 chunk 700 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 456 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 778 optimal weight: 0.6980 chunk 646 optimal weight: 3.9990 chunk 360 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 408 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN F 93 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN I 25 GLN K 90 ASN M 304 GLN Q 83 ASN T 43 GLN T 117 GLN U 11 ASN U 71 GLN V 134 GLN W 24 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN Y 91 GLN Z 33 GLN a 189 ASN d 23 GLN e 86 ASN h 82 GLN i 322 GLN l 109 HIS u 64 ASN v 65 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 69903 Z= 0.148 Angle : 0.516 10.844 94495 Z= 0.263 Chirality : 0.040 0.234 10215 Planarity : 0.005 0.056 11770 Dihedral : 13.446 178.573 10747 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.40 % Favored : 96.54 % Rotamer: Outliers : 2.77 % Allowed : 18.72 % Favored : 78.51 % 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: 1.57 (0.08), residues: 4306 sheet: 0.11 (0.25), residues: 401 loop : -0.54 (0.10), residues: 3466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.018 0.001 HIS J 323 PHE 0.031 0.001 PHE i 292 TYR 0.026 0.001 TYR r 406 ARG 0.009 0.000 ARG F 26 *********************** 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 1302 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1104 time to evaluate : 5.902 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 184 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.6463 (ttmm) REVERT: A 214 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8086 (mm-30) REVERT: F 40 ARG cc_start: 0.6818 (ptp-170) cc_final: 0.6551 (ptp-170) REVERT: G 139 MET cc_start: 0.7650 (mmp) cc_final: 0.7135 (mpm) REVERT: I 70 MET cc_start: 0.8473 (tmt) cc_final: 0.8129 (tmm) REVERT: K 71 SER cc_start: 0.7604 (t) cc_final: 0.7245 (p) REVERT: L 73 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7712 (mtmt) REVERT: L 86 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8590 (m-40) REVERT: N 12 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: N 21 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7293 (tpp80) REVERT: N 101 LYS cc_start: 0.8643 (mmmt) cc_final: 0.8410 (mmtt) REVERT: O 64 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7489 (tp30) REVERT: O 159 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6832 (mptt) REVERT: O 224 SER cc_start: 0.8785 (t) cc_final: 0.8575 (t) REVERT: Q 42 GLU cc_start: 0.8313 (tt0) cc_final: 0.8069 (tt0) REVERT: Q 57 GLU cc_start: 0.7823 (tt0) cc_final: 0.7503 (tm-30) REVERT: V 106 ARG cc_start: 0.6109 (OUTLIER) cc_final: 0.5139 (mtt-85) REVERT: V 107 SER cc_start: 0.8386 (t) cc_final: 0.8093 (p) REVERT: W 52 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8625 (mmtt) REVERT: W 135 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8531 (m) REVERT: X 137 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8153 (mtmt) REVERT: e 83 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8690 (t0) REVERT: e 116 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7280 (mm-30) REVERT: e 124 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7313 (mpt-90) REVERT: h 24 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6629 (tm-30) REVERT: h 42 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8267 (mt-10) REVERT: i 149 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.7963 (tp) REVERT: i 154 MET cc_start: 0.9109 (tpt) cc_final: 0.8825 (tpt) REVERT: i 269 GLU cc_start: 0.8760 (tp30) cc_final: 0.8409 (tp30) REVERT: i 282 MET cc_start: 0.9307 (mtp) cc_final: 0.9038 (mtm) REVERT: j 1 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6306 (tmt) REVERT: j 44 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7257 (mpt) REVERT: k 97 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.6904 (mm-40) REVERT: l 197 ASP cc_start: 0.8613 (p0) cc_final: 0.8402 (p0) REVERT: l 373 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8931 (tt) REVERT: l 514 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8047 (ttmt) REVERT: l 525 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8249 (mpp) REVERT: l 562 LEU cc_start: 0.8907 (tp) cc_final: 0.8665 (tt) REVERT: m 1 MET cc_start: 0.2065 (mpt) cc_final: 0.1486 (mtm) REVERT: m 102 CYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6386 (m) REVERT: n 41 LYS cc_start: 0.8853 (mttm) cc_final: 0.8347 (mtpp) REVERT: p 127 ARG cc_start: 0.8067 (ttp80) cc_final: 0.7619 (ttp-110) REVERT: p 141 GLN cc_start: 0.7994 (tt0) cc_final: 0.7588 (mt0) REVERT: r 114 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: s 61 LEU cc_start: 0.8582 (mt) cc_final: 0.8222 (tt) REVERT: s 133 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8931 (mm) REVERT: s 222 MET cc_start: 0.9337 (mtp) cc_final: 0.9085 (mtm) REVERT: u 73 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: u 88 CYS cc_start: 0.7528 (t) cc_final: 0.7097 (t) REVERT: v 35 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7924 (mppt) REVERT: v 38 GLU cc_start: 0.7510 (pm20) cc_final: 0.7160 (tt0) REVERT: w 116 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8483 (tttp) REVERT: w 227 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7152 (mmm) REVERT: w 253 CYS cc_start: 0.4615 (OUTLIER) cc_final: 0.4278 (t) outliers start: 198 outliers final: 66 residues processed: 1209 average time/residue: 1.6363 time to fit residues: 2534.5712 Evaluate side-chains 1156 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1062 time to evaluate : 5.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain J residue 298 TYR Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain M residue 677 GLN Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 135 SER Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain b residue 108 ASP Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 136 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 272 LEU Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 461 SER Chi-restraints excluded: chain l residue 514 LYS Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 102 CYS Chi-restraints excluded: chain o residue 121 LEU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 387 SER Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 133 LEU Chi-restraints excluded: chain u residue 73 GLN Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 45 GLU Chi-restraints excluded: chain v residue 68 LYS Chi-restraints excluded: chain v residue 113 LYS Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 116 LYS Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 253 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 443 optimal weight: 2.9990 chunk 568 optimal weight: 2.9990 chunk 440 optimal weight: 5.9990 chunk 655 optimal weight: 8.9990 chunk 434 optimal weight: 0.9990 chunk 775 optimal weight: 9.9990 chunk 485 optimal weight: 9.9990 chunk 473 optimal weight: 10.0000 chunk 358 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN F 93 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN I 25 GLN K 90 ASN M 304 GLN O 144 ASN Q 250 ASN T 43 GLN T 117 GLN U 11 ASN U 71 GLN V 134 GLN W 24 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 46 GLN ** Y 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN d 23 GLN i 322 GLN l 109 HIS l 579 ASN p 62 GLN p 124 GLN r 304 GLN r 440 HIS u 64 ASN v 54 GLN v 65 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 69903 Z= 0.276 Angle : 0.579 11.211 94495 Z= 0.294 Chirality : 0.044 0.318 10215 Planarity : 0.005 0.079 11770 Dihedral : 13.388 179.461 10732 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.96 % Favored : 95.96 % Rotamer: Outliers : 2.60 % Allowed : 19.45 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.09), residues: 8173 helix: 1.51 (0.08), residues: 4312 sheet: 0.14 (0.26), residues: 392 loop : -0.54 (0.10), residues: 3469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP w 353 HIS 0.018 0.001 HIS J 323 PHE 0.035 0.002 PHE i 292 TYR 0.022 0.002 TYR u 85 ARG 0.017 0.000 ARG P 44 *********************** 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 1258 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1072 time to evaluate : 5.810 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 184 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.6472 (ttmm) REVERT: A 214 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8129 (mm-30) REVERT: G 139 MET cc_start: 0.7704 (mmp) cc_final: 0.6642 (mpp) REVERT: I 70 MET cc_start: 0.8508 (tmt) cc_final: 0.8196 (tmm) REVERT: K 71 SER cc_start: 0.7610 (t) cc_final: 0.7269 (p) REVERT: K 80 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7333 (mm-30) REVERT: L 73 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7689 (mtmt) REVERT: L 86 ASN cc_start: 0.9216 (OUTLIER) cc_final: 0.8562 (m-40) REVERT: N 12 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7270 (mp10) REVERT: N 21 ARG cc_start: 0.7622 (ttm-80) cc_final: 0.7314 (tpp80) REVERT: N 101 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8409 (mmtt) REVERT: O 64 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7503 (tp30) REVERT: O 159 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7073 (mptt) REVERT: Q 42 GLU cc_start: 0.8325 (tt0) cc_final: 0.8084 (tt0) REVERT: Q 57 GLU cc_start: 0.7828 (tt0) cc_final: 0.7499 (tm-30) REVERT: Q 356 ILE cc_start: 0.9498 (OUTLIER) cc_final: 0.9002 (pp) REVERT: V 106 ARG cc_start: 0.6196 (OUTLIER) cc_final: 0.5252 (mtm-85) REVERT: V 107 SER cc_start: 0.8474 (t) cc_final: 0.8095 (m) REVERT: W 22 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8472 (mttm) REVERT: X 137 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.7693 (mtmt) REVERT: e 83 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8827 (t0) REVERT: e 116 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: e 124 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7742 (mpt-90) REVERT: h 24 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6605 (tm-30) REVERT: h 42 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8316 (mt-10) REVERT: i 149 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8031 (tp) REVERT: i 154 MET cc_start: 0.9175 (tpt) cc_final: 0.8830 (tpt) REVERT: j 1 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6318 (tmt) REVERT: j 44 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7246 (mpt) REVERT: j 109 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8416 (mptt) REVERT: k 97 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.6899 (mm-40) REVERT: l 197 ASP cc_start: 0.8676 (p0) cc_final: 0.8457 (p0) REVERT: l 373 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8950 (tt) REVERT: l 503 GLU cc_start: 0.7670 (tp30) cc_final: 0.7272 (tp30) REVERT: l 525 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8240 (mpp) REVERT: l 562 LEU cc_start: 0.9023 (tp) cc_final: 0.8756 (tt) REVERT: o 26 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.8236 (m) REVERT: p 127 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7614 (ttp-110) REVERT: p 141 GLN cc_start: 0.8066 (tt0) cc_final: 0.7621 (mt0) REVERT: p 176 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6829 (mt-10) REVERT: r 114 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: r 454 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8653 (pp) REVERT: s 133 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8975 (mm) REVERT: s 143 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: s 222 MET cc_start: 0.9429 (mtp) cc_final: 0.9202 (mtm) REVERT: s 233 MET cc_start: 0.9351 (tmm) cc_final: 0.9093 (tmm) REVERT: u 88 CYS cc_start: 0.7553 (t) cc_final: 0.7140 (t) REVERT: v 35 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7937 (mppt) REVERT: v 38 GLU cc_start: 0.7505 (pm20) cc_final: 0.7186 (tt0) REVERT: w 227 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7060 (mmm) REVERT: w 253 CYS cc_start: 0.4700 (OUTLIER) cc_final: 0.4399 (t) REVERT: w 254 GLU cc_start: 0.5734 (OUTLIER) cc_final: 0.5270 (pm20) outliers start: 186 outliers final: 103 residues processed: 1170 average time/residue: 1.6938 time to fit residues: 2547.5933 Evaluate side-chains 1184 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1049 time to evaluate : 5.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 47 SER 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 49 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 470 LYS Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain M residue 677 GLN Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 220 SER Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain S residue 59 ARG Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 22 LYS Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 108 ASP Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 136 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain i residue 11 MET Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 109 LYS Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 272 LEU Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 461 SER Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 514 LYS Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain o residue 26 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 121 LEU Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain r residue 387 SER Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 133 LEU Chi-restraints excluded: chain s residue 143 GLU Chi-restraints excluded: chain u residue 73 GLN 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 42 THR Chi-restraints excluded: chain v residue 45 GLU Chi-restraints excluded: chain v residue 113 LYS Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 116 LYS Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 218 ILE Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 254 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 480 optimal weight: 7.9990 chunk 309 optimal weight: 0.9980 chunk 463 optimal weight: 0.7980 chunk 233 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 493 optimal weight: 6.9990 chunk 528 optimal weight: 0.7980 chunk 383 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 609 optimal weight: 7.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN E 45 ASN F 93 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN I 25 GLN K 90 ASN M 304 GLN P 77 GLN T 43 GLN U 11 ASN U 71 GLN V 134 GLN W 24 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 46 GLN ** Y 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN d 23 GLN i 322 GLN l 34 ASN l 109 HIS l 579 ASN p 124 GLN r 304 GLN r 440 HIS u 64 ASN u 104 GLN v 65 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 69903 Z= 0.184 Angle : 0.533 10.921 94495 Z= 0.271 Chirality : 0.041 0.274 10215 Planarity : 0.005 0.055 11770 Dihedral : 13.039 177.821 10732 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.65 % Favored : 96.28 % Rotamer: Outliers : 2.43 % Allowed : 19.63 % Favored : 77.93 % 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: 0.99 (0.09), residues: 8173 helix: 1.62 (0.08), residues: 4304 sheet: 0.15 (0.26), residues: 393 loop : -0.48 (0.10), residues: 3476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP w 353 HIS 0.017 0.001 HIS J 323 PHE 0.032 0.001 PHE i 292 TYR 0.023 0.001 TYR u 85 ARG 0.011 0.000 ARG F 26 *********************** 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 1250 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1076 time to evaluate : 5.889 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 184 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7191 (ttmm) REVERT: A 214 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8146 (mm-30) REVERT: G 139 MET cc_start: 0.7672 (mmp) cc_final: 0.6826 (mpp) REVERT: J 85 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.8557 (ptt180) REVERT: K 71 SER cc_start: 0.7613 (t) cc_final: 0.7306 (p) REVERT: L 73 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7744 (mtmt) REVERT: L 86 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8627 (m-40) REVERT: M 310 GLU cc_start: 0.7664 (pp20) cc_final: 0.7296 (mp0) REVERT: N 12 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7206 (mp10) REVERT: N 21 ARG cc_start: 0.7642 (ttm-80) cc_final: 0.7314 (tpp80) REVERT: N 101 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8434 (mmtt) REVERT: O 64 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: O 159 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.6921 (mptt) REVERT: P 85 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8244 (mt-10) REVERT: Q 42 GLU cc_start: 0.8308 (tt0) cc_final: 0.8075 (tt0) REVERT: Q 57 GLU cc_start: 0.7830 (tt0) cc_final: 0.7512 (tm-30) REVERT: V 106 ARG cc_start: 0.6103 (OUTLIER) cc_final: 0.5137 (mtt-85) REVERT: V 107 SER cc_start: 0.8443 (t) cc_final: 0.8112 (p) REVERT: Z 33 GLN cc_start: 0.8411 (tp40) cc_final: 0.8082 (mm-40) REVERT: e 83 ASP cc_start: 0.9087 (OUTLIER) cc_final: 0.8733 (t0) REVERT: e 116 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7318 (mm-30) REVERT: e 124 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7730 (mpt-90) REVERT: h 24 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: h 42 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8244 (mt-10) REVERT: i 149 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8002 (tp) REVERT: j 1 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6298 (tmt) REVERT: j 44 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7249 (mpt) REVERT: k 97 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.6884 (mm-40) REVERT: l 197 ASP cc_start: 0.8640 (p0) cc_final: 0.8423 (p0) REVERT: l 373 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8957 (tt) REVERT: l 503 GLU cc_start: 0.7654 (tp30) cc_final: 0.7263 (tp30) REVERT: l 514 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8051 (ttmt) REVERT: l 525 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.8241 (mpp) REVERT: m 1 MET cc_start: 0.1819 (mpt) cc_final: 0.1243 (mtm) REVERT: m 102 CYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6505 (m) REVERT: o 26 SER cc_start: 0.8575 (OUTLIER) cc_final: 0.8221 (m) REVERT: p 127 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7589 (ttp-110) REVERT: p 141 GLN cc_start: 0.8021 (tt0) cc_final: 0.7568 (mt0) REVERT: p 176 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6839 (mt-10) REVERT: r 114 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: s 61 LEU cc_start: 0.8614 (mt) cc_final: 0.8238 (tt) REVERT: s 133 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8949 (mm) REVERT: s 143 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: s 222 MET cc_start: 0.9383 (mtp) cc_final: 0.9136 (mtm) REVERT: s 227 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8622 (tp30) REVERT: u 73 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7990 (mt0) REVERT: u 88 CYS cc_start: 0.7532 (t) cc_final: 0.7122 (t) REVERT: v 35 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7936 (mppt) REVERT: v 38 GLU cc_start: 0.7538 (pm20) cc_final: 0.7248 (tt0) REVERT: w 227 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.7113 (mmm) REVERT: w 253 CYS cc_start: 0.4654 (OUTLIER) cc_final: 0.4350 (t) outliers start: 174 outliers final: 93 residues processed: 1174 average time/residue: 1.6892 time to fit residues: 2533.2423 Evaluate side-chains 1175 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1052 time to evaluate : 5.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 47 SER 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 49 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 470 LYS Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain M residue 677 GLN Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain X residue 92 LYS Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 108 ASP Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 136 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 272 LEU Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 461 SER Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 514 LYS Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 102 CYS Chi-restraints excluded: chain o residue 26 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 121 LEU Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 387 SER Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 133 LEU Chi-restraints excluded: chain s residue 143 GLU Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain u residue 73 GLN Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 89 ILE Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 45 GLU Chi-restraints excluded: chain v residue 68 LYS Chi-restraints excluded: chain v residue 113 LYS Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 116 LYS Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 253 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 1.9990 chunk 743 optimal weight: 7.9990 chunk 678 optimal weight: 1.9990 chunk 723 optimal weight: 0.6980 chunk 435 optimal weight: 0.3980 chunk 314 optimal weight: 0.9990 chunk 567 optimal weight: 0.4980 chunk 221 optimal weight: 9.9990 chunk 653 optimal weight: 6.9990 chunk 683 optimal weight: 2.9990 chunk 720 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN F 93 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN I 25 GLN K 90 ASN M 304 GLN P 77 GLN T 43 GLN T 117 GLN U 11 ASN U 71 GLN V 134 GLN W 24 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 46 GLN ** Y 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN d 23 GLN i 322 GLN l 109 HIS l 579 ASN p 62 GLN p 124 GLN r 304 GLN u 64 ASN u 104 GLN v 65 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 69903 Z= 0.153 Angle : 0.520 12.928 94495 Z= 0.263 Chirality : 0.040 0.262 10215 Planarity : 0.004 0.088 11770 Dihedral : 12.705 178.511 10732 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.74 % Favored : 96.21 % Rotamer: Outliers : 2.13 % Allowed : 19.98 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.09), residues: 8173 helix: 1.70 (0.08), residues: 4309 sheet: 0.11 (0.25), residues: 405 loop : -0.41 (0.11), residues: 3459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP w 353 HIS 0.017 0.001 HIS J 323 PHE 0.068 0.001 PHE l 340 TYR 0.024 0.001 TYR u 85 ARG 0.021 0.000 ARG P 44 *********************** 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 1228 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1076 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: symmetry clash REVERT: A 184 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7163 (ttmm) REVERT: A 214 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8099 (mm-30) REVERT: G 139 MET cc_start: 0.7628 (mmp) cc_final: 0.6774 (mpp) REVERT: K 71 SER cc_start: 0.7666 (t) cc_final: 0.7430 (p) REVERT: L 73 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7741 (mtmt) REVERT: L 86 ASN cc_start: 0.9183 (OUTLIER) cc_final: 0.8648 (m-40) REVERT: M 310 GLU cc_start: 0.7580 (pp20) cc_final: 0.7265 (mp0) REVERT: N 12 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7000 (mp10) REVERT: N 21 ARG cc_start: 0.7632 (ttm-80) cc_final: 0.7298 (tpp80) REVERT: N 101 LYS cc_start: 0.8632 (mmmt) cc_final: 0.8426 (mmtt) REVERT: O 64 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7462 (tp30) REVERT: O 224 SER cc_start: 0.8808 (t) cc_final: 0.8595 (t) REVERT: Q 42 GLU cc_start: 0.8304 (tt0) cc_final: 0.8071 (tt0) REVERT: Q 57 GLU cc_start: 0.7835 (tt0) cc_final: 0.7522 (tm-30) REVERT: Q 62 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7753 (tptm) REVERT: V 106 ARG cc_start: 0.6121 (OUTLIER) cc_final: 0.5155 (mtt-85) REVERT: V 107 SER cc_start: 0.8422 (t) cc_final: 0.8138 (p) REVERT: W 52 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8657 (mmtt) REVERT: X 125 GLU cc_start: 0.8666 (tp30) cc_final: 0.8438 (tp30) REVERT: X 137 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8112 (mtmt) REVERT: Z 33 GLN cc_start: 0.8434 (tp40) cc_final: 0.8087 (mm-40) REVERT: b 116 VAL cc_start: 0.8715 (m) cc_final: 0.8513 (t) REVERT: e 83 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8728 (t0) REVERT: e 116 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: h 24 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.6501 (tm-30) REVERT: h 42 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8146 (mt-10) REVERT: i 149 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.7969 (tp) REVERT: j 1 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6282 (tmt) REVERT: j 44 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7220 (mpt) REVERT: k 97 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.6862 (mm-40) REVERT: l 197 ASP cc_start: 0.8611 (p0) cc_final: 0.8399 (p0) REVERT: l 373 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8980 (tp) REVERT: l 486 MET cc_start: 0.8707 (ttm) cc_final: 0.8236 (ttp) REVERT: l 503 GLU cc_start: 0.7642 (tp30) cc_final: 0.7266 (tp30) REVERT: l 514 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8066 (ttmt) REVERT: l 525 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.8243 (mpp) REVERT: m 1 MET cc_start: 0.1611 (mpt) cc_final: 0.1051 (mtm) REVERT: m 102 CYS cc_start: 0.6756 (OUTLIER) cc_final: 0.6394 (m) REVERT: m 135 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: m 173 ARG cc_start: 0.8315 (ttm-80) cc_final: 0.7921 (ttm-80) REVERT: n 41 LYS cc_start: 0.8858 (mttm) cc_final: 0.8343 (mtpp) REVERT: o 26 SER cc_start: 0.8564 (OUTLIER) cc_final: 0.8218 (m) REVERT: p 127 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7582 (ttp-110) REVERT: p 141 GLN cc_start: 0.7973 (tt0) cc_final: 0.7570 (mt0) REVERT: p 176 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6850 (mt-10) REVERT: r 114 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7943 (tm-30) REVERT: s 61 LEU cc_start: 0.8553 (mt) cc_final: 0.8203 (tt) REVERT: s 222 MET cc_start: 0.9356 (mtp) cc_final: 0.9108 (mtm) REVERT: s 243 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8728 (mt) REVERT: u 12 ASP cc_start: 0.7770 (t0) cc_final: 0.7405 (t0) REVERT: u 73 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: u 88 CYS cc_start: 0.7507 (t) cc_final: 0.7084 (t) REVERT: v 35 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7939 (mppt) REVERT: w 37 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6055 (tm-30) REVERT: w 227 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7087 (mmm) REVERT: w 253 CYS cc_start: 0.4642 (OUTLIER) cc_final: 0.4371 (t) outliers start: 152 outliers final: 84 residues processed: 1161 average time/residue: 1.6290 time to fit residues: 2427.8385 Evaluate side-chains 1168 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1056 time to evaluate : 5.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain B residue 47 SER 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 49 LEU Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain J residue 298 TYR Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 470 LYS Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain X residue 92 LYS Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 136 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 272 LEU Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 461 SER Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 514 LYS Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 102 CYS Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 26 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 121 LEU Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 387 SER Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 243 LEU Chi-restraints excluded: chain u residue 73 GLN Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 45 GLU Chi-restraints excluded: chain v residue 68 LYS Chi-restraints excluded: chain v residue 113 LYS Chi-restraints excluded: chain w residue 37 GLN Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 116 LYS Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 253 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 474 optimal weight: 9.9990 chunk 764 optimal weight: 6.9990 chunk 466 optimal weight: 3.9990 chunk 362 optimal weight: 8.9990 chunk 531 optimal weight: 4.9990 chunk 801 optimal weight: 3.9990 chunk 738 optimal weight: 0.8980 chunk 638 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 493 optimal weight: 0.0050 chunk 391 optimal weight: 0.7980 overall best weight: 1.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN E 45 ASN F 93 ASN G 115 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN I 25 GLN K 90 ASN M 304 GLN T 43 GLN U 11 ASN U 71 GLN V 134 GLN W 24 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 46 GLN ** Y 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN d 23 GLN i 322 GLN l 109 HIS l 579 ASN p 62 GLN p 124 GLN r 304 GLN r 440 HIS u 64 ASN v 65 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 69903 Z= 0.220 Angle : 0.557 18.320 94495 Z= 0.281 Chirality : 0.042 0.265 10215 Planarity : 0.005 0.061 11770 Dihedral : 12.674 177.309 10728 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.78 % Favored : 96.15 % Rotamer: Outliers : 1.99 % Allowed : 20.05 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.09), residues: 8173 helix: 1.65 (0.08), residues: 4306 sheet: 0.18 (0.26), residues: 393 loop : -0.42 (0.10), residues: 3474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP w 353 HIS 0.016 0.001 HIS J 323 PHE 0.033 0.002 PHE i 292 TYR 0.026 0.001 TYR u 85 ARG 0.015 0.000 ARG F 26 ********************** 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 1206 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1064 time to evaluate : 5.842 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 184 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7193 (ttmm) REVERT: A 214 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8144 (mm-30) REVERT: G 139 MET cc_start: 0.7548 (mmp) cc_final: 0.6858 (mpp) REVERT: J 85 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8560 (ptt180) REVERT: K 71 SER cc_start: 0.7678 (t) cc_final: 0.7474 (p) REVERT: L 73 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7756 (mtmt) REVERT: L 86 ASN cc_start: 0.9197 (OUTLIER) cc_final: 0.8668 (m-40) REVERT: M 310 GLU cc_start: 0.7629 (pp20) cc_final: 0.7272 (mp0) REVERT: N 12 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.6991 (mp10) REVERT: N 21 ARG cc_start: 0.7618 (ttm-80) cc_final: 0.7306 (tpp80) REVERT: N 101 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8443 (mmtt) REVERT: O 64 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7476 (tp30) REVERT: Q 42 GLU cc_start: 0.8313 (tt0) cc_final: 0.8079 (tt0) REVERT: Q 57 GLU cc_start: 0.7848 (tt0) cc_final: 0.7527 (tm-30) REVERT: V 106 ARG cc_start: 0.6124 (OUTLIER) cc_final: 0.5087 (mtt-85) REVERT: V 107 SER cc_start: 0.8441 (t) cc_final: 0.8158 (m) REVERT: X 125 GLU cc_start: 0.8671 (tp30) cc_final: 0.8405 (tp30) REVERT: X 137 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.7626 (mtmt) REVERT: Z 33 GLN cc_start: 0.8443 (tp40) cc_final: 0.8093 (mm-40) REVERT: e 83 ASP cc_start: 0.9125 (OUTLIER) cc_final: 0.8778 (t0) REVERT: e 116 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: h 24 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.6557 (tm-30) REVERT: h 42 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: i 149 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.7987 (tp) REVERT: j 1 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6305 (tmt) REVERT: j 44 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7237 (mpt) REVERT: k 97 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.6892 (mm-40) REVERT: l 197 ASP cc_start: 0.8643 (p0) cc_final: 0.8435 (p0) REVERT: l 373 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8974 (tp) REVERT: l 503 GLU cc_start: 0.7655 (tp30) cc_final: 0.7273 (tp30) REVERT: l 525 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.8244 (mpp) REVERT: m 1 MET cc_start: 0.1885 (mpt) cc_final: 0.1340 (mtm) REVERT: m 102 CYS cc_start: 0.6819 (OUTLIER) cc_final: 0.6418 (m) REVERT: m 173 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.7994 (ttm-80) REVERT: n 41 LYS cc_start: 0.8860 (mttm) cc_final: 0.8345 (mtpp) REVERT: o 26 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8226 (m) REVERT: p 127 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7597 (ttp-110) REVERT: p 141 GLN cc_start: 0.8031 (tt0) cc_final: 0.7603 (mt0) REVERT: p 176 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6869 (mt-10) REVERT: r 114 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: s 61 LEU cc_start: 0.8610 (mt) cc_final: 0.8250 (tt) REVERT: s 143 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7642 (tm-30) REVERT: s 222 MET cc_start: 0.9407 (mtp) cc_final: 0.9158 (mtm) REVERT: s 227 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8650 (tp30) REVERT: s 243 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8786 (mt) REVERT: v 35 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7944 (mppt) REVERT: v 54 GLN cc_start: 0.8525 (pt0) cc_final: 0.8151 (pm20) REVERT: w 37 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6093 (tm-30) REVERT: w 227 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.7097 (mmm) REVERT: w 253 CYS cc_start: 0.4706 (OUTLIER) cc_final: 0.4414 (t) outliers start: 142 outliers final: 89 residues processed: 1147 average time/residue: 1.6750 time to fit residues: 2461.6807 Evaluate side-chains 1169 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1053 time to evaluate : 6.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain B residue 47 SER 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 49 LEU Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 470 LYS Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain X residue 92 LYS Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 136 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 272 LEU Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 461 SER Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 514 LYS Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 102 CYS Chi-restraints excluded: chain o residue 26 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 121 LEU Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain r residue 387 SER Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 143 GLU Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 243 LEU Chi-restraints excluded: chain u residue 73 GLN Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 68 LYS Chi-restraints excluded: chain v residue 113 LYS Chi-restraints excluded: chain w residue 37 GLN Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 116 LYS Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 253 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 507 optimal weight: 0.9980 chunk 680 optimal weight: 0.7980 chunk 195 optimal weight: 10.0000 chunk 588 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 177 optimal weight: 0.6980 chunk 639 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 656 optimal weight: 10.0000 chunk 80 optimal weight: 0.3980 chunk 117 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN F 93 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN I 9 GLN I 25 GLN K 90 ASN M 304 GLN T 43 GLN U 11 ASN U 71 GLN V 134 GLN W 24 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 46 GLN ** Y 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN d 23 GLN i 322 GLN l 109 HIS l 579 ASN p 124 GLN ** r 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 304 GLN r 440 HIS u 104 GLN v 61 HIS v 65 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.094716 restraints weight = 89918.021| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.35 r_work: 0.2901 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 69903 Z= 0.145 Angle : 0.513 20.064 94495 Z= 0.258 Chirality : 0.040 0.243 10215 Planarity : 0.004 0.072 11770 Dihedral : 12.224 178.916 10728 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.47 % Favored : 96.48 % Rotamer: Outliers : 1.82 % Allowed : 20.32 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.09), residues: 8173 helix: 1.78 (0.08), residues: 4309 sheet: 0.18 (0.25), residues: 405 loop : -0.33 (0.11), residues: 3459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP w 353 HIS 0.015 0.001 HIS J 323 PHE 0.034 0.001 PHE i 292 TYR 0.024 0.001 TYR u 85 ARG 0.022 0.000 ARG P 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32403.21 seconds wall clock time: 559 minutes 54.68 seconds (33594.68 seconds total)