Starting phenix.real_space_refine on Thu Mar 14 23:13:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2r_32265/03_2024/7w2r_32265_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2r_32265/03_2024/7w2r_32265.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2r_32265/03_2024/7w2r_32265_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2r_32265/03_2024/7w2r_32265_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2r_32265/03_2024/7w2r_32265_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2r_32265/03_2024/7w2r_32265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2r_32265/03_2024/7w2r_32265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2r_32265/03_2024/7w2r_32265_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2r_32265/03_2024/7w2r_32265_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 46 5.49 5 Mg 1 5.21 5 S 482 5.16 5 C 44117 2.51 5 N 11233 2.21 5 O 12220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 129": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 78": "OE1" <-> "OE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "J PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 234": "OE1" <-> "OE2" Residue "J GLU 365": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L GLU 132": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 161": "OE1" <-> "OE2" Residue "M GLU 244": "OE1" <-> "OE2" Residue "M GLU 369": "OE1" <-> "OE2" Residue "M GLU 370": "OE1" <-> "OE2" Residue "M GLU 396": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "M GLU 660": "OE1" <-> "OE2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P GLU 169": "OE1" <-> "OE2" Residue "P PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 194": "OE1" <-> "OE2" Residue "P GLU 215": "OE1" <-> "OE2" Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 259": "OE1" <-> "OE2" Residue "Q GLU 260": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "T GLU 64": "OE1" <-> "OE2" Residue "T GLU 105": "OE1" <-> "OE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "V GLU 138": "OE1" <-> "OE2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W GLU 123": "OE1" <-> "OE2" Residue "W GLU 132": "OE1" <-> "OE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X GLU 125": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Z GLU 25": "OE1" <-> "OE2" Residue "Z GLU 49": "OE1" <-> "OE2" Residue "a GLU 97": "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 "a GLU 155": "OE1" <-> "OE2" Residue "b GLU 27": "OE1" <-> "OE2" Residue "b GLU 122": "OE1" <-> "OE2" Residue "c GLU 60": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 148": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 53": "OE1" <-> "OE2" Residue "d TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "d GLU 172": "OE1" <-> "OE2" Residue "e GLU 57": "OE1" <-> "OE2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e GLU 123": "OE1" <-> "OE2" Residue "e GLU 130": "OE1" <-> "OE2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "h GLU 37": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "i GLU 117": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "j GLU 38": "OE1" <-> "OE2" Residue "j PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 105": "OE1" <-> "OE2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "j GLU 115": "OE1" <-> "OE2" Residue "k GLU 34": "OE1" <-> "OE2" Residue "l GLU 60": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 102": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 397": "OE1" <-> "OE2" Residue "l GLU 445": "OE1" <-> "OE2" Residue "m GLU 81": "OE1" <-> "OE2" Residue "m TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "p GLU 50": "OE1" <-> "OE2" Residue "r GLU 47": "OE1" <-> "OE2" Residue "r GLU 114": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "r GLU 335": "OE1" <-> "OE2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s GLU 202": "OE1" <-> "OE2" Residue "s GLU 206": "OE1" <-> "OE2" Residue "s GLU 214": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "u GLU 50": "OE1" <-> "OE2" Residue "u TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "w GLU 115": "OE1" <-> "OE2" Residue "w GLU 226": "OE1" <-> "OE2" Residue "w GLU 254": "OE1" <-> "OE2" Residue "w GLU 303": "OE1" <-> "OE2" Residue "w GLU 316": "OE1" <-> "OE2" Residue "w GLU 345": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 68128 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: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1732 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 192} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "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: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 559 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 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: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1459 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 164} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 577} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "m" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1277 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "w" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2579 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 130 Unusual residues: {'DCQ': 1, 'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "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: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 134 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "g" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 87 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "j" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 150 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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: "o" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 255 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "s" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 168 Unusual residues: {' UQ': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 25 Chain: "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 47.506 49.005 173.000 1.00 15.88 S ATOM 3060 SG CYS A 425 46.829 45.967 178.953 1.00 19.00 S ATOM 2738 SG CYS A 385 44.166 44.772 173.207 1.00 34.98 S ATOM 2699 SG CYS A 379 42.203 49.789 176.918 1.00 19.53 S ATOM 3961 SG CYS B 113 36.876 64.178 137.838 1.00 23.13 S ATOM 3980 SG CYS B 116 41.811 61.890 141.895 1.00 9.85 S ATOM 4003 SG CYS B 119 43.027 64.412 136.366 1.00 16.54 S ATOM 4332 SG CYS B 162 40.386 58.647 137.018 1.00 9.29 S ATOM 4030 SG CYS B 123 49.176 67.017 131.815 1.00 0.00 S ATOM 4256 SG CYS B 152 47.307 65.150 125.938 1.00 5.14 S ATOM 4303 SG CYS B 158 45.417 61.438 130.747 1.00 6.19 S ATOM 4282 SG CYS B 155 51.454 61.747 129.270 1.00 7.91 S ATOM 5724 SG CYS C 166 54.046 65.060 121.753 1.00 18.07 S ATOM 4996 SG CYS C 72 54.502 66.337 115.418 1.00 10.30 S ATOM 4990 SG CYS C 71 59.766 64.580 118.334 1.00 11.14 S ATOM 5494 SG CYS C 136 56.516 70.004 120.448 1.00 14.38 S ATOM 14949 SG CYS M 131 40.981 62.348 153.883 1.00 28.72 S ATOM 14928 SG CYS M 128 44.594 57.669 150.936 1.00 14.19 S ATOM 14989 SG CYS M 137 46.690 61.224 156.002 1.00 6.38 S ATOM 15321 SG CYS M 179 45.019 61.576 167.119 1.00 15.34 S ATOM 15675 SG CYS M 226 41.987 64.280 162.716 1.00 3.79 S ATOM 15345 SG CYS M 182 39.561 64.452 168.709 1.00 21.72 S ATOM 15298 SG CYS M 176 39.321 58.875 165.500 1.00 8.03 S ATOM 14546 SG CYS M 78 56.320 56.863 171.024 1.00 25.21 S ATOM 14647 SG CYS M 92 54.646 59.008 173.321 1.00 12.46 S ATOM 14435 SG CYS M 64 50.287 59.039 171.023 1.00 13.42 S ATOM 14521 SG CYS M 75 51.239 56.951 168.027 1.00 16.59 S ATOM 21484 SG CYS O 135 31.257 32.077 181.468 1.00 40.93 S ATOM 21518 SG CYS O 140 31.152 28.829 182.786 1.00 48.56 S ATOM 21798 SG CYS O 176 35.980 33.807 183.828 1.00 53.74 S ATOM 21821 SG CYS O 180 36.079 30.367 184.746 1.00 45.45 S ATOM 28547 SG CYS T 86 29.039 51.157 146.163 1.00 28.50 S ATOM 28725 SG CYS T 111 30.540 54.630 147.003 1.00 21.69 S ATOM 28747 SG CYS T 114 28.673 54.151 143.948 1.00 30.39 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.66 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.66 Time building chain proxies: 26.85, per 1000 atoms: 0.39 Number of scatterers: 68128 At special positions: 0 Unit cell: (220.211, 214.84, 229.879, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 482 16.00 P 46 15.00 Mg 1 11.99 O 12220 8.00 N 11233 7.00 C 44117 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=2.04 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " distance=2.03 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.03 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.04 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=1.60 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: 21.10 Conformation dependent library (CDL) restraints added in 9.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " 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="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " 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="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb=" SF4 M 802 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 114 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " Number of angles added : 3 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: 351 helices and 30 sheets defined 53.0% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.66 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.705A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 4.690A 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 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.628A 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 263 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 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.314A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.112A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 457 Proline residue: A 434 - end of helix removed outlier: 3.612A 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 77 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 211 removed outlier: 5.660A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 79 removed outlier: 3.684A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 111 through 122 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'E' and resid 25 through 50 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.176A 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: 4.388A 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 31 through 39 Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 95 Processing helix chain 'G' and resid 76 through 88 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 137 removed outlier: 3.732A 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: 3.942A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 61 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 76 removed outlier: 3.988A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 3.517A pdb=" N MET J 92 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 223 removed outlier: 4.206A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 4.770A 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 273 through 284 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.885A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 323 Processing helix chain 'J' and resid 335 through 338 Processing helix chain 'J' and resid 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: 5.704A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 4.851A 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 removed outlier: 3.726A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 77 through 80' Processing helix chain 'K' and resid 85 through 95 removed outlier: 4.425A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 69 through 73 Processing helix chain 'L' and resid 131 through 140 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.853A 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: 3.869A 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 378 through 380 No H-bonds generated for 'chain 'M' and resid 378 through 380' Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 390 through 396 removed outlier: 3.677A pdb=" N VAL M 394 " --> pdb=" O THR M 390 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU M 395 " --> pdb=" O ILE M 391 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU M 396 " --> pdb=" O ALA M 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 390 through 396' Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 removed outlier: 3.790A pdb=" N SER M 457 " --> pdb=" O ASP M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 467 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 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 654 Processing helix chain 'M' and resid 665 through 674 removed outlier: 4.075A pdb=" N LEU M 674 " --> pdb=" O GLU M 670 " (cutoff:3.500A) Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.664A 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: 3.820A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.341A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 141 No H-bonds generated for 'chain 'O' and resid 138 through 141' Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 198 through 209 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.626A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix removed outlier: 3.521A pdb=" N ASP P 102 " --> pdb=" O PHE P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 174 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: 3.999A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.828A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 139 Proline residue: Q 134 - end of helix removed outlier: 3.952A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.639A 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: 3.782A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 262 removed outlier: 3.760A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.805A 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: 4.604A 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 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: 3.501A pdb=" N GLY Q 434 " --> pdb=" O ALA Q 430 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU Q 435 " --> pdb=" O HIS Q 431 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.487A 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 30 Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 42 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'U' and resid 3 through 15 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 Processing helix chain 'U' and resid 79 through 82 No H-bonds generated for 'chain 'U' and resid 79 through 82' Processing helix chain 'V' and resid 3 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 32 through 99 Proline residue: W 73 - end of helix removed outlier: 3.797A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 125 Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.018A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) 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 137 removed outlier: 4.659A pdb=" N LYS X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) 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: 3.864A pdb=" N LEU Y 81 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Y' and resid 94 through 97 No H-bonds generated for 'chain 'Y' and resid 94 through 97' Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 39 removed outlier: 3.708A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 54 removed outlier: 3.557A pdb=" N SER Z 54 " --> pdb=" O TRP Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 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 removed outlier: 3.885A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 109 through 112' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 26 Processing helix chain 'b' and resid 69 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 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 129 through 149 Processing helix chain 'd' and resid 29 through 58 removed outlier: 4.621A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix removed outlier: 3.583A pdb=" N LYS d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 124 removed outlier: 3.935A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.446A 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 95 Processing helix chain 'e' and resid 100 through 107 Processing helix chain 'e' and resid 115 through 131 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 removed outlier: 3.820A 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: 3.935A 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 removed outlier: 3.659A pdb=" N GLU h 89 " --> pdb=" O LYS h 85 " (cutoff:3.500A) 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 45 Proline residue: i 42 - end of helix removed outlier: 3.776A pdb=" N MET i 45 " --> pdb=" O ILE i 41 " (cutoff:3.500A) 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: 4.304A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 132 Processing helix chain 'i' and resid 134 through 148 removed outlier: 3.893A pdb=" N ALA i 137 " --> pdb=" O GLN i 134 " (cutoff:3.500A) Proline residue: i 138 - end of helix removed outlier: 3.548A pdb=" N SER i 146 " --> pdb=" O CYS i 143 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLN i 147 " --> pdb=" O GLN i 144 " (cutoff:3.500A) Processing helix chain 'i' and resid 151 through 171 removed outlier: 4.005A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 192 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.638A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 273 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.488A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.013A 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: 3.533A pdb=" N LEU j 63 " --> pdb=" O ALA j 59 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU j 64 " --> pdb=" O ILE j 60 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.494A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.398A 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 27 through 51 Processing helix chain 'k' and resid 55 through 85 removed outlier: 3.885A 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: 3.734A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.722A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 26 through 28 No H-bonds generated for 'chain 'l' and resid 26 through 28' Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.368A 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: 4.032A 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: 3.967A 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: 4.076A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.291A 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 269 removed outlier: 4.447A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) Proline residue: l 265 - end of helix removed outlier: 3.905A pdb=" N GLU l 268 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.494A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 Processing helix chain 'l' and resid 322 through 349 removed outlier: 4.030A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 381 Processing helix chain 'l' and resid 389 through 400 removed outlier: 4.588A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.679A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 471 removed outlier: 5.586A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN l 471 " --> pdb=" O ILE l 467 " (cutoff:3.500A) Processing helix chain 'l' and resid 484 through 487 No H-bonds generated for 'chain 'l' and resid 484 through 487' Processing helix chain 'l' and resid 489 through 509 removed outlier: 3.874A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.499A 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 532 Proline residue: l 530 - end of helix 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 46 Processing helix chain 'm' and resid 50 through 74 removed outlier: 5.179A pdb=" N GLY m 62 " --> pdb=" O LEU m 58 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY m 63 " --> pdb=" O ILE m 59 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) Processing helix chain 'm' and resid 87 through 108 Processing helix chain 'm' and resid 124 through 127 Processing helix chain 'm' and resid 138 through 149 removed outlier: 3.808A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR m 147 " --> pdb=" O ILE m 143 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N SER m 148 " --> pdb=" O ALA m 144 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 removed outlier: 3.776A pdb=" N ARG m 173 " --> pdb=" O MET m 169 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 35 removed outlier: 6.039A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.760A pdb=" N LEU n 35 " --> pdb=" O SER n 31 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 20 through 23 Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.667A 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 77 through 79 No H-bonds generated for 'chain 'o' and resid 77 through 79' 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: 4.571A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 74 Processing helix chain 'p' and resid 93 through 97 removed outlier: 4.281A pdb=" N CYS p 96 " --> pdb=" O ARG p 93 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 142 removed outlier: 4.793A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 5.081A 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 removed outlier: 4.128A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.282A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.953A 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: 3.739A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.623A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 142 through 170 removed outlier: 3.905A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY r 156 " --> pdb=" O TYR r 152 " (cutoff:3.500A) Proline residue: r 159 - end of helix Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.566A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.057A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 235 through 246 removed outlier: 4.233A pdb=" N GLY r 239 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 removed outlier: 3.960A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) Processing helix chain 'r' and resid 259 through 277 removed outlier: 3.716A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 removed outlier: 3.633A pdb=" N ILE r 286 " --> pdb=" O LEU r 282 " (cutoff:3.500A) Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.653A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 392 through 415 removed outlier: 3.610A pdb=" N TYR r 409 " --> pdb=" O LEU r 405 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 448 Proline residue: r 443 - end of helix removed outlier: 3.903A pdb=" N THR r 448 " --> pdb=" O LEU r 444 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 31 Proline residue: s 12 - end of helix removed outlier: 3.578A 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: 4.309A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 3.523A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.181A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.702A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 192 removed outlier: 4.903A pdb=" N TRP s 179 " --> pdb=" O PHE s 176 " (cutoff:3.500A) Proline residue: s 180 - end of helix Processing helix chain 's' and resid 204 through 207 No H-bonds generated for 'chain 's' and resid 204 through 207' Processing helix chain 's' and resid 210 through 212 No H-bonds generated for 'chain 's' and resid 210 through 212' Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 291 removed outlier: 3.885A 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 22 through 35 removed outlier: 5.019A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 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 80 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 124 Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 93 through 97 removed outlier: 3.639A pdb=" N THR w 97 " --> pdb=" O TYR w 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 93 through 97' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 166 through 175 removed outlier: 3.512A pdb=" N GLU w 171 " --> pdb=" O VAL w 168 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.223A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.790A 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 250 removed outlier: 5.255A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix Processing helix chain 'w' and resid 261 through 264 removed outlier: 3.617A pdb=" N GLU w 264 " --> pdb=" O ARG w 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 261 through 264' Processing helix chain 'w' and resid 266 through 275 removed outlier: 3.570A pdb=" N TYR w 275 " --> pdb=" O GLU w 271 " (cutoff:3.500A) Processing helix chain 'w' and resid 283 through 285 No H-bonds generated for 'chain 'w' and resid 283 through 285' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 309 removed outlier: 5.076A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 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 239 through 244 removed outlier: 6.350A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 5.969A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.377A 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: 6.717A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.337A 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: 6.478A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.515A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 228 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= O, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 365 through 368 removed outlier: 4.656A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.106A 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: 8.330A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.431A 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: 3.512A pdb=" N GLY N 40 " --> pdb=" O TYR N 48 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.576A 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: 6.437A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.932A 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: 6.839A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 6.324A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 77 through 79 Processing sheet with id= Z, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= AA, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= AB, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.529A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'w' and resid 60 through 64 removed outlier: 7.089A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'w' and resid 84 through 86 2941 hydrogen bonds defined for protein. 8307 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: 20.03 Time building geometry restraints manager: 23.15 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: 27756 1.40 - 1.62: 41099 1.62 - 1.84: 879 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 69814 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.262 0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.631 -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 1.300 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.27e+02 ... (remaining 69809 not shown) Histogram of bond angle deviations from ideal: 73.55 - 85.95: 76 85.95 - 98.35: 2 98.35 - 110.74: 23709 110.74 - 123.14: 67387 123.14 - 135.54: 3211 Bond angle restraints: 94385 Sorted by residual: angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 124.08 -16.34 1.95e+00 2.62e-01 6.99e+01 angle pdb=" C LEU j 73 " pdb=" N PRO j 74 " pdb=" CA PRO j 74 " ideal model delta sigma weight residual 119.87 128.19 -8.32 1.04e+00 9.25e-01 6.40e+01 angle pdb=" C ARG P 44 " pdb=" N PRO P 45 " pdb=" CA PRO P 45 " ideal model delta sigma weight residual 119.05 127.00 -7.95 1.11e+00 8.12e-01 5.12e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 117.33 -13.49 1.91e+00 2.73e-01 4.96e+01 angle pdb=" C51 CDL N 201 " pdb=" CB5 CDL N 201 " pdb=" OB6 CDL N 201 " ideal model delta sigma weight residual 111.33 120.40 -9.07 1.32e+00 5.72e-01 4.71e+01 ... (remaining 94380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 40499 35.65 - 71.30: 1743 71.30 - 106.94: 113 106.94 - 142.59: 17 142.59 - 178.24: 9 Dihedral angle restraints: 42381 sinusoidal: 18288 harmonic: 24093 Sorted by residual: dihedral pdb=" CB CYS u 78 " pdb=" SG CYS u 78 " pdb=" SG CYS u 110 " pdb=" CB CYS u 110 " ideal model delta sinusoidal sigma weight residual -86.00 -151.40 65.40 1 1.00e+01 1.00e-02 5.60e+01 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 75.83 -178.24 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 86.00 -145.99 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 42378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 9482 0.082 - 0.164: 690 0.164 - 0.246: 29 0.246 - 0.328: 8 0.328 - 0.410: 4 Chirality restraints: 10213 Sorted by residual: chirality pdb=" CA PHE s 19 " pdb=" N PHE s 19 " pdb=" C PHE s 19 " pdb=" CB PHE s 19 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CA TRP u 86 " pdb=" N TRP u 86 " pdb=" C TRP u 86 " pdb=" CB TRP u 86 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA ARG P 44 " pdb=" N ARG P 44 " pdb=" C ARG P 44 " pdb=" CB ARG P 44 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 10210 not shown) Planarity restraints: 11761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 UQ J 402 " -0.467 2.00e-02 2.50e+03 4.06e-01 2.06e+03 pdb=" C23 UQ J 402 " 0.520 2.00e-02 2.50e+03 pdb=" C24 UQ J 402 " 0.399 2.00e-02 2.50e+03 pdb=" C25 UQ J 402 " -0.421 2.00e-02 2.50e+03 pdb=" C26 UQ J 402 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 403 " 0.350 2.00e-02 2.50e+03 3.23e-01 1.30e+03 pdb=" C18 UQ s 403 " -0.337 2.00e-02 2.50e+03 pdb=" C19 UQ s 403 " -0.387 2.00e-02 2.50e+03 pdb=" C20 UQ s 403 " 0.004 2.00e-02 2.50e+03 pdb=" C21 UQ s 403 " 0.369 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ J 402 " 0.313 2.00e-02 2.50e+03 3.11e-01 1.21e+03 pdb=" C18 UQ J 402 " -0.578 2.00e-02 2.50e+03 pdb=" C19 UQ J 402 " 0.219 2.00e-02 2.50e+03 pdb=" C20 UQ J 402 " 0.058 2.00e-02 2.50e+03 pdb=" C21 UQ J 402 " -0.013 2.00e-02 2.50e+03 ... (remaining 11758 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5213 2.74 - 3.28: 66990 3.28 - 3.82: 117466 3.82 - 4.36: 147007 4.36 - 4.90: 245445 Nonbonded interactions: 582121 Sorted by model distance: nonbonded pdb=" O THR H 48 " pdb=" OG1 THR H 52 " model vdw 2.197 2.440 nonbonded pdb=" OH TYR w 118 " pdb=" O2' ADP w 401 " model vdw 2.199 2.440 nonbonded pdb=" OH TYR X 90 " pdb=" OD1 ASP X 114 " model vdw 2.206 2.440 nonbonded pdb=" O ASN l 505 " pdb=" OG1 THR l 508 " model vdw 2.207 2.440 nonbonded pdb=" OE2 GLU Q 176 " pdb=" OH TYR Q 311 " model vdw 2.209 2.440 ... (remaining 582116 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 69 through 93 or (resid 94 through 97 and (name N or name \ CA or name C or name O or name CB )) or resid 98 through 101 or (resid 102 and ( \ name N or name CA or name C or name O or name CB )) or resid 103 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=0.66 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.050 Extract box with map and model: 8.860 Check model and map are aligned: 0.720 Set scattering table: 0.470 Process input model: 154.700 Find NCS groups from input model: 2.090 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:9.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.319 69814 Z= 0.500 Angle : 0.806 17.199 94385 Z= 0.411 Chirality : 0.044 0.410 10213 Planarity : 0.009 0.406 11761 Dihedral : 18.322 178.241 26822 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 1.27 % Allowed : 15.77 % Favored : 82.95 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.09), residues: 8173 helix: 1.61 (0.08), residues: 4323 sheet: 0.30 (0.24), residues: 441 loop : -0.34 (0.11), residues: 3409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP c 145 HIS 0.010 0.001 HIS u 77 PHE 0.034 0.001 PHE i 292 TYR 0.033 0.001 TYR J 216 ARG 0.009 0.000 ARG o 42 *********************** 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 1072 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 981 time to evaluate : 6.027 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8572 (mt-10) REVERT: l 496 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7157 (ttt) REVERT: n 34 LYS cc_start: 0.7735 (mtmt) cc_final: 0.7532 (mtpm) REVERT: r 114 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8236 (tm-30) outliers start: 91 outliers final: 71 residues processed: 1054 average time/residue: 1.5715 time to fit residues: 2137.1520 Evaluate side-chains 1038 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 966 time to evaluate : 5.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 426 ASP Chi-restraints excluded: chain M residue 500 ILE Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 140 CYS Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain e residue 139 SER Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 75 ARG Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 67 SER Chi-restraints excluded: chain i residue 182 SER Chi-restraints excluded: chain i residue 215 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 316 THR Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 380 LEU Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 290 SER Chi-restraints excluded: chain r residue 305 THR Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 149 GLU Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 309 THR Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 679 optimal weight: 1.9990 chunk 610 optimal weight: 0.9990 chunk 338 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 411 optimal weight: 3.9990 chunk 325 optimal weight: 6.9990 chunk 630 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 383 optimal weight: 4.9990 chunk 469 optimal weight: 4.9990 chunk 731 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 86 ASN M 336 ASN M 663 ASN O 153 GLN P 123 GLN T 43 GLN Y 54 GLN c 115 ASN d 123 GLN h 21 GLN i 47 ASN l 603 ASN n 11 HIS r 192 ASN w 219 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.0500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 69814 Z= 0.298 Angle : 0.582 10.668 94385 Z= 0.291 Chirality : 0.043 0.206 10213 Planarity : 0.005 0.060 11761 Dihedral : 14.482 177.176 10771 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Rotamer: Outliers : 3.08 % Allowed : 14.15 % Favored : 82.77 % 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: 1.00 (0.09), residues: 8173 helix: 1.55 (0.08), residues: 4326 sheet: 0.30 (0.25), residues: 431 loop : -0.38 (0.10), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.007 0.001 HIS u 77 PHE 0.032 0.002 PHE i 292 TYR 0.022 0.002 TYR J 216 ARG 0.008 0.000 ARG I 103 *********************** 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 1198 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 978 time to evaluate : 6.259 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: E 111 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: E 117 ASP cc_start: 0.8185 (p0) cc_final: 0.7928 (p0) REVERT: I 58 ASP cc_start: 0.8844 (t0) cc_final: 0.8573 (t0) REVERT: J 142 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7350 (tp30) REVERT: M 39 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: M 696 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.8818 (mtt) REVERT: P 173 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.8018 (mpm) REVERT: Q 42 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: Q 214 TYR cc_start: 0.8996 (m-10) cc_final: 0.8680 (m-10) REVERT: Q 258 LEU cc_start: 0.9212 (tp) cc_final: 0.8979 (tp) REVERT: W 30 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7547 (mt) REVERT: W 85 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: W 98 MET cc_start: 0.7884 (mmm) cc_final: 0.7679 (mmt) REVERT: Y 41 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6815 (pp20) REVERT: Z 49 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.7399 (mm-30) REVERT: a 114 LYS cc_start: 0.8981 (ttpt) cc_final: 0.8460 (ttmm) REVERT: a 176 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8203 (ptpp) REVERT: c 141 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8362 (mt) REVERT: d 131 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8234 (mt0) REVERT: e 72 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.7714 (p0) REVERT: h 53 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7950 (tm-30) REVERT: i 282 MET cc_start: 0.9042 (mtm) cc_final: 0.8790 (mtp) REVERT: j 44 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7710 (ttt) REVERT: k 36 MET cc_start: 0.9286 (mtm) cc_final: 0.9067 (mtp) REVERT: l 401 MET cc_start: 0.8279 (mmm) cc_final: 0.7997 (mtp) REVERT: l 496 MET cc_start: 0.7509 (ttm) cc_final: 0.7220 (ttp) REVERT: o 112 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8777 (ttmt) REVERT: s 62 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8415 (mtm-85) REVERT: u 17 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: u 49 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8760 (mt-10) REVERT: v 101 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7187 (tp30) outliers start: 220 outliers final: 86 residues processed: 1106 average time/residue: 1.5729 time to fit residues: 2249.6450 Evaluate side-chains 1068 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 961 time to evaluate : 5.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 484 SER Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 555 ILE Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 148 ILE Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 173 MET Chi-restraints excluded: chain Q residue 42 GLU Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain Z residue 80 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 176 LYS Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 131 GLN Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 119 THR Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 206 LEU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain k residue 6 MET Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain k residue 43 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 338 MET Chi-restraints excluded: chain l residue 461 SER Chi-restraints excluded: chain l residue 572 LYS Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 11 THR Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 102 CYS Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 305 THR Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 62 ARG Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 49 GLU Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain v residue 101 GLU Chi-restraints excluded: chain w residue 47 GLU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 287 ASP Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 406 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 chunk 608 optimal weight: 8.9990 chunk 497 optimal weight: 6.9990 chunk 201 optimal weight: 0.9980 chunk 732 optimal weight: 2.9990 chunk 791 optimal weight: 10.0000 chunk 652 optimal weight: 5.9990 chunk 726 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 587 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 277 ASN E 45 ASN L 86 ASN M 336 ASN M 663 ASN O 153 GLN P 123 GLN T 43 GLN T 74 GLN Z 33 GLN c 115 ASN ** d 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 ASN e 115 GLN h 21 GLN i 47 ASN ** l 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 11 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 69814 Z= 0.281 Angle : 0.560 10.818 94385 Z= 0.283 Chirality : 0.043 0.206 10213 Planarity : 0.005 0.057 11761 Dihedral : 13.653 177.681 10698 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.49 % Favored : 96.44 % Rotamer: Outliers : 3.29 % Allowed : 14.71 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.09), residues: 8173 helix: 1.57 (0.08), residues: 4304 sheet: 0.25 (0.25), residues: 431 loop : -0.37 (0.10), residues: 3438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.009 0.001 HIS u 77 PHE 0.033 0.002 PHE i 292 TYR 0.023 0.002 TYR r 406 ARG 0.008 0.000 ARG I 103 *********************** 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 1241 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1006 time to evaluate : 6.388 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 257 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.6951 (mtt180) REVERT: E 117 ASP cc_start: 0.8230 (p0) cc_final: 0.7973 (p0) REVERT: I 58 ASP cc_start: 0.8844 (t0) cc_final: 0.8484 (t0) REVERT: J 117 ARG cc_start: 0.7926 (ttp-110) cc_final: 0.7626 (ttm-80) REVERT: J 142 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7318 (tp30) REVERT: M 39 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: M 54 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: M 675 VAL cc_start: 0.6929 (OUTLIER) cc_final: 0.6681 (p) REVERT: M 696 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.8841 (mtt) REVERT: N 9 ARG cc_start: 0.7267 (mtm-85) cc_final: 0.6551 (mtm180) REVERT: P 173 MET cc_start: 0.9398 (OUTLIER) cc_final: 0.7975 (mpm) REVERT: Q 42 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: W 30 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7572 (mt) REVERT: W 85 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: W 91 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8302 (tp) REVERT: Y 41 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6817 (pp20) REVERT: Z 49 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8402 (mm-30) REVERT: a 114 LYS cc_start: 0.9046 (ttpt) cc_final: 0.8598 (ttmm) REVERT: a 176 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8223 (ptpp) REVERT: b 24 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.8502 (tptt) REVERT: c 129 MET cc_start: 0.8799 (mtm) cc_final: 0.8444 (mtp) REVERT: c 141 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8341 (mt) REVERT: d 81 ASP cc_start: 0.8843 (t0) cc_final: 0.8623 (t0) REVERT: d 131 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8244 (mt0) REVERT: e 56 GLN cc_start: 0.7580 (mm-40) cc_final: 0.7152 (mm-40) REVERT: e 72 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.7735 (p0) REVERT: e 127 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8163 (ttmt) REVERT: h 53 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: h 55 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7622 (mt-10) REVERT: i 282 MET cc_start: 0.9030 (mtm) cc_final: 0.8768 (mtp) REVERT: j 44 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7631 (ttt) REVERT: l 150 MET cc_start: 0.9222 (mmm) cc_final: 0.8891 (mmm) REVERT: l 496 MET cc_start: 0.7477 (ttm) cc_final: 0.7249 (ttp) REVERT: p 66 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7596 (mp10) REVERT: p 141 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7567 (tp-100) REVERT: r 263 MET cc_start: 0.9303 (mmt) cc_final: 0.8987 (mmt) REVERT: s 62 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8428 (mtm-85) REVERT: u 17 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: u 49 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8771 (mt-10) REVERT: v 91 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8900 (mm-30) REVERT: v 101 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7124 (tp30) REVERT: w 316 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.7934 (mp0) outliers start: 235 outliers final: 103 residues processed: 1152 average time/residue: 1.5677 time to fit residues: 2344.8610 Evaluate side-chains 1087 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 956 time to evaluate : 5.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 484 SER Chi-restraints excluded: chain M residue 555 ILE Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 148 ILE Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 173 MET Chi-restraints excluded: chain Q residue 42 GLU Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 176 LYS Chi-restraints excluded: chain b residue 24 LYS Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain d residue 76 GLU Chi-restraints excluded: chain d residue 131 GLN Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 127 LYS Chi-restraints excluded: chain e residue 139 SER Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 206 LEU Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain k residue 43 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 127 THR Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 461 SER Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 572 LYS Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 11 THR 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 n residue 4 VAL Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 254 THR Chi-restraints excluded: chain r residue 305 THR Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain r residue 444 LEU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 62 ARG Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 49 GLU Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain v residue 101 GLU Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 287 ASP Chi-restraints excluded: chain w residue 309 THR Chi-restraints excluded: chain w residue 316 GLU Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 0.8980 chunk 550 optimal weight: 10.0000 chunk 380 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 349 optimal weight: 0.6980 chunk 491 optimal weight: 6.9990 chunk 734 optimal weight: 7.9990 chunk 778 optimal weight: 3.9990 chunk 383 optimal weight: 4.9990 chunk 696 optimal weight: 5.9990 chunk 209 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN L 86 ASN M 336 ASN M 558 GLN M 663 ASN O 153 GLN P 123 GLN T 43 GLN Z 33 GLN c 115 ASN ** d 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN i 47 ASN l 446 ASN ** l 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 11 HIS ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 69814 Z= 0.243 Angle : 0.538 10.570 94385 Z= 0.272 Chirality : 0.042 0.201 10213 Planarity : 0.005 0.057 11761 Dihedral : 13.198 177.852 10686 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.44 % Favored : 96.49 % Rotamer: Outliers : 3.14 % Allowed : 15.30 % Favored : 81.57 % 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: 1.08 (0.09), residues: 8173 helix: 1.62 (0.08), residues: 4311 sheet: 0.26 (0.25), residues: 443 loop : -0.34 (0.11), residues: 3419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP u 86 HIS 0.007 0.001 HIS u 77 PHE 0.032 0.001 PHE i 292 TYR 0.020 0.001 TYR r 406 ARG 0.006 0.000 ARG h 75 *********************** 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 1200 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 976 time to evaluate : 6.100 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 117 ASP cc_start: 0.8370 (p0) cc_final: 0.8155 (p0) REVERT: I 58 ASP cc_start: 0.8850 (t0) cc_final: 0.8482 (t0) REVERT: J 117 ARG cc_start: 0.7877 (ttp-110) cc_final: 0.7604 (ttm-80) REVERT: J 142 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7316 (tp30) REVERT: M 39 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: M 54 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8075 (pt0) REVERT: M 543 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7852 (mptp) REVERT: M 675 VAL cc_start: 0.6947 (OUTLIER) cc_final: 0.6713 (p) REVERT: M 696 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.8820 (mtt) REVERT: P 173 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.9187 (mmp) REVERT: Q 42 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: Q 435 LEU cc_start: 0.9450 (tp) cc_final: 0.9250 (tp) REVERT: W 30 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7600 (mt) REVERT: W 85 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: X 136 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7873 (mt-10) REVERT: Z 49 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8415 (mm-30) REVERT: a 114 LYS cc_start: 0.9048 (ttpt) cc_final: 0.8651 (ttmm) REVERT: a 176 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8214 (ptpp) REVERT: b 24 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.8428 (tptt) REVERT: c 129 MET cc_start: 0.8775 (mtm) cc_final: 0.8424 (mtp) REVERT: d 131 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8251 (mt0) REVERT: d 168 LYS cc_start: 0.8255 (tmtp) cc_final: 0.7862 (tmtp) REVERT: e 56 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7080 (mm-40) REVERT: e 72 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.7698 (p0) REVERT: h 53 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: h 102 GLU cc_start: 0.8096 (tt0) cc_final: 0.7888 (pt0) REVERT: i 282 MET cc_start: 0.8958 (mtm) cc_final: 0.8729 (mtp) REVERT: k 36 MET cc_start: 0.9303 (mtm) cc_final: 0.9066 (mtp) REVERT: l 88 MET cc_start: 0.8758 (tpp) cc_final: 0.8553 (tpt) REVERT: l 150 MET cc_start: 0.9249 (mmm) cc_final: 0.8870 (mmm) REVERT: l 401 MET cc_start: 0.8195 (mmm) cc_final: 0.7924 (mtp) REVERT: l 496 MET cc_start: 0.7545 (ttm) cc_final: 0.7312 (ttp) REVERT: n 33 GLU cc_start: 0.7952 (pt0) cc_final: 0.7740 (pt0) REVERT: p 66 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: r 14 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8658 (ttp) REVERT: r 263 MET cc_start: 0.9290 (mmt) cc_final: 0.8994 (mmt) REVERT: s 31 MET cc_start: 0.9525 (OUTLIER) cc_final: 0.9006 (mtt) REVERT: u 17 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: u 37 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8378 (t0) REVERT: u 49 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8773 (mt-10) REVERT: v 91 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8926 (mm-30) REVERT: v 101 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7077 (tp30) outliers start: 224 outliers final: 117 residues processed: 1108 average time/residue: 1.5937 time to fit residues: 2277.1589 Evaluate side-chains 1095 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 955 time to evaluate : 6.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 175 LYS Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 484 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 543 LYS Chi-restraints excluded: chain M residue 555 ILE Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 628 GLU Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 148 ILE Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 173 MET Chi-restraints excluded: chain Q residue 42 GLU Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 176 LYS Chi-restraints excluded: chain b residue 24 LYS Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 68 ASP Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain d residue 76 GLU Chi-restraints excluded: chain d residue 131 GLN Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 139 SER Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 206 LEU Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain k residue 43 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 127 THR Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 316 THR Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 461 SER Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 572 LYS Chi-restraints excluded: chain m residue 1 MET 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 n residue 4 VAL Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain r residue 14 MET Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 254 THR Chi-restraints excluded: chain r residue 305 THR Chi-restraints excluded: chain r residue 444 LEU Chi-restraints excluded: chain s residue 31 MET Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 37 ASP Chi-restraints excluded: chain u residue 49 GLU Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain v residue 101 GLU Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 287 ASP Chi-restraints excluded: chain w residue 309 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 1.9990 chunk 441 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 579 optimal weight: 3.9990 chunk 321 optimal weight: 5.9990 chunk 664 optimal weight: 8.9990 chunk 537 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 397 optimal weight: 7.9990 chunk 698 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN I 25 GLN L 86 ASN M 336 ASN M 558 GLN M 663 ASN O 153 GLN P 123 GLN T 43 GLN c 115 ASN ** d 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN f 62 HIS i 47 ASN ** l 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 580 GLN r 192 ASN s 258 ASN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 43 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 69814 Z= 0.338 Angle : 0.589 10.920 94385 Z= 0.297 Chirality : 0.044 0.219 10213 Planarity : 0.005 0.059 11761 Dihedral : 13.058 177.269 10682 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.79 % Favored : 96.13 % Rotamer: Outliers : 3.58 % Allowed : 15.27 % Favored : 81.15 % 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: 1.46 (0.08), residues: 4315 sheet: 0.29 (0.25), residues: 425 loop : -0.41 (0.10), residues: 3433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP c 145 HIS 0.015 0.001 HIS u 77 PHE 0.031 0.002 PHE i 292 TYR 0.020 0.002 TYR o 77 ARG 0.009 0.000 ARG I 103 *********************** 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 1226 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 970 time to evaluate : 7.896 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.6978 (mtt180) REVERT: I 58 ASP cc_start: 0.8879 (t0) cc_final: 0.8614 (t0) REVERT: J 117 ARG cc_start: 0.7961 (ttp-110) cc_final: 0.7640 (ttm-80) REVERT: J 142 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7359 (tp30) REVERT: M 39 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: M 543 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7829 (mptp) REVERT: M 675 VAL cc_start: 0.7184 (OUTLIER) cc_final: 0.6965 (p) REVERT: M 696 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.8843 (mtt) REVERT: N 9 ARG cc_start: 0.7226 (mtm-85) cc_final: 0.6480 (mtm180) REVERT: P 173 MET cc_start: 0.9441 (OUTLIER) cc_final: 0.9177 (mmp) REVERT: Q 258 LEU cc_start: 0.9153 (tp) cc_final: 0.8936 (tp) REVERT: Q 435 LEU cc_start: 0.9480 (tp) cc_final: 0.9268 (tp) REVERT: S 59 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7224 (mtp85) REVERT: W 30 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7633 (mt) REVERT: W 85 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: W 91 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8346 (tp) REVERT: Z 49 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8490 (mm-30) REVERT: a 176 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8267 (ptpp) REVERT: b 24 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8451 (tptt) REVERT: c 129 MET cc_start: 0.8793 (mtm) cc_final: 0.8446 (mtp) REVERT: c 141 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8361 (mt) REVERT: d 131 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8255 (mt0) REVERT: e 56 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7236 (mm-40) REVERT: e 72 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.7781 (p0) REVERT: h 53 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: h 55 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: h 102 GLU cc_start: 0.8210 (tt0) cc_final: 0.7935 (pt0) REVERT: i 282 MET cc_start: 0.9044 (mtm) cc_final: 0.8770 (mtp) REVERT: i 318 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: k 36 MET cc_start: 0.9329 (mtm) cc_final: 0.9110 (mtp) REVERT: l 150 MET cc_start: 0.9271 (mmm) cc_final: 0.9069 (mmm) REVERT: l 401 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7857 (mtp) REVERT: l 496 MET cc_start: 0.7558 (ttm) cc_final: 0.7330 (ttp) REVERT: o 112 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8811 (ttmt) REVERT: p 66 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: r 14 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8672 (ttp) REVERT: r 263 MET cc_start: 0.9309 (mmt) cc_final: 0.9073 (mmt) REVERT: s 91 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8998 (mtt) REVERT: s 227 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: u 17 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: u 37 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8383 (t0) REVERT: u 49 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8802 (mt-10) REVERT: v 91 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8879 (mm-30) REVERT: v 101 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7179 (tp30) REVERT: w 316 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.7824 (mp0) outliers start: 256 outliers final: 137 residues processed: 1125 average time/residue: 1.5627 time to fit residues: 2273.6122 Evaluate side-chains 1120 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 952 time to evaluate : 6.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 175 LYS Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 484 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 543 LYS Chi-restraints excluded: chain M residue 555 ILE Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 148 ILE Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 173 MET Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 59 ARG Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain Z residue 80 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 176 LYS Chi-restraints excluded: chain b residue 24 LYS Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 76 GLU Chi-restraints excluded: chain d residue 131 GLN Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 139 SER Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 119 THR Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 206 LEU Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 318 GLU Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain k residue 43 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 127 THR Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 316 THR Chi-restraints excluded: chain l residue 380 LEU Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 461 SER Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 572 LYS Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 11 THR Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 94 VAL Chi-restraints excluded: chain m residue 102 CYS Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain r residue 14 MET Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 254 THR Chi-restraints excluded: chain r residue 305 THR Chi-restraints excluded: chain r residue 444 LEU Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 37 ASP Chi-restraints excluded: chain u residue 49 GLU Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain v residue 101 GLU Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 47 GLU Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 309 THR Chi-restraints excluded: chain w residue 316 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 0.1980 chunk 700 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 456 optimal weight: 4.9990 chunk 192 optimal weight: 0.3980 chunk 778 optimal weight: 2.9990 chunk 646 optimal weight: 6.9990 chunk 360 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 408 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN E 45 ASN I 25 GLN L 86 ASN M 336 ASN M 558 GLN M 663 ASN M 688 GLN O 153 GLN P 123 GLN S 61 HIS T 43 GLN c 115 ASN ** d 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN i 47 ASN l 351 ASN ** l 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 192 ASN s 258 ASN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 69814 Z= 0.183 Angle : 0.510 10.736 94385 Z= 0.258 Chirality : 0.040 0.191 10213 Planarity : 0.004 0.054 11761 Dihedral : 12.572 178.253 10680 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.73 % Rotamer: Outliers : 2.76 % Allowed : 16.49 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.09), residues: 8173 helix: 1.73 (0.08), residues: 4289 sheet: 0.25 (0.25), residues: 443 loop : -0.31 (0.11), residues: 3441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP u 86 HIS 0.013 0.001 HIS u 77 PHE 0.032 0.001 PHE i 292 TYR 0.022 0.001 TYR r 406 ARG 0.006 0.000 ARG v 115 *********************** 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 1202 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1005 time to evaluate : 6.067 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7935 (tpt170) REVERT: G 140 CYS cc_start: 0.8168 (p) cc_final: 0.7814 (p) REVERT: I 58 ASP cc_start: 0.8828 (t0) cc_final: 0.8556 (t0) REVERT: J 117 ARG cc_start: 0.7858 (ttp-110) cc_final: 0.7583 (ttm-80) REVERT: J 142 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7320 (tp30) REVERT: M 39 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: M 54 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8015 (pt0) REVERT: M 543 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7830 (mptp) REVERT: M 546 PHE cc_start: 0.8169 (m-80) cc_final: 0.7470 (t80) REVERT: M 675 VAL cc_start: 0.6891 (OUTLIER) cc_final: 0.6681 (p) REVERT: M 696 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.8806 (mtt) REVERT: N 9 ARG cc_start: 0.7171 (mtm-85) cc_final: 0.6403 (mtm180) REVERT: P 63 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8202 (mt0) REVERT: S 53 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7807 (mtp180) REVERT: W 78 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8397 (mt-10) REVERT: W 85 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: W 91 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8395 (tp) REVERT: W 98 MET cc_start: 0.7942 (mmt) cc_final: 0.7701 (mmp) REVERT: X 136 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7748 (mt-10) REVERT: Y 96 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: Z 49 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8433 (mm-30) REVERT: a 176 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8180 (ptpp) REVERT: b 24 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8385 (tptt) REVERT: b 27 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7641 (mt-10) REVERT: c 141 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8319 (mt) REVERT: e 56 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7205 (mm-40) REVERT: e 72 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.7647 (p0) REVERT: h 53 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: h 55 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: i 159 MET cc_start: 0.8995 (tpt) cc_final: 0.8644 (tpt) REVERT: j 8 LEU cc_start: 0.8586 (tp) cc_final: 0.8316 (tp) REVERT: l 102 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: l 401 MET cc_start: 0.8089 (mmm) cc_final: 0.7800 (mtp) REVERT: l 496 MET cc_start: 0.7550 (ttm) cc_final: 0.7315 (ttp) REVERT: p 66 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7460 (mt0) REVERT: r 14 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8673 (ttp) REVERT: r 378 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8048 (mt-10) REVERT: s 31 MET cc_start: 0.9518 (OUTLIER) cc_final: 0.9003 (mtt) REVERT: s 307 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9011 (tp) REVERT: u 17 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: u 37 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8382 (t0) REVERT: u 49 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8758 (mt-10) REVERT: v 101 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7062 (tp30) outliers start: 197 outliers final: 86 residues processed: 1131 average time/residue: 1.5940 time to fit residues: 2323.9374 Evaluate side-chains 1085 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 970 time to evaluate : 6.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 175 LYS Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 484 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 543 LYS Chi-restraints excluded: chain M residue 555 ILE Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 628 GLU Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 148 ILE Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 53 ARG Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain Y residue 75 HIS Chi-restraints excluded: chain Y residue 96 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 176 LYS Chi-restraints excluded: chain b residue 24 LYS Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain d residue 76 GLU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 206 LEU Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 102 GLU Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 454 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 173 ARG Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain r residue 14 MET Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 254 THR Chi-restraints excluded: chain r residue 305 THR Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain r residue 444 LEU Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 31 MET Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 307 LEU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 37 ASP Chi-restraints excluded: chain u residue 49 GLU Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain u residue 149 GLU Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain v residue 101 GLU Chi-restraints excluded: chain v residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 443 optimal weight: 0.6980 chunk 568 optimal weight: 7.9990 chunk 440 optimal weight: 2.9990 chunk 655 optimal weight: 9.9990 chunk 434 optimal weight: 0.0040 chunk 775 optimal weight: 7.9990 chunk 485 optimal weight: 9.9990 chunk 473 optimal weight: 10.0000 chunk 358 optimal weight: 6.9990 overall best weight: 2.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN G 115 GLN I 25 GLN L 86 ASN M 336 ASN M 558 GLN M 663 ASN O 153 GLN P 123 GLN T 43 GLN c 115 ASN ** d 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN i 47 ASN l 471 ASN r 192 ASN s 99 ASN s 258 ASN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 43 GLN w 219 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 69814 Z= 0.312 Angle : 0.575 11.333 94385 Z= 0.290 Chirality : 0.043 0.215 10213 Planarity : 0.005 0.058 11761 Dihedral : 12.604 177.549 10678 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.82 % Favored : 96.11 % Rotamer: Outliers : 3.01 % Allowed : 16.60 % Favored : 80.39 % 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: 1.00 (0.09), residues: 8173 helix: 1.55 (0.08), residues: 4308 sheet: 0.22 (0.25), residues: 443 loop : -0.36 (0.10), residues: 3422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP c 145 HIS 0.014 0.001 HIS u 77 PHE 0.032 0.002 PHE i 292 TYR 0.020 0.002 TYR d 63 ARG 0.010 0.000 ARG I 103 *********************** 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 1180 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 965 time to evaluate : 7.125 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7978 (tpt170) REVERT: A 257 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7007 (mtt180) REVERT: G 140 CYS cc_start: 0.8136 (p) cc_final: 0.7816 (p) REVERT: I 58 ASP cc_start: 0.8873 (t0) cc_final: 0.8512 (t0) REVERT: J 117 ARG cc_start: 0.7938 (ttp-110) cc_final: 0.7626 (ttm-80) REVERT: J 142 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7346 (tp30) REVERT: M 39 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: M 54 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8105 (pt0) REVERT: M 543 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7822 (mptp) REVERT: M 696 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.8857 (mtt) REVERT: N 6 VAL cc_start: 0.5608 (OUTLIER) cc_final: 0.5303 (t) REVERT: N 9 ARG cc_start: 0.7165 (mtm-85) cc_final: 0.6392 (mtm180) REVERT: Q 258 LEU cc_start: 0.9125 (tp) cc_final: 0.8916 (tp) REVERT: S 53 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7803 (mtp180) REVERT: S 59 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7174 (mtp85) REVERT: W 85 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: W 91 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8397 (tp) REVERT: X 136 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7791 (mt-10) REVERT: Z 49 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8496 (mm-30) REVERT: a 176 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8255 (ptpp) REVERT: c 129 MET cc_start: 0.8768 (mtm) cc_final: 0.8416 (mtp) REVERT: c 141 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8338 (mt) REVERT: d 131 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: e 56 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7248 (mm-40) REVERT: e 72 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.7751 (p0) REVERT: h 53 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: i 318 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: k 36 MET cc_start: 0.9331 (mtm) cc_final: 0.9081 (mtp) REVERT: l 366 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8313 (mtt) REVERT: l 401 MET cc_start: 0.8057 (mmm) cc_final: 0.7605 (mtp) REVERT: l 496 MET cc_start: 0.7518 (ttm) cc_final: 0.7276 (ttp) REVERT: p 66 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7623 (mp10) REVERT: r 14 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8454 (ttp) REVERT: r 114 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: r 263 MET cc_start: 0.9260 (mmt) cc_final: 0.8938 (mmt) REVERT: r 378 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: u 6 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7142 (tm-30) REVERT: u 17 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: u 37 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8401 (t0) REVERT: u 49 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8760 (mt-10) REVERT: v 101 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7134 (tp30) REVERT: w 296 MET cc_start: 0.9146 (mmm) cc_final: 0.8886 (mmp) outliers start: 215 outliers final: 121 residues processed: 1101 average time/residue: 1.6009 time to fit residues: 2276.5409 Evaluate side-chains 1108 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 958 time to evaluate : 6.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 175 LYS Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 360 ARG Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 484 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 543 LYS Chi-restraints excluded: chain M residue 555 ILE Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 148 ILE Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 53 ARG Chi-restraints excluded: chain S residue 59 ARG Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain U residue 83 ASN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain X residue 92 LYS Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 101 ILE Chi-restraints excluded: chain a residue 176 LYS Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 76 GLU Chi-restraints excluded: chain d residue 131 GLN Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 139 SER Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 206 LEU Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 215 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 318 GLU Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 380 LEU Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 572 LYS Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 94 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 111 LYS Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain r residue 14 MET Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 254 THR Chi-restraints excluded: chain r residue 305 THR Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain r residue 444 LEU Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 37 ASP Chi-restraints excluded: chain u residue 49 GLU Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain u residue 149 GLU Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain v residue 101 GLU Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 47 GLU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 309 THR Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 480 optimal weight: 8.9990 chunk 309 optimal weight: 2.9990 chunk 463 optimal weight: 8.9990 chunk 233 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 493 optimal weight: 0.0670 chunk 528 optimal weight: 0.8980 chunk 383 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 609 optimal weight: 7.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN I 25 GLN L 86 ASN M 336 ASN M 558 GLN M 663 ASN O 153 GLN P 123 GLN T 43 GLN W 90 ASN c 115 ASN ** d 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN i 47 ASN j 83 ASN k 91 GLN ** l 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 192 ASN s 258 ASN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 219 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 69814 Z= 0.249 Angle : 0.548 11.520 94385 Z= 0.277 Chirality : 0.042 0.208 10213 Planarity : 0.005 0.056 11761 Dihedral : 12.441 177.846 10678 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.43 % Rotamer: Outliers : 2.86 % Allowed : 16.89 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.09), residues: 8173 helix: 1.60 (0.08), residues: 4306 sheet: 0.21 (0.25), residues: 443 loop : -0.35 (0.11), residues: 3424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP c 145 HIS 0.013 0.001 HIS u 77 PHE 0.034 0.001 PHE i 292 TYR 0.024 0.001 TYR d 63 ARG 0.009 0.000 ARG I 103 *********************** 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 1174 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 970 time to evaluate : 6.406 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7925 (tpt170) REVERT: A 52 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.6569 (mpt-90) REVERT: G 140 CYS cc_start: 0.8136 (p) cc_final: 0.7866 (p) REVERT: I 29 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7856 (mm110) REVERT: I 58 ASP cc_start: 0.8846 (t0) cc_final: 0.8480 (t0) REVERT: J 117 ARG cc_start: 0.7883 (ttp-110) cc_final: 0.7598 (ttm-80) REVERT: J 142 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7341 (tp30) REVERT: K 72 THR cc_start: 0.7591 (p) cc_final: 0.7362 (t) REVERT: M 39 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: M 54 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8046 (pt0) REVERT: M 543 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7849 (mptp) REVERT: M 696 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.8851 (mtt) REVERT: N 9 ARG cc_start: 0.7143 (mtm-85) cc_final: 0.6377 (mtm180) REVERT: Q 73 LYS cc_start: 0.7831 (mmtm) cc_final: 0.7629 (mptt) REVERT: Q 258 LEU cc_start: 0.9115 (tp) cc_final: 0.8910 (tp) REVERT: S 53 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7791 (mtp180) REVERT: S 59 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7167 (mtp85) REVERT: W 85 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: W 91 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8429 (tp) REVERT: X 136 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7806 (mt-10) REVERT: Y 96 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: Z 49 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8522 (mm-30) REVERT: a 176 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8227 (ptpp) REVERT: c 129 MET cc_start: 0.8764 (mtm) cc_final: 0.8423 (mtp) REVERT: c 141 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8359 (mt) REVERT: d 131 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8264 (mt0) REVERT: e 56 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7220 (mm-40) REVERT: e 72 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.7707 (p0) REVERT: h 53 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: h 80 LYS cc_start: 0.7814 (mtpm) cc_final: 0.7560 (mtpm) REVERT: l 401 MET cc_start: 0.8071 (mmm) cc_final: 0.7617 (mtp) REVERT: l 496 MET cc_start: 0.7572 (ttm) cc_final: 0.7343 (ttp) REVERT: m 1 MET cc_start: 0.3849 (mtt) cc_final: 0.3479 (ttm) REVERT: p 66 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7654 (mp10) REVERT: r 14 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8481 (ttp) REVERT: r 114 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7856 (tm-30) REVERT: u 6 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7113 (tm-30) REVERT: u 17 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: u 37 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8406 (t0) REVERT: u 49 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8758 (mt-10) REVERT: v 21 ARG cc_start: 0.7233 (mtp85) cc_final: 0.6893 (mtt180) REVERT: v 101 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7119 (tp30) outliers start: 204 outliers final: 127 residues processed: 1107 average time/residue: 1.6203 time to fit residues: 2318.1732 Evaluate side-chains 1113 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 959 time to evaluate : 6.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 175 LYS Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 360 ARG Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 459 ASN Chi-restraints excluded: chain M residue 484 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 543 LYS Chi-restraints excluded: chain M residue 555 ILE Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 628 GLU Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 148 ILE Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 53 ARG Chi-restraints excluded: chain S residue 59 ARG Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain U residue 83 ASN Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 96 GLU Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 101 ILE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 176 LYS Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 76 GLU Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain d residue 131 GLN Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 137 MET Chi-restraints excluded: chain e residue 139 SER Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 206 LEU Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 380 LEU Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 461 SER Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 111 LYS Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain r residue 14 MET Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 254 THR Chi-restraints excluded: chain r residue 305 THR Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain r residue 444 LEU Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 37 ASP Chi-restraints excluded: chain u residue 49 GLU Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain u residue 149 GLU Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain v residue 101 GLU Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 309 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 0.8980 chunk 743 optimal weight: 0.9990 chunk 678 optimal weight: 0.8980 chunk 723 optimal weight: 0.7980 chunk 435 optimal weight: 0.0980 chunk 314 optimal weight: 2.9990 chunk 567 optimal weight: 0.7980 chunk 221 optimal weight: 0.0070 chunk 653 optimal weight: 4.9990 chunk 683 optimal weight: 0.8980 chunk 720 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN L 86 ASN M 336 ASN M 558 GLN M 663 ASN M 688 GLN O 153 GLN P 123 GLN T 43 GLN c 115 ASN d 123 GLN e 115 GLN i 47 ASN j 83 ASN ** l 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 258 ASN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 55 GLN w 219 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 69814 Z= 0.145 Angle : 0.497 13.514 94385 Z= 0.250 Chirality : 0.039 0.271 10213 Planarity : 0.004 0.053 11761 Dihedral : 11.808 179.280 10678 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.86 % Rotamer: Outliers : 1.88 % Allowed : 17.93 % Favored : 80.20 % 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: 1.33 (0.09), residues: 8173 helix: 1.85 (0.08), residues: 4299 sheet: 0.29 (0.25), residues: 450 loop : -0.24 (0.11), residues: 3424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP l 144 HIS 0.010 0.001 HIS u 77 PHE 0.032 0.001 PHE i 292 TYR 0.024 0.001 TYR r 406 ARG 0.008 0.000 ARG I 103 *********************** 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 1178 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1044 time to evaluate : 6.082 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 TYR cc_start: 0.9193 (OUTLIER) cc_final: 0.7176 (t80) REVERT: G 140 CYS cc_start: 0.8178 (p) cc_final: 0.7941 (p) REVERT: I 58 ASP cc_start: 0.8795 (t0) cc_final: 0.8411 (t0) REVERT: J 117 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7568 (ttm-80) REVERT: J 142 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7309 (tp30) REVERT: J 319 VAL cc_start: 0.8979 (t) cc_final: 0.8777 (m) REVERT: K 72 THR cc_start: 0.7527 (p) cc_final: 0.7295 (t) REVERT: M 39 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: M 543 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7842 (mptp) REVERT: M 546 PHE cc_start: 0.8139 (m-80) cc_final: 0.7462 (t80) REVERT: M 696 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8789 (mtt) REVERT: N 9 ARG cc_start: 0.7089 (mtm-85) cc_final: 0.6310 (mtm180) REVERT: P 63 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8183 (mt0) REVERT: W 91 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8420 (tp) REVERT: Z 49 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8413 (mm-30) REVERT: a 176 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8146 (ptpp) REVERT: c 145 TRP cc_start: 0.8483 (t60) cc_final: 0.8059 (t60) REVERT: e 56 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7125 (mm-40) REVERT: h 80 LYS cc_start: 0.7871 (mtpm) cc_final: 0.7631 (mtpm) REVERT: i 29 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8688 (mt) REVERT: i 318 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: j 8 LEU cc_start: 0.8568 (tp) cc_final: 0.8211 (tp) REVERT: k 36 MET cc_start: 0.9320 (mtm) cc_final: 0.9054 (mtp) REVERT: l 401 MET cc_start: 0.8037 (mmm) cc_final: 0.7551 (mtp) REVERT: l 496 MET cc_start: 0.7526 (ttm) cc_final: 0.7289 (ttp) REVERT: p 66 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7541 (mt0) REVERT: r 114 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: r 355 MET cc_start: 0.9032 (tpp) cc_final: 0.8831 (mmt) REVERT: u 17 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: u 37 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8418 (t0) REVERT: v 21 ARG cc_start: 0.7229 (mtp85) cc_final: 0.6897 (mtt180) REVERT: v 91 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8950 (mm-30) REVERT: v 101 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7071 (tp30) outliers start: 134 outliers final: 63 residues processed: 1129 average time/residue: 1.6091 time to fit residues: 2357.3853 Evaluate side-chains 1068 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 989 time to evaluate : 6.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 360 ARG Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 543 LYS Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 628 GLU Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain U residue 83 ASN Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 101 ILE Chi-restraints excluded: chain a residue 176 LYS Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 206 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 318 GLU Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain l residue 14 ILE Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 461 SER Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 254 THR Chi-restraints excluded: chain r residue 444 LEU Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 37 ASP Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain v residue 101 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 474 optimal weight: 0.8980 chunk 764 optimal weight: 7.9990 chunk 466 optimal weight: 8.9990 chunk 362 optimal weight: 0.7980 chunk 531 optimal weight: 0.5980 chunk 801 optimal weight: 6.9990 chunk 738 optimal weight: 0.8980 chunk 638 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 493 optimal weight: 0.0980 chunk 391 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN I 25 GLN L 86 ASN M 336 ASN M 558 GLN M 663 ASN O 153 GLN P 123 GLN T 43 GLN c 83 GLN c 115 ASN ** d 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN i 47 ASN k 91 GLN ** l 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 11 HIS o 123 GLN s 258 ASN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 219 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.096 69814 Z= 0.143 Angle : 0.497 13.558 94385 Z= 0.249 Chirality : 0.039 0.191 10213 Planarity : 0.004 0.052 11761 Dihedral : 11.475 179.503 10669 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.89 % Rotamer: Outliers : 1.40 % Allowed : 18.92 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.09), residues: 8173 helix: 1.91 (0.08), residues: 4315 sheet: 0.39 (0.25), residues: 445 loop : -0.16 (0.11), residues: 3413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP u 86 HIS 0.010 0.001 HIS u 77 PHE 0.033 0.001 PHE i 292 TYR 0.025 0.001 TYR J 216 ARG 0.015 0.000 ARG N 131 ********************** 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 1110 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1010 time to evaluate : 6.174 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.7342 (t80) REVERT: G 80 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7735 (tttp) REVERT: G 140 CYS cc_start: 0.8138 (p) cc_final: 0.7894 (p) REVERT: J 117 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7577 (ttm-80) REVERT: J 142 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7295 (tp30) REVERT: K 72 THR cc_start: 0.7503 (p) cc_final: 0.7299 (t) REVERT: M 39 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: M 543 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7834 (mptp) REVERT: M 546 PHE cc_start: 0.8126 (m-80) cc_final: 0.7487 (t80) REVERT: M 696 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8771 (mtt) REVERT: N 6 VAL cc_start: 0.5566 (OUTLIER) cc_final: 0.5243 (t) REVERT: N 9 ARG cc_start: 0.7067 (mtm-85) cc_final: 0.6266 (mtm180) REVERT: S 53 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7724 (mtp180) REVERT: W 91 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8362 (tp) REVERT: Z 49 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.6967 (mm-30) REVERT: a 176 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8137 (ptpp) REVERT: c 145 TRP cc_start: 0.8515 (t60) cc_final: 0.8097 (t60) REVERT: e 56 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7170 (mm-40) REVERT: h 80 LYS cc_start: 0.7884 (mtpm) cc_final: 0.7554 (mtpm) REVERT: i 29 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8688 (mt) REVERT: l 88 MET cc_start: 0.8657 (tpt) cc_final: 0.8451 (tpp) REVERT: l 496 MET cc_start: 0.7528 (ttm) cc_final: 0.7289 (ttp) REVERT: p 66 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7497 (mt0) REVERT: r 114 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: r 355 MET cc_start: 0.9066 (tpp) cc_final: 0.8827 (mmp) REVERT: u 17 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: v 21 ARG cc_start: 0.7248 (mtp85) cc_final: 0.6924 (mtt180) REVERT: v 83 GLU cc_start: 0.8566 (mp0) cc_final: 0.8321 (mp0) REVERT: v 101 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7034 (tp30) outliers start: 100 outliers final: 63 residues processed: 1078 average time/residue: 1.6112 time to fit residues: 2251.1586 Evaluate side-chains 1072 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 994 time to evaluate : 6.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 360 ARG Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 543 LYS Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain S residue 53 ARG Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain U residue 83 ASN Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 75 HIS Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 101 ILE Chi-restraints excluded: chain a residue 176 LYS Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 68 ASP Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 206 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 254 THR Chi-restraints excluded: chain r residue 444 LEU Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain v residue 101 GLU Chi-restraints excluded: chain v residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 507 optimal weight: 3.9990 chunk 680 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 588 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 639 optimal weight: 7.9990 chunk 267 optimal weight: 7.9990 chunk 656 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 76 ASN I 25 GLN L 86 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 336 ASN M 558 GLN M 663 ASN O 153 GLN P 123 GLN T 43 GLN c 115 ASN ** d 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN i 47 ASN k 91 GLN n 11 HIS o 123 GLN r 192 ASN s 230 ASN s 235 ASN s 258 ASN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 219 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.094364 restraints weight = 93905.567| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.23 r_work: 0.2838 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 69814 Z= 0.333 Angle : 0.602 13.351 94385 Z= 0.302 Chirality : 0.044 0.217 10213 Planarity : 0.005 0.058 11761 Dihedral : 11.934 177.481 10668 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.15 % Rotamer: Outliers : 1.95 % Allowed : 18.66 % Favored : 79.40 % 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: 1.08 (0.09), residues: 8173 helix: 1.60 (0.08), residues: 4308 sheet: 0.27 (0.25), residues: 433 loop : -0.31 (0.11), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 145 HIS 0.014 0.001 HIS u 77 PHE 0.031 0.002 PHE i 292 TYR 0.025 0.002 TYR d 63 ARG 0.010 0.001 ARG I 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29950.89 seconds wall clock time: 518 minutes 25.54 seconds (31105.54 seconds total)