Starting phenix.real_space_refine on Sat Feb 17 04:53:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4g_32304/02_2024/7w4g_32304_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4g_32304/02_2024/7w4g_32304.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4g_32304/02_2024/7w4g_32304_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4g_32304/02_2024/7w4g_32304_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4g_32304/02_2024/7w4g_32304_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4g_32304/02_2024/7w4g_32304.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4g_32304/02_2024/7w4g_32304.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4g_32304/02_2024/7w4g_32304_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4g_32304/02_2024/7w4g_32304_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 47 5.49 5 Mg 1 5.21 5 S 482 5.16 5 C 44209 2.51 5 N 11245 2.21 5 O 12247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 78": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "J GLU 135": "OE1" <-> "OE2" Residue "J GLU 346": "OE1" <-> "OE2" Residue "J GLU 367": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "M GLU 217": "OE1" <-> "OE2" Residue "M GLU 310": "OE1" <-> "OE2" Residue "M GLU 369": "OE1" <-> "OE2" Residue "M GLU 647": "OE1" <-> "OE2" Residue "M GLU 660": "OE1" <-> "OE2" Residue "M GLU 670": "OE1" <-> "OE2" Residue "M GLU 716": "OE1" <-> "OE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N GLU 50": "OE1" <-> "OE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "O GLU 207": "OE1" <-> "OE2" Residue "O GLU 236": "OE1" <-> "OE2" Residue "P GLU 83": "OE1" <-> "OE2" Residue "P ARG 125": "NH1" <-> "NH2" Residue "P GLU 215": "OE1" <-> "OE2" Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q GLU 57": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 125": "OE1" <-> "OE2" Residue "Q GLU 246": "OE1" <-> "OE2" Residue "Q GLU 335": "OE1" <-> "OE2" Residue "Q GLU 460": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 35": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 123": "OE1" <-> "OE2" Residue "X GLU 125": "OE1" <-> "OE2" Residue "X GLU 129": "OE1" <-> "OE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "Z GLU 85": "OE1" <-> "OE2" Residue "a GLU 97": "OE1" <-> "OE2" Residue "a GLU 111": "OE1" <-> "OE2" Residue "a GLU 130": "OE1" <-> "OE2" Residue "a GLU 143": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "b GLU 17": "OE1" <-> "OE2" Residue "b GLU 27": "OE1" <-> "OE2" Residue "b TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 47": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 53": "OE1" <-> "OE2" Residue "d GLU 76": "OE1" <-> "OE2" Residue "d GLU 130": "OE1" <-> "OE2" Residue "d PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 57": "OE1" <-> "OE2" Residue "g PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "h GLU 24": "OE1" <-> "OE2" Residue "h GLU 39": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 55": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "i GLU 269": "OE1" <-> "OE2" Residue "j GLU 32": "OE1" <-> "OE2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "l PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 102": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 353": "OE1" <-> "OE2" Residue "l ASP 393": "OD1" <-> "OD2" Residue "l GLU 503": "OE1" <-> "OE2" Residue "m GLU 77": "OE1" <-> "OE2" Residue "m GLU 139": "OE1" <-> "OE2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p GLU 84": "OE1" <-> "OE2" Residue "p GLU 95": "OE1" <-> "OE2" Residue "p GLU 131": "OE1" <-> "OE2" Residue "p GLU 136": "OE1" <-> "OE2" Residue "p GLU 142": "OE1" <-> "OE2" Residue "p GLU 152": "OE1" <-> "OE2" Residue "p GLU 160": "OE1" <-> "OE2" Residue "p GLU 176": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "r TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 378": "OE1" <-> "OE2" Residue "s PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "s GLU 202": "OE1" <-> "OE2" Residue "s GLU 214": "OE1" <-> "OE2" Residue "u GLU 11": "OE1" <-> "OE2" Residue "u GLU 17": "OE1" <-> "OE2" Residue "u GLU 109": "OE1" <-> "OE2" Residue "u GLU 149": "OE1" <-> "OE2" Residue "u GLU 153": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 45": "OE1" <-> "OE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "w GLU 47": "OE1" <-> "OE2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "w GLU 115": "OE1" <-> "OE2" Residue "w GLU 171": "OE1" <-> "OE2" Residue "w GLU 197": "OE1" <-> "OE2" Residue "w GLU 238": "OE1" <-> "OE2" Residue "w GLU 248": "OE1" <-> "OE2" Residue "w GLU 251": "OE1" <-> "OE2" Residue "w GLU 267": "OE1" <-> "OE2" Residue "w GLU 271": "OE1" <-> "OE2" Residue "w GLU 274": "OE1" <-> "OE2" Residue "w GLU 345": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 68260 Number of models: 1 Model: "" Number of chains: 68 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: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3459 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 566 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1167 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} 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: "X" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 703 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1005 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "h" Number of atoms: 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: 4816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4816 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 28, 'TRANS': 577} Chain: "m" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1292 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "w" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'PEE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 125 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1, 'UQ1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "J" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {' UQ': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'PEE': 1, 'UQ1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 194 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "i" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'PLX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 336 Unusual residues: {'CDL': 2, 'PEE': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "m" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 94 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "r" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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 47.694 49.730 171.310 1.00 22.53 S ATOM 3060 SG CYS A 425 47.244 46.270 177.019 1.00 23.63 S ATOM 2738 SG CYS A 385 44.743 45.118 171.289 1.00 29.37 S ATOM 2699 SG CYS A 379 42.374 50.032 175.113 1.00 24.03 S ATOM 3961 SG CYS B 113 36.688 65.477 136.163 1.00 35.69 S ATOM 3980 SG CYS B 116 41.787 63.198 140.094 1.00 4.54 S ATOM 4003 SG CYS B 119 42.935 65.887 134.736 1.00 8.98 S ATOM 4332 SG CYS B 162 40.510 60.098 135.184 1.00 13.24 S ATOM 4030 SG CYS B 123 49.079 69.007 130.325 1.00 9.83 S ATOM 4256 SG CYS B 152 47.258 67.222 124.389 1.00 18.70 S ATOM 4303 SG CYS B 158 45.421 63.413 129.086 1.00 25.98 S ATOM 4282 SG CYS B 155 51.501 63.836 127.716 1.00 14.13 S ATOM 5724 SG CYS C 166 53.922 67.512 120.175 1.00 8.20 S ATOM 4996 SG CYS C 72 54.509 69.070 113.881 1.00 3.87 S ATOM 4990 SG CYS C 71 59.763 67.498 117.010 1.00 17.11 S ATOM 5494 SG CYS C 136 56.140 72.636 119.190 1.00 9.41 S ATOM 14949 SG CYS M 131 40.852 63.273 152.188 1.00 23.05 S ATOM 14928 SG CYS M 128 44.620 58.820 149.226 1.00 11.69 S ATOM 14989 SG CYS M 137 46.410 62.353 154.582 1.00 8.55 S ATOM 15321 SG CYS M 179 44.645 62.157 165.474 1.00 19.83 S ATOM 15675 SG CYS M 226 41.669 64.857 161.232 1.00 15.16 S ATOM 15345 SG CYS M 182 39.137 64.791 167.255 1.00 11.49 S ATOM 15298 SG CYS M 176 39.062 59.306 163.769 1.00 15.39 S ATOM 14546 SG CYS M 78 56.440 57.926 169.756 1.00 31.63 S ATOM 14647 SG CYS M 92 54.465 59.840 172.098 1.00 19.37 S ATOM 14435 SG CYS M 64 50.100 59.782 169.542 1.00 18.18 S ATOM 14521 SG CYS M 75 51.451 57.873 166.726 1.00 22.85 S ATOM 21484 SG CYS O 135 32.215 31.870 178.939 1.00 53.37 S ATOM 21518 SG CYS O 140 32.427 28.369 180.246 1.00 57.05 S ATOM 21798 SG CYS O 176 36.527 33.448 181.762 1.00 52.77 S ATOM 21821 SG CYS O 180 37.125 30.159 182.753 1.00 53.13 S ATOM 28560 SG CYS T 86 29.492 51.822 143.991 1.00 23.17 S ATOM 28738 SG CYS T 111 30.669 55.123 144.736 1.00 23.07 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.67 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.67 Time building chain proxies: 27.49, per 1000 atoms: 0.40 Number of scatterers: 68260 At special positions: 0 Unit cell: (212.993, 225.069, 228.363, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 482 16.00 P 47 15.00 Mg 1 11.99 O 12247 8.00 N 11245 7.00 C 44209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " distance=2.03 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.03 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.04 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.94 Conformation dependent library (CDL) restraints added in 9.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="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="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb=" SF4 C 301 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb=" SF4 M 802 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15532 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 353 helices and 28 sheets defined 52.6% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.49 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 95 through 102 removed outlier: 4.234A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.626A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 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: 4.338A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.062A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 Proline residue: A 434 - end of helix removed outlier: 3.517A pdb=" N ARG A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.531A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 206 removed outlier: 5.687A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'E' and resid 25 through 49 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 69 Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.389A 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 94 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 135 No H-bonds generated for 'chain 'G' and resid 132 through 135' Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.881A 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 75 removed outlier: 4.255A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 5.351A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 222 removed outlier: 3.608A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 295 through 307 removed outlier: 4.015A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 322 Processing helix chain 'J' and resid 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: 5.805A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 4.961A 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 'K' and resid 77 through 80 Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.392A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (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 removed outlier: 4.268A pdb=" N LYS L 73 " --> pdb=" O GLU L 70 " (cutoff:3.500A) 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: 3.909A 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: 3.884A 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 298 removed outlier: 4.992A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 332 Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 378 through 380 No H-bonds generated for 'chain 'M' and resid 378 through 380' Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 390 through 395 removed outlier: 3.742A pdb=" N VAL M 394 " --> pdb=" O THR M 390 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU M 395 " --> pdb=" O ILE M 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 390 through 395' Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 425 Processing helix chain 'M' and resid 449 through 456 Processing helix chain 'M' and resid 461 through 467 Processing helix chain 'M' and resid 478 through 481 Processing helix chain 'M' and resid 484 through 503 removed outlier: 4.581A pdb=" N THR M 487 " --> pdb=" O SER M 484 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER M 503 " --> pdb=" O ILE M 500 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 528 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.704A 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: 3.788A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 90 removed outlier: 4.202A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 198 through 209 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.458A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.780A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET P 173 " --> pdb=" O ILE P 170 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 41 through 47 removed outlier: 4.060A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 91 No H-bonds generated for 'chain 'Q' and resid 89 through 91' Processing helix chain 'Q' and resid 120 through 126 Processing helix chain 'Q' and resid 133 through 139 removed outlier: 3.851A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.521A 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: 3.862A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 262 removed outlier: 3.807A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.769A 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: 4.288A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 311 through 313 No H-bonds generated for 'chain 'Q' and resid 311 through 313' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 371 No H-bonds generated for 'chain 'Q' and resid 368 through 371' Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 438 removed outlier: 3.621A pdb=" N LEU Q 435 " --> pdb=" O HIS Q 431 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.497A 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 removed outlier: 3.557A pdb=" N ILE S 5 " --> pdb=" O TRP S 2 " (cutoff:3.500A) Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix removed outlier: 3.700A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'U' and resid 4 through 15 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 Processing helix chain 'U' and resid 79 through 82 No H-bonds generated for 'chain 'U' and resid 79 through 82' Processing helix chain 'V' and resid 3 through 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: 3.851A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 137 Processing helix chain 'W' and resid 139 through 142 No H-bonds generated for 'chain 'W' and resid 139 through 142' Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 137 removed outlier: 4.241A 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: 3.747A pdb=" N LEU Y 81 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Y' and resid 94 through 97 No H-bonds generated for 'chain 'Y' and resid 94 through 97' Processing helix chain 'Z' and resid 28 through 38 Processing helix chain 'Z' and resid 46 through 54 removed outlier: 4.618A pdb=" N TRP Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ARG Z 52 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR Z 53 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 26 Processing helix chain 'b' and resid 70 through 73 No H-bonds generated for 'chain 'b' and resid 70 through 73' Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'b' and resid 90 through 92 No H-bonds generated for 'chain 'b' and resid 90 through 92' Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 83 through 85 No H-bonds generated for 'chain 'c' and resid 83 through 85' Processing helix chain 'c' and resid 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: 5.003A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix removed outlier: 3.647A 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 116 Processing helix chain 'd' and resid 118 through 124 removed outlier: 3.724A pdb=" N TYR d 121 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ARG d 122 " --> pdb=" O GLU d 119 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN d 124 " --> pdb=" O TYR d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 175 Processing helix chain 'e' and resid 80 through 95 Processing helix chain 'e' and resid 98 through 107 Processing helix chain 'e' and resid 115 through 131 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 removed outlier: 3.883A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 44 Processing helix chain 'h' and resid 49 through 55 removed outlier: 4.079A pdb=" N LYS h 54 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'h' and resid 96 through 98 No H-bonds generated for 'chain 'h' and resid 96 through 98' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 45 Proline residue: i 42 - end of helix removed outlier: 3.979A 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: 4.248A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.827A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 171 removed outlier: 4.009A 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: 3.641A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 252 Processing helix chain 'i' and resid 258 through 272 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.325A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 3.990A 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: 3.967A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU j 68 " --> pdb=" O LEU j 64 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.581A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.462A 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: 4.025A 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 4 through 23 removed outlier: 3.621A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.998A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.501A pdb=" N VAL l 49 " --> pdb=" O THR l 45 " (cutoff:3.500A) Proline residue: l 50 - end of helix Processing helix chain 'l' and resid 84 through 107 Proline residue: l 91 - end of helix removed outlier: 3.808A 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: 3.913A 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: 4.086A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.126A 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 255 through 262 Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.190A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 3.764A pdb=" N ILE l 293 " --> pdb=" O ALA l 289 " (cutoff:3.500A) removed outlier: 4.863A 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: 4.171A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 380 Processing helix chain 'l' and resid 389 through 399 removed outlier: 4.899A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.913A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 471 removed outlier: 5.986A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 484 through 487 No H-bonds generated for 'chain 'l' and resid 484 through 487' Processing helix chain 'l' and resid 489 through 509 removed outlier: 3.642A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR l 509 " --> pdb=" O ASN l 505 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 526 through 533 Proline residue: l 530 - end of helix removed outlier: 4.101A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 Processing helix chain 'm' and resid 50 through 74 Processing helix chain 'm' and resid 87 through 109 Processing helix chain 'm' and resid 124 through 127 removed outlier: 3.773A pdb=" N ILE m 127 " --> pdb=" O ASP m 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 124 through 127' Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.241A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 4 through 14 removed outlier: 6.462A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 34 removed outlier: 3.683A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 20 through 22 No H-bonds generated for 'chain 'o' and resid 20 through 22' Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.709A 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 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 51 removed outlier: 4.390A 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: 4.312A pdb=" N CYS p 96 " --> pdb=" O ARG p 93 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 4.786A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 171 No H-bonds generated for 'chain 'p' and resid 168 through 171' Processing helix chain 'r' and resid 2 through 16 Proline residue: r 7 - end of helix Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.302A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 63 through 82 Proline residue: r 74 - end of helix removed outlier: 4.683A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 109 Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.819A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 140 through 171 removed outlier: 3.747A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE r 151 " --> pdb=" O TYR r 148 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 4.268A pdb=" N THR r 171 " --> pdb=" O GLN r 168 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.567A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.249A 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 248 removed outlier: 3.508A pdb=" N LEU r 238 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY r 239 " --> pdb=" O LEU r 236 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR r 247 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR r 248 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 254 through 257 No H-bonds generated for 'chain 'r' and resid 254 through 257' Processing helix chain 'r' and resid 259 through 277 removed outlier: 3.826A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 removed outlier: 3.579A pdb=" N ILE r 286 " --> pdb=" O LEU r 282 " (cutoff:3.500A) Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.619A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 351 No H-bonds generated for 'chain 'r' and resid 348 through 351' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 414 removed outlier: 3.550A pdb=" N ILE r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N MET r 396 " --> pdb=" O ILE r 393 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR r 403 " --> pdb=" O MET r 400 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA r 404 " --> pdb=" O MET r 401 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix Processing helix chain 'r' and resid 451 through 454 removed outlier: 3.554A pdb=" N ILE r 454 " --> pdb=" O PRO r 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 451 through 454' Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.769A 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: 4.344A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 3.992A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.043A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 Processing helix chain 's' and resid 174 through 176 No H-bonds generated for 'chain 's' and resid 174 through 176' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 204 through 207 No H-bonds generated for 'chain 's' and resid 204 through 207' Processing helix chain 's' and resid 210 through 212 No H-bonds generated for 'chain 's' and resid 210 through 212' Processing helix chain 's' and resid 217 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 291 removed outlier: 3.954A 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 10 through 13 Processing helix chain 'u' and resid 22 through 27 Processing helix chain 'u' and resid 29 through 35 Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 79 through 91 Processing helix chain 'u' and resid 102 through 115 Processing helix chain 'v' and resid 3 through 9 Processing helix chain 'v' and resid 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 81 through 123 Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 94 through 97 Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 166 through 175 removed outlier: 4.075A pdb=" N ARG w 175 " --> pdb=" O ALA w 172 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.327A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 252 removed outlier: 5.476A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix removed outlier: 3.964A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS w 252 " --> pdb=" O GLU w 248 " (cutoff:3.500A) Processing helix chain 'w' and resid 266 through 275 removed outlier: 3.856A pdb=" N TYR w 275 " --> pdb=" O GLU w 271 " (cutoff:3.500A) Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 309 removed outlier: 5.181A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 333 Processing helix chain 'w' and resid 341 through 343 No H-bonds generated for 'chain 'w' and resid 341 through 343' Processing helix chain 'w' and resid 345 through 347 No H-bonds generated for 'chain 'w' and resid 345 through 347' Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 240 through 244 removed outlier: 7.249A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.009A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.634A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.411A 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 56 removed outlier: 3.650A pdb=" N GLU F 18 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 8.025A pdb=" N PHE J 263 " --> pdb=" O ALA J 198 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU J 164 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE J 201 " --> pdb=" O LEU J 164 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N HIS J 166 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER J 168 " --> pdb=" O PRO J 203 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 228 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 removed outlier: 6.391A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL M 270 " --> pdb=" O ARG M 266 " (cutoff:3.500A) 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 366 through 368 removed outlier: 8.558A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.286A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.424A 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: 3.589A pdb=" N GLY N 40 " --> pdb=" O TYR N 48 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.662A 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: 6.605A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.926A 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: 6.771A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (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: 6.299A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.364A 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 76 through 78 removed outlier: 6.941A pdb=" N GLN T 117 " --> pdb=" O SER T 77 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y 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 62 through 67 removed outlier: 6.498A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'w' and resid 255 through 259 removed outlier: 6.469A pdb=" N VAL w 204 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N TYR w 258 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR w 206 " --> pdb=" O TYR w 258 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL w 157 " --> pdb=" O ILE w 60 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL w 62 " --> pdb=" O VAL w 157 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU w 159 " --> pdb=" O VAL w 62 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N GLY w 64 " --> pdb=" O LEU w 159 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG w 84 " --> pdb=" O VAL w 158 " (cutoff:3.500A) 2924 hydrogen bonds defined for protein. 8127 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: 23.05 Time building geometry restraints manager: 23.11 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: 27807 1.40 - 1.62: 41186 1.62 - 1.84: 876 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 69949 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 1.291 0.237 2.00e-02 2.50e+03 1.40e+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 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.26e+02 ... (remaining 69944 not shown) Histogram of bond angle deviations from ideal: 73.61 - 85.99: 76 85.99 - 98.37: 4 98.37 - 110.75: 23648 110.75 - 123.13: 67612 123.13 - 135.50: 3212 Bond angle restraints: 94552 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 107.74 123.92 -16.18 1.95e+00 2.62e-01 6.86e+01 angle pdb=" C11 CDL l 702 " pdb=" CA5 CDL l 702 " pdb=" OA6 CDL l 702 " ideal model delta sigma weight residual 111.33 121.44 -10.11 1.32e+00 5.72e-01 5.84e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 117.91 -14.07 1.91e+00 2.73e-01 5.40e+01 angle pdb=" C11 CDL l 703 " pdb=" CA5 CDL l 703 " pdb=" OA6 CDL l 703 " ideal model delta sigma weight residual 111.33 120.93 -9.60 1.32e+00 5.72e-01 5.27e+01 angle pdb=" N ARG P 125 " pdb=" CA ARG P 125 " pdb=" C ARG P 125 " ideal model delta sigma weight residual 111.28 118.96 -7.68 1.09e+00 8.42e-01 4.97e+01 ... (remaining 94547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 40617 35.00 - 70.00: 1813 70.00 - 105.00: 161 105.00 - 140.00: 21 140.00 - 175.00: 13 Dihedral angle restraints: 42625 sinusoidal: 18530 harmonic: 24095 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual -102.41 70.48 -172.89 1 2.00e+01 2.50e-03 4.78e+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 69.44 -129.44 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -136.02 50.02 1 1.00e+01 1.00e-02 3.43e+01 ... (remaining 42622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 9243 0.072 - 0.144: 911 0.144 - 0.216: 26 0.216 - 0.288: 8 0.288 - 0.360: 4 Chirality restraints: 10192 Sorted by residual: chirality pdb=" C3B NDP J 401 " pdb=" C2B NDP J 401 " pdb=" C4B NDP J 401 " pdb=" O3B NDP J 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA MET E 68 " pdb=" N MET E 68 " pdb=" C MET E 68 " pdb=" CB MET E 68 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 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 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 10189 not shown) Planarity restraints: 11778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 403 " 0.409 2.00e-02 2.50e+03 3.66e-01 1.68e+03 pdb=" C18 UQ s 403 " -0.409 2.00e-02 2.50e+03 pdb=" C19 UQ s 403 " -0.409 2.00e-02 2.50e+03 pdb=" C20 UQ s 403 " -0.001 2.00e-02 2.50e+03 pdb=" C21 UQ s 403 " 0.410 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ1 Q 501 " -0.364 2.00e-02 2.50e+03 3.20e-01 1.28e+03 pdb=" C11 UQ1 Q 501 " -0.000 2.00e-02 2.50e+03 pdb=" C7 UQ1 Q 501 " -0.350 2.00e-02 2.50e+03 pdb=" C8 UQ1 Q 501 " 0.339 2.00e-02 2.50e+03 pdb=" C9 UQ1 Q 501 " 0.376 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 403 " -0.064 2.00e-02 2.50e+03 2.54e-01 8.05e+02 pdb=" C11 UQ s 403 " 0.109 2.00e-02 2.50e+03 pdb=" C7 UQ s 403 " -0.232 2.00e-02 2.50e+03 pdb=" C8 UQ s 403 " 0.436 2.00e-02 2.50e+03 pdb=" C9 UQ s 403 " -0.248 2.00e-02 2.50e+03 ... (remaining 11775 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1594 2.70 - 3.25: 65517 3.25 - 3.80: 109639 3.80 - 4.35: 149775 4.35 - 4.90: 246367 Nonbonded interactions: 572892 Sorted by model distance: nonbonded pdb=" OG1 THR M 715 " pdb=" OE1 GLU M 716 " model vdw 2.149 2.440 nonbonded pdb=" OE1 GLU A 217 " pdb=" NH2 ARG L 171 " model vdw 2.203 2.520 nonbonded pdb=" O LEU i 128 " pdb=" OG1 THR i 132 " model vdw 2.204 2.440 nonbonded pdb=" OH TYR a 133 " pdb=" OE1 GLU d 87 " model vdw 2.212 2.440 nonbonded pdb=" OG SER K 103 " pdb=" O TRP L 166 " model vdw 2.219 2.440 ... (remaining 572887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 69 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 156 or resid 201)) selection = (chain 'X' and (resid 69 through 149 or (resid 150 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 156 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.67 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 8.570 Check model and map are aligned: 0.870 Set scattering table: 0.530 Process input model: 162.270 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 178.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.317 69949 Z= 0.502 Angle : 0.815 17.079 94552 Z= 0.407 Chirality : 0.043 0.360 10192 Planarity : 0.009 0.366 11778 Dihedral : 18.856 174.999 27066 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 0.24 % Allowed : 16.56 % Favored : 83.20 % 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: 1.04 (0.09), residues: 8173 helix: 1.77 (0.08), residues: 4275 sheet: 0.03 (0.24), residues: 451 loop : -0.59 (0.11), residues: 3447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.005 0.001 HIS J 37 PHE 0.036 0.001 PHE i 292 TYR 0.024 0.001 TYR l 422 ARG 0.009 0.000 ARG J 299 *********************** 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 1156 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1139 time to evaluate : 7.056 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: I 41 LEU cc_start: 0.8891 (mp) cc_final: 0.8690 (mt) REVERT: N 12 GLN cc_start: 0.7327 (tp40) cc_final: 0.6980 (mt0) REVERT: Q 62 LYS cc_start: 0.7408 (tppt) cc_final: 0.7058 (tptm) REVERT: Z 14 MET cc_start: 0.2856 (ttt) cc_final: 0.2421 (ttt) REVERT: e 77 ASP cc_start: 0.8419 (t0) cc_final: 0.8195 (t0) REVERT: i 98 MET cc_start: 0.9105 (tpp) cc_final: 0.8682 (tpp) REVERT: l 571 MET cc_start: 0.9184 (ttp) cc_final: 0.8838 (ttm) REVERT: o 24 ASP cc_start: 0.7527 (t0) cc_final: 0.7283 (t0) REVERT: o 117 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7472 (mm-40) REVERT: p 65 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7612 (ttm170) REVERT: u 68 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8140 (mp) outliers start: 17 outliers final: 9 residues processed: 1148 average time/residue: 0.6886 time to fit residues: 1330.4141 Evaluate side-chains 1107 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1096 time to evaluate : 5.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain m residue 74 MET Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 65 ARG Chi-restraints excluded: chain s residue 38 ASN Chi-restraints excluded: chain u residue 68 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 679 optimal weight: 5.9990 chunk 610 optimal weight: 0.9980 chunk 338 optimal weight: 0.8980 chunk 208 optimal weight: 0.3980 chunk 411 optimal weight: 0.8980 chunk 325 optimal weight: 8.9990 chunk 630 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 383 optimal weight: 2.9990 chunk 469 optimal weight: 0.9980 chunk 731 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS I 25 GLN K 75 ASN K 78 HIS ** M 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 154 GLN e 132 ASN g 81 GLN u 77 HIS ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.0422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 69949 Z= 0.151 Angle : 0.512 10.698 94552 Z= 0.255 Chirality : 0.040 0.209 10192 Planarity : 0.004 0.066 11778 Dihedral : 14.961 172.901 10886 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 1.62 % Allowed : 15.79 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.09), residues: 8173 helix: 1.89 (0.08), residues: 4273 sheet: 0.18 (0.25), residues: 439 loop : -0.48 (0.11), residues: 3461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.005 0.001 HIS r 30 PHE 0.033 0.001 PHE i 292 TYR 0.021 0.001 TYR l 422 ARG 0.006 0.000 ARG h 32 *********************** 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 1252 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1136 time to evaluate : 5.902 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 90 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7897 (t80) REVERT: K 98 MET cc_start: 0.8245 (mmm) cc_final: 0.7547 (mmm) REVERT: N 12 GLN cc_start: 0.7184 (tp40) cc_final: 0.6913 (mt0) REVERT: Q 62 LYS cc_start: 0.7374 (tppt) cc_final: 0.7049 (tptm) REVERT: S 59 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7692 (mtt90) REVERT: W 51 MET cc_start: 0.8413 (ttp) cc_final: 0.8206 (ptt) REVERT: d 78 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7137 (mt-10) REVERT: e 77 ASP cc_start: 0.8440 (t0) cc_final: 0.8115 (t0) REVERT: e 90 VAL cc_start: 0.9149 (t) cc_final: 0.8903 (t) REVERT: i 18 MET cc_start: 0.8634 (mmm) cc_final: 0.8370 (mmp) REVERT: i 89 MET cc_start: 0.8587 (ttt) cc_final: 0.8056 (ttt) REVERT: i 98 MET cc_start: 0.8969 (tpp) cc_final: 0.8597 (tpp) REVERT: l 59 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: l 140 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8693 (tt) REVERT: l 338 MET cc_start: 0.8937 (ttp) cc_final: 0.8425 (ttt) REVERT: o 24 ASP cc_start: 0.7446 (t0) cc_final: 0.7233 (t0) REVERT: o 117 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7413 (mm-40) REVERT: p 159 LYS cc_start: 0.7597 (ttmt) cc_final: 0.7389 (ttmm) REVERT: s 155 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8348 (tt) REVERT: w 45 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7041 (pp) REVERT: w 105 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7660 (m-30) outliers start: 116 outliers final: 64 residues processed: 1204 average time/residue: 0.6611 time to fit residues: 1369.7520 Evaluate side-chains 1160 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1089 time to evaluate : 5.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 90 TYR Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 212 ARG Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 50 MET Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 154 GLN Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 113 CYS Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 22 SER Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 46 ASN Chi-restraints excluded: chain m residue 74 MET Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain n residue 28 ASP Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 274 SER Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 285 LEU Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain s residue 178 SER Chi-restraints excluded: chain s residue 209 SER Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 118 VAL Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 81 LEU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 105 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 406 optimal weight: 0.9990 chunk 226 optimal weight: 20.0000 chunk 608 optimal weight: 0.0470 chunk 497 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 chunk 732 optimal weight: 0.0070 chunk 791 optimal weight: 8.9990 chunk 652 optimal weight: 8.9990 chunk 726 optimal weight: 0.9990 chunk 249 optimal weight: 4.9990 chunk 587 optimal weight: 7.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS F 93 ASN I 25 GLN K 75 ASN M 498 GLN P 77 GLN ** T 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 132 ASN i 171 ASN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 69949 Z= 0.132 Angle : 0.485 10.659 94552 Z= 0.242 Chirality : 0.039 0.215 10192 Planarity : 0.004 0.062 11778 Dihedral : 13.789 173.476 10863 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 1.66 % Allowed : 16.39 % Favored : 81.94 % 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: 1.34 (0.10), residues: 8173 helix: 2.00 (0.08), residues: 4262 sheet: 0.32 (0.25), residues: 438 loop : -0.43 (0.11), residues: 3473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.006 0.001 HIS K 78 PHE 0.032 0.001 PHE i 292 TYR 0.021 0.001 TYR l 422 ARG 0.006 0.000 ARG J 299 *********************** 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 1272 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1153 time to evaluate : 5.967 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: G 139 MET cc_start: 0.7396 (tpp) cc_final: 0.7107 (mmm) REVERT: H 94 MET cc_start: 0.8952 (mmm) cc_final: 0.8719 (mmm) REVERT: K 98 MET cc_start: 0.8237 (mmm) cc_final: 0.7545 (mmm) REVERT: M 643 ARG cc_start: 0.8581 (mtt180) cc_final: 0.8328 (mtt180) REVERT: S 54 ILE cc_start: 0.9102 (mm) cc_final: 0.8868 (mm) REVERT: S 59 ARG cc_start: 0.7904 (mtt90) cc_final: 0.7679 (mtt90) REVERT: Z 14 MET cc_start: 0.2899 (ttt) cc_final: 0.2419 (ttt) REVERT: e 77 ASP cc_start: 0.8419 (t0) cc_final: 0.8146 (t0) REVERT: i 89 MET cc_start: 0.8605 (ttt) cc_final: 0.8178 (ttt) REVERT: j 97 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8709 (mt) REVERT: l 140 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8646 (tt) REVERT: l 338 MET cc_start: 0.8928 (ttp) cc_final: 0.8446 (ttt) REVERT: l 486 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8239 (ttm) REVERT: o 24 ASP cc_start: 0.7422 (t0) cc_final: 0.7192 (t0) REVERT: p 159 LYS cc_start: 0.7503 (ttmt) cc_final: 0.7217 (ttmm) REVERT: r 340 ARG cc_start: 0.9040 (mtm-85) cc_final: 0.8839 (mtm-85) REVERT: s 155 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8367 (tt) REVERT: v 39 MET cc_start: 0.8159 (tpt) cc_final: 0.7851 (tpt) REVERT: w 45 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.6969 (pp) REVERT: w 105 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7656 (m-30) outliers start: 119 outliers final: 70 residues processed: 1217 average time/residue: 0.6857 time to fit residues: 1417.2401 Evaluate side-chains 1167 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1091 time to evaluate : 5.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 326 ASP Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 113 CYS Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 74 MET Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain n residue 28 ASP Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 274 SER Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 285 LEU Chi-restraints excluded: chain r residue 299 VAL Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 98 MET Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain s residue 178 SER Chi-restraints excluded: chain s residue 209 SER Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 118 VAL Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 81 LEU Chi-restraints excluded: chain w residue 105 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 7.9990 chunk 550 optimal weight: 9.9990 chunk 380 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 349 optimal weight: 3.9990 chunk 491 optimal weight: 7.9990 chunk 734 optimal weight: 6.9990 chunk 778 optimal weight: 9.9990 chunk 383 optimal weight: 10.0000 chunk 696 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS F 93 ASN I 25 GLN J 37 HIS ** M 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN c 154 GLN d 134 GLN e 132 ASN ** g 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 268 GLN r 81 GLN r 251 ASN r 304 GLN u 73 GLN u 99 HIS ** w 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 300 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 69949 Z= 0.550 Angle : 0.712 13.699 94552 Z= 0.357 Chirality : 0.050 0.224 10192 Planarity : 0.006 0.074 11778 Dihedral : 14.339 175.508 10863 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 3.02 % Allowed : 15.77 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.09), residues: 8173 helix: 1.36 (0.08), residues: 4284 sheet: 0.13 (0.25), residues: 412 loop : -0.75 (0.10), residues: 3477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP u 86 HIS 0.011 0.002 HIS J 37 PHE 0.031 0.003 PHE i 292 TYR 0.030 0.003 TYR l 587 ARG 0.009 0.001 ARG B 98 *********************** 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 1317 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1101 time to evaluate : 5.785 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 65 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8139 (pm20) REVERT: B 110 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8838 (tp30) REVERT: E 87 LYS cc_start: 0.8893 (tptt) cc_final: 0.8494 (ttmt) REVERT: G 117 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8146 (mt-10) REVERT: G 128 PHE cc_start: 0.8076 (p90) cc_final: 0.7674 (p90) REVERT: G 139 MET cc_start: 0.7754 (tpp) cc_final: 0.7419 (mmm) REVERT: I 27 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8797 (ptt90) REVERT: J 113 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8861 (mmtt) REVERT: K 98 MET cc_start: 0.8367 (mmm) cc_final: 0.7769 (mmm) REVERT: O 219 ARG cc_start: 0.7724 (mtp85) cc_final: 0.7496 (mtp85) REVERT: P 125 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8169 (ttp80) REVERT: Q 308 TYR cc_start: 0.9239 (OUTLIER) cc_final: 0.8405 (p90) REVERT: S 64 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8524 (mmtm) REVERT: W 51 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8485 (ptt) REVERT: c 57 MET cc_start: 0.9265 (mtp) cc_final: 0.9013 (mtm) REVERT: c 81 ARG cc_start: 0.8665 (mmm-85) cc_final: 0.8414 (mtp85) REVERT: c 154 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8751 (tp40) REVERT: d 78 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: h 24 GLU cc_start: 0.7976 (tp30) cc_final: 0.7502 (tp30) REVERT: j 16 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8625 (mm) REVERT: j 109 LYS cc_start: 0.8174 (mmtp) cc_final: 0.7917 (mmtm) REVERT: l 140 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8938 (tt) REVERT: l 338 MET cc_start: 0.9030 (ttp) cc_final: 0.8634 (ttt) REVERT: l 571 MET cc_start: 0.9203 (ttp) cc_final: 0.8869 (ttm) REVERT: m 135 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: o 24 ASP cc_start: 0.7351 (t0) cc_final: 0.7132 (t0) REVERT: p 57 MET cc_start: 0.7561 (mmp) cc_final: 0.7317 (mmp) REVERT: p 59 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8355 (tttp) REVERT: p 159 LYS cc_start: 0.7710 (ttmt) cc_final: 0.7421 (ttmm) REVERT: r 1 MET cc_start: 0.8209 (ptm) cc_final: 0.8008 (ptm) REVERT: w 45 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7382 (pp) REVERT: w 105 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: w 241 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.6413 (t80) outliers start: 216 outliers final: 139 residues processed: 1227 average time/residue: 0.6961 time to fit residues: 1441.6600 Evaluate side-chains 1219 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1065 time to evaluate : 5.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 212 ARG Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain J residue 366 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 320 GLU Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 633 THR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 125 ARG Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 279 THR Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 25 GLU Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 125 SER Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 154 GLN Chi-restraints excluded: chain c residue 164 ASN Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 113 CYS Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 102 ASP Chi-restraints excluded: chain h residue 22 SER Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 73 MET Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 42 ASP Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 3 LEU 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 59 GLN Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 229 LEU Chi-restraints excluded: chain l residue 393 ASP Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 423 SER Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 572 LYS Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 11 THR Chi-restraints excluded: chain m residue 46 ASN Chi-restraints excluded: chain m residue 74 MET Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 160 SER Chi-restraints excluded: chain n residue 28 ASP Chi-restraints excluded: chain o residue 22 GLU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 205 VAL Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 274 SER Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 285 LEU Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 98 MET Chi-restraints excluded: chain s residue 178 SER Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 118 VAL Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 70 LYS Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 81 LEU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 105 ASP Chi-restraints excluded: chain w residue 230 THR Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 0.9990 chunk 441 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 579 optimal weight: 5.9990 chunk 321 optimal weight: 0.7980 chunk 664 optimal weight: 0.7980 chunk 537 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 397 optimal weight: 0.8980 chunk 698 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 37 GLN I 25 GLN K 75 ASN M 498 GLN O 187 GLN P 77 GLN ** T 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 59 ASN h 21 GLN i 171 ASN s 304 HIS u 77 HIS w 107 GLN w 300 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 69949 Z= 0.165 Angle : 0.516 10.529 94552 Z= 0.260 Chirality : 0.040 0.171 10192 Planarity : 0.004 0.063 11778 Dihedral : 13.388 174.456 10863 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.45 % Rotamer: Outliers : 1.82 % Allowed : 16.94 % Favored : 81.25 % 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: 1.04 (0.09), residues: 8173 helix: 1.73 (0.08), residues: 4287 sheet: 0.08 (0.24), residues: 455 loop : -0.53 (0.11), residues: 3431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.005 0.001 HIS K 78 PHE 0.031 0.001 PHE i 292 TYR 0.020 0.001 TYR r 406 ARG 0.007 0.000 ARG J 299 *********************** 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 1270 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1140 time to evaluate : 5.837 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: B 65 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7519 (pm20) REVERT: B 110 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8780 (tp30) REVERT: E 87 LYS cc_start: 0.8784 (tptt) cc_final: 0.8460 (ttmt) REVERT: G 139 MET cc_start: 0.7691 (tpp) cc_final: 0.7327 (mmm) REVERT: J 113 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8751 (mmtt) REVERT: K 98 MET cc_start: 0.8256 (mmm) cc_final: 0.7649 (mmm) REVERT: L 78 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8272 (ttt90) REVERT: L 148 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7816 (mt-10) REVERT: M 483 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.7434 (ptm160) REVERT: M 636 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7855 (p90) REVERT: O 219 ARG cc_start: 0.7727 (mtp85) cc_final: 0.7520 (mtp85) REVERT: Q 101 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8848 (mt) REVERT: Q 185 MET cc_start: 0.9361 (tpp) cc_final: 0.9093 (tpt) REVERT: Q 308 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.8406 (p90) REVERT: S 64 LYS cc_start: 0.8665 (mmtt) cc_final: 0.8333 (mmtm) REVERT: S 67 GLU cc_start: 0.8138 (pm20) cc_final: 0.7855 (pm20) REVERT: V 58 ARG cc_start: 0.8496 (ttp80) cc_final: 0.8294 (ttp80) REVERT: W 9 ASP cc_start: 0.9150 (t0) cc_final: 0.8844 (t0) REVERT: X 106 LYS cc_start: 0.8028 (mttt) cc_final: 0.7634 (mttp) REVERT: d 78 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7111 (mt-10) REVERT: e 83 ASP cc_start: 0.8361 (t0) cc_final: 0.8106 (t0) REVERT: j 16 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8631 (mm) REVERT: l 140 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8738 (tt) REVERT: l 338 MET cc_start: 0.8988 (ttp) cc_final: 0.8669 (ttt) REVERT: m 135 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: o 24 ASP cc_start: 0.7654 (t0) cc_final: 0.7343 (t0) REVERT: p 57 MET cc_start: 0.7387 (mmp) cc_final: 0.7124 (mmp) REVERT: p 159 LYS cc_start: 0.7798 (ttmt) cc_final: 0.7582 (ttmt) REVERT: s 24 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8069 (tp30) REVERT: v 81 LYS cc_start: 0.8219 (mmmt) cc_final: 0.7964 (mttt) REVERT: w 45 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7101 (pp) REVERT: w 105 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7544 (m-30) REVERT: w 241 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.6386 (t80) outliers start: 130 outliers final: 81 residues processed: 1220 average time/residue: 0.6659 time to fit residues: 1370.5946 Evaluate side-chains 1197 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1101 time to evaluate : 5.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 212 ARG Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 563 ASP Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 52 ARG Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 125 SER Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 113 CYS Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain h residue 22 SER Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 453 SER Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain m residue 74 MET Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 28 ASP Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 274 SER Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 285 LEU Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain s residue 178 SER Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 81 LEU Chi-restraints excluded: chain w residue 105 ASP Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 0.0570 chunk 700 optimal weight: 6.9990 chunk 153 optimal weight: 0.5980 chunk 456 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 chunk 778 optimal weight: 10.0000 chunk 646 optimal weight: 3.9990 chunk 360 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 chunk 408 optimal weight: 7.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN H 37 GLN I 25 GLN P 77 GLN e 132 ASN h 21 GLN ** w 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 69949 Z= 0.155 Angle : 0.504 10.661 94552 Z= 0.252 Chirality : 0.040 0.259 10192 Planarity : 0.004 0.063 11778 Dihedral : 12.816 172.212 10863 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 1.89 % Allowed : 16.99 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.09), residues: 8173 helix: 1.85 (0.08), residues: 4284 sheet: 0.17 (0.24), residues: 455 loop : -0.45 (0.11), residues: 3434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.005 0.001 HIS K 78 PHE 0.032 0.001 PHE i 292 TYR 0.022 0.001 TYR l 422 ARG 0.008 0.000 ARG J 299 *********************** 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 1265 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1130 time to evaluate : 5.804 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: B 65 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7531 (pm20) REVERT: B 110 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8760 (tp30) REVERT: E 87 LYS cc_start: 0.8783 (tptt) cc_final: 0.8460 (ttmt) REVERT: I 27 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8770 (ptt90) REVERT: I 41 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8558 (mp) REVERT: K 98 MET cc_start: 0.8242 (mmm) cc_final: 0.7612 (mmm) REVERT: L 148 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7881 (mt-10) REVERT: M 483 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7333 (ptm160) REVERT: M 636 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7815 (p90) REVERT: Q 60 HIS cc_start: 0.6478 (m-70) cc_final: 0.6214 (m-70) REVERT: Q 101 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8860 (mt) REVERT: Q 185 MET cc_start: 0.9348 (tpp) cc_final: 0.9062 (tpt) REVERT: Q 308 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.8368 (p90) REVERT: S 67 GLU cc_start: 0.8118 (pm20) cc_final: 0.7853 (pm20) REVERT: T 122 HIS cc_start: 0.5661 (p90) cc_final: 0.4131 (m-70) REVERT: W 9 ASP cc_start: 0.9133 (t0) cc_final: 0.8821 (t0) REVERT: X 106 LYS cc_start: 0.7950 (mttt) cc_final: 0.7616 (mttp) REVERT: b 93 LYS cc_start: 0.8114 (mtmt) cc_final: 0.7866 (mttp) REVERT: d 78 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: j 16 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8625 (mm) REVERT: l 140 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8709 (tt) REVERT: l 338 MET cc_start: 0.8986 (ttp) cc_final: 0.8647 (ttt) REVERT: m 135 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: o 24 ASP cc_start: 0.7620 (t0) cc_final: 0.7328 (t0) REVERT: p 57 MET cc_start: 0.7407 (mmp) cc_final: 0.7142 (mmp) REVERT: p 159 LYS cc_start: 0.7814 (ttmt) cc_final: 0.7556 (ttmm) REVERT: r 152 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.8776 (m-80) REVERT: s 24 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8161 (tp30) REVERT: v 36 GLU cc_start: 0.7595 (tt0) cc_final: 0.7358 (tt0) REVERT: v 81 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7889 (mmtp) REVERT: w 45 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7053 (pp) REVERT: w 105 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7533 (m-30) REVERT: w 241 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.6524 (t80) outliers start: 135 outliers final: 95 residues processed: 1218 average time/residue: 0.6714 time to fit residues: 1381.5896 Evaluate side-chains 1209 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1097 time to evaluate : 5.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 90 TYR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 212 ARG Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 563 ASP Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 52 ARG Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 123 GLU Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 125 SER Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 113 CYS Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 22 SER Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain i residue 318 GLU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 453 SER Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 28 ASP Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 152 TYR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 274 SER Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 285 LEU Chi-restraints excluded: chain r residue 299 VAL Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain s residue 178 SER Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 81 LEU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 105 ASP Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 443 optimal weight: 4.9990 chunk 568 optimal weight: 5.9990 chunk 440 optimal weight: 2.9990 chunk 655 optimal weight: 5.9990 chunk 434 optimal weight: 6.9990 chunk 775 optimal weight: 10.0000 chunk 485 optimal weight: 7.9990 chunk 473 optimal weight: 10.0000 chunk 358 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS H 37 GLN O 187 GLN e 132 ASN ** g 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN u 73 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.122 69949 Z= 0.507 Angle : 0.689 13.472 94552 Z= 0.345 Chirality : 0.049 0.250 10192 Planarity : 0.006 0.079 11778 Dihedral : 13.500 170.675 10860 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 2.71 % Allowed : 16.77 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.09), residues: 8173 helix: 1.37 (0.08), residues: 4285 sheet: -0.01 (0.25), residues: 428 loop : -0.74 (0.11), residues: 3460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP u 86 HIS 0.009 0.002 HIS r 30 PHE 0.033 0.002 PHE i 292 TYR 0.031 0.002 TYR l 587 ARG 0.009 0.001 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1282 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1088 time to evaluate : 5.906 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: B 65 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8036 (pm20) REVERT: B 110 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8840 (tp30) REVERT: E 87 LYS cc_start: 0.8885 (tptt) cc_final: 0.8483 (ttmt) REVERT: I 27 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8835 (ptt90) REVERT: K 98 MET cc_start: 0.8357 (mmm) cc_final: 0.7769 (mmm) REVERT: M 483 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.7078 (ptm160) REVERT: M 636 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.7922 (p90) REVERT: Q 60 HIS cc_start: 0.6582 (m-70) cc_final: 0.6333 (m-70) REVERT: Q 68 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7412 (m-30) REVERT: Q 101 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9083 (mt) REVERT: Q 308 TYR cc_start: 0.9247 (OUTLIER) cc_final: 0.8427 (p90) REVERT: S 68 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8664 (m-40) REVERT: X 106 LYS cc_start: 0.7987 (mttt) cc_final: 0.7613 (mttp) REVERT: Z 14 MET cc_start: 0.2706 (ttt) cc_final: 0.2343 (ttt) REVERT: c 57 MET cc_start: 0.9310 (mtp) cc_final: 0.9025 (mtm) REVERT: d 78 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7224 (mt-10) REVERT: e 145 ASN cc_start: 0.8684 (p0) cc_final: 0.8358 (p0) REVERT: f 67 LEU cc_start: 0.8588 (tt) cc_final: 0.8335 (tp) REVERT: j 16 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8583 (mm) REVERT: l 59 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8470 (tt0) REVERT: l 140 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8915 (tt) REVERT: l 338 MET cc_start: 0.9088 (ttp) cc_final: 0.8759 (ttt) REVERT: l 571 MET cc_start: 0.9197 (ttp) cc_final: 0.8877 (ttm) REVERT: m 135 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8046 (m-80) REVERT: o 24 ASP cc_start: 0.7588 (t0) cc_final: 0.7317 (t0) REVERT: o 30 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8332 (mmt-90) REVERT: p 57 MET cc_start: 0.7553 (mmp) cc_final: 0.7345 (mmp) REVERT: s 24 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8135 (tp30) REVERT: s 59 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: s 225 MET cc_start: 0.8489 (mtt) cc_final: 0.8276 (mtt) REVERT: u 78 CYS cc_start: 0.6779 (m) cc_final: 0.6433 (t) REVERT: w 45 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7352 (pp) REVERT: w 105 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7587 (m-30) outliers start: 194 outliers final: 143 residues processed: 1203 average time/residue: 0.6718 time to fit residues: 1363.1384 Evaluate side-chains 1219 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1057 time to evaluate : 5.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 90 TYR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 212 ARG Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain J residue 366 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 563 ASP Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 253 PHE Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain T residue 52 ARG Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 50 MET Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 25 GLU Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 123 PHE Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 125 SER Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 164 ASN Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 4 SER Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 113 CYS Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain h residue 22 SER Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 42 ASP Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 127 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 267 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 453 SER Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 11 THR Chi-restraints excluded: chain m residue 46 ASN Chi-restraints excluded: chain m residue 74 MET Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 160 SER Chi-restraints excluded: chain n residue 28 ASP Chi-restraints excluded: chain o residue 30 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 274 SER Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 285 LEU Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 178 SER Chi-restraints excluded: chain s residue 271 LEU Chi-restraints excluded: chain s residue 313 SER Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 153 GLU Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 70 LYS Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 81 LEU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 105 ASP Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 480 optimal weight: 0.8980 chunk 309 optimal weight: 2.9990 chunk 463 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 493 optimal weight: 4.9990 chunk 528 optimal weight: 0.8980 chunk 383 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 609 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 37 GLN M 260 ASN M 278 HIS O 187 GLN P 77 GLN ** T 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 122 HIS h 21 GLN r 338 HIS u 16 GLN u 77 HIS w 107 GLN ** w 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 300 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 69949 Z= 0.162 Angle : 0.522 10.638 94552 Z= 0.263 Chirality : 0.040 0.304 10192 Planarity : 0.004 0.064 11778 Dihedral : 12.717 170.679 10860 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 1.93 % Allowed : 17.55 % Favored : 80.52 % 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: 1.69 (0.08), residues: 4301 sheet: 0.07 (0.24), residues: 459 loop : -0.53 (0.11), residues: 3413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.005 0.001 HIS A 133 PHE 0.031 0.001 PHE i 292 TYR 0.020 0.001 TYR l 422 ARG 0.009 0.000 ARG J 299 *********************** 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 1246 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1108 time to evaluate : 5.856 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: B 65 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: B 110 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8800 (tp30) REVERT: E 87 LYS cc_start: 0.8780 (tptt) cc_final: 0.8455 (ttmt) REVERT: I 27 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8844 (ptt90) REVERT: K 98 MET cc_start: 0.8237 (mmm) cc_final: 0.7631 (mmm) REVERT: M 271 MET cc_start: 0.9233 (mmp) cc_final: 0.9005 (mmp) REVERT: M 483 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7293 (ptm160) REVERT: M 636 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7899 (p90) REVERT: P 125 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8219 (ttt180) REVERT: Q 60 HIS cc_start: 0.6460 (m-70) cc_final: 0.6209 (m-70) REVERT: Q 101 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8885 (mt) REVERT: Q 185 MET cc_start: 0.9343 (tpp) cc_final: 0.9058 (tpt) REVERT: Q 308 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.8455 (p90) REVERT: W 9 ASP cc_start: 0.9163 (t0) cc_final: 0.8853 (t0) REVERT: X 106 LYS cc_start: 0.7821 (mttt) cc_final: 0.7544 (mttp) REVERT: Y 88 ASP cc_start: 0.8088 (t0) cc_final: 0.7769 (t70) REVERT: Z 14 MET cc_start: 0.2452 (ttt) cc_final: 0.2155 (ttt) REVERT: b 93 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7907 (mttp) REVERT: c 57 MET cc_start: 0.9183 (mtp) cc_final: 0.8927 (mtm) REVERT: d 78 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7140 (mt-10) REVERT: j 16 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8531 (mm) REVERT: l 140 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8763 (tt) REVERT: l 338 MET cc_start: 0.8976 (ttp) cc_final: 0.8605 (ttt) REVERT: m 87 LYS cc_start: 0.8321 (mtmt) cc_final: 0.7595 (tmtt) REVERT: m 135 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: o 30 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8172 (mmt-90) REVERT: p 57 MET cc_start: 0.7305 (mmp) cc_final: 0.7094 (mmp) REVERT: s 24 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8111 (tp30) REVERT: v 81 LYS cc_start: 0.8191 (mmmt) cc_final: 0.7988 (mttt) REVERT: w 45 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7131 (pp) REVERT: w 105 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: w 241 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.6438 (t80) outliers start: 138 outliers final: 107 residues processed: 1196 average time/residue: 0.6770 time to fit residues: 1367.7895 Evaluate side-chains 1201 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1077 time to evaluate : 5.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 212 ARG Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 563 ASP Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 125 ARG Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 52 ARG Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 25 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain b residue 123 PHE Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 125 SER Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 113 CYS Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 22 SER Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 453 SER Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 28 ASP Chi-restraints excluded: chain o residue 30 ARG Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 274 SER Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 285 LEU Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain s residue 178 SER Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 153 GLU Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 81 LEU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 105 ASP Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 0.7980 chunk 743 optimal weight: 0.9990 chunk 678 optimal weight: 3.9990 chunk 723 optimal weight: 4.9990 chunk 435 optimal weight: 1.9990 chunk 314 optimal weight: 4.9990 chunk 567 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 chunk 653 optimal weight: 3.9990 chunk 683 optimal weight: 4.9990 chunk 720 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 37 GLN P 77 GLN T 122 HIS h 21 GLN u 77 HIS w 107 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 69949 Z= 0.173 Angle : 0.519 11.050 94552 Z= 0.260 Chirality : 0.040 0.316 10192 Planarity : 0.004 0.063 11778 Dihedral : 12.294 171.778 10860 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.17 % Favored : 95.79 % Rotamer: Outliers : 1.84 % Allowed : 17.83 % Favored : 80.32 % 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: 1.16 (0.09), residues: 8173 helix: 1.82 (0.08), residues: 4280 sheet: 0.13 (0.25), residues: 456 loop : -0.47 (0.11), residues: 3437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.006 0.001 HIS A 133 PHE 0.032 0.001 PHE i 292 TYR 0.022 0.001 TYR l 422 ARG 0.009 0.000 ARG J 299 *********************** 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 1246 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1114 time to evaluate : 5.831 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: B 65 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: B 110 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8736 (tp30) REVERT: E 87 LYS cc_start: 0.8780 (tptt) cc_final: 0.8451 (ttmt) REVERT: I 27 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8782 (ptt90) REVERT: J 298 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7595 (t80) REVERT: K 98 MET cc_start: 0.8290 (mmm) cc_final: 0.7649 (mmm) REVERT: M 483 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.7206 (ptm160) REVERT: M 636 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.7871 (p90) REVERT: M 673 LYS cc_start: 0.7877 (ptpt) cc_final: 0.7337 (mtmt) REVERT: P 125 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8184 (ttt180) REVERT: Q 60 HIS cc_start: 0.6393 (m-70) cc_final: 0.6134 (m-70) REVERT: Q 62 LYS cc_start: 0.7472 (tppt) cc_final: 0.7182 (tptm) REVERT: Q 101 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8852 (mt) REVERT: Q 185 MET cc_start: 0.9379 (tpp) cc_final: 0.9081 (tpt) REVERT: Q 308 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.8418 (p90) REVERT: W 9 ASP cc_start: 0.9147 (t0) cc_final: 0.8831 (t0) REVERT: X 106 LYS cc_start: 0.7919 (mttt) cc_final: 0.7677 (mttp) REVERT: Y 88 ASP cc_start: 0.8134 (t0) cc_final: 0.7818 (t70) REVERT: Z 14 MET cc_start: 0.2491 (ttt) cc_final: 0.2211 (ttt) REVERT: b 93 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7902 (mttp) REVERT: c 57 MET cc_start: 0.9167 (mtp) cc_final: 0.8929 (mtm) REVERT: d 78 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7145 (mt-10) REVERT: j 16 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8539 (mm) REVERT: j 109 LYS cc_start: 0.8147 (mmtp) cc_final: 0.7844 (mmtt) REVERT: l 1 MET cc_start: 0.6574 (OUTLIER) cc_final: 0.5738 (tmm) REVERT: l 140 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8755 (tt) REVERT: l 338 MET cc_start: 0.8952 (ttp) cc_final: 0.8602 (ttt) REVERT: m 87 LYS cc_start: 0.8332 (mtmt) cc_final: 0.7643 (tmtt) REVERT: m 135 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7941 (m-80) REVERT: o 30 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8184 (mmt-90) REVERT: p 57 MET cc_start: 0.7361 (mmp) cc_final: 0.7142 (mmp) REVERT: s 24 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8108 (tp30) REVERT: s 59 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8266 (pt0) REVERT: v 81 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7919 (mmtp) REVERT: w 45 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7103 (pp) REVERT: w 105 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: w 241 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.6453 (t80) outliers start: 132 outliers final: 101 residues processed: 1195 average time/residue: 0.6646 time to fit residues: 1336.8132 Evaluate side-chains 1213 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1092 time to evaluate : 5.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 212 ARG Chi-restraints excluded: chain J residue 298 TYR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 563 ASP Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 125 ARG Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 52 ARG Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 25 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain b residue 123 PHE Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 125 SER Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 113 CYS Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 22 SER Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 267 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 453 SER Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 46 ASN Chi-restraints excluded: chain m residue 74 MET Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 28 ASP Chi-restraints excluded: chain o residue 30 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 274 SER Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 285 LEU Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain s residue 178 SER Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 153 GLU Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 81 LEU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 105 ASP Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 474 optimal weight: 6.9990 chunk 764 optimal weight: 9.9990 chunk 466 optimal weight: 5.9990 chunk 362 optimal weight: 0.7980 chunk 531 optimal weight: 0.9980 chunk 801 optimal weight: 6.9990 chunk 738 optimal weight: 0.0980 chunk 638 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 493 optimal weight: 6.9990 chunk 391 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 37 GLN P 77 GLN T 122 HIS g 81 GLN u 77 HIS w 107 GLN ** w 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 69949 Z= 0.168 Angle : 0.518 14.503 94552 Z= 0.259 Chirality : 0.040 0.322 10192 Planarity : 0.004 0.063 11778 Dihedral : 12.048 171.765 10860 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 1.84 % Allowed : 17.78 % Favored : 80.38 % 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: 1.20 (0.10), residues: 8173 helix: 1.84 (0.08), residues: 4280 sheet: 0.15 (0.24), residues: 461 loop : -0.44 (0.11), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.007 0.001 HIS A 133 PHE 0.032 0.001 PHE i 292 TYR 0.022 0.001 TYR l 422 ARG 0.009 0.000 ARG J 299 ********************** 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 1233 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1101 time to evaluate : 5.885 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 65 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7529 (pm20) REVERT: B 110 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8737 (tp30) REVERT: E 87 LYS cc_start: 0.8768 (tptt) cc_final: 0.8429 (ttmt) REVERT: H 94 MET cc_start: 0.8938 (mmm) cc_final: 0.8630 (mmm) REVERT: I 27 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8735 (ptt90) REVERT: K 98 MET cc_start: 0.8269 (mmm) cc_final: 0.7626 (mmm) REVERT: M 483 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7275 (ptm160) REVERT: M 636 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7862 (p90) REVERT: M 673 LYS cc_start: 0.7875 (ptpt) cc_final: 0.7348 (mtmt) REVERT: P 125 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8177 (ttt180) REVERT: Q 60 HIS cc_start: 0.6514 (m-70) cc_final: 0.6272 (m-70) REVERT: Q 62 LYS cc_start: 0.7387 (tppt) cc_final: 0.7083 (tptm) REVERT: Q 101 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8870 (mt) REVERT: Q 185 MET cc_start: 0.9368 (tpp) cc_final: 0.9067 (tpt) REVERT: Q 308 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.8373 (p90) REVERT: X 106 LYS cc_start: 0.7902 (mttt) cc_final: 0.7671 (mttp) REVERT: Y 88 ASP cc_start: 0.8086 (t0) cc_final: 0.7749 (t70) REVERT: Z 14 MET cc_start: 0.2464 (ttt) cc_final: 0.2175 (ttt) REVERT: b 93 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7902 (mttp) REVERT: c 57 MET cc_start: 0.9144 (mtp) cc_final: 0.8902 (mtm) REVERT: d 78 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7102 (mt-10) REVERT: j 16 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8552 (mm) REVERT: j 109 LYS cc_start: 0.8115 (mmtp) cc_final: 0.7839 (mmtt) REVERT: l 1 MET cc_start: 0.6514 (OUTLIER) cc_final: 0.5808 (tmm) REVERT: l 140 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8694 (tt) REVERT: l 338 MET cc_start: 0.8927 (ttp) cc_final: 0.8621 (ttt) REVERT: m 87 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7657 (tmtt) REVERT: m 135 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: o 30 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8163 (mmt-90) REVERT: p 57 MET cc_start: 0.7356 (mmp) cc_final: 0.7136 (mmp) REVERT: s 22 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8958 (tp) REVERT: s 24 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8161 (tp30) REVERT: s 59 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8261 (pt0) REVERT: s 85 MET cc_start: 0.8760 (mtp) cc_final: 0.8396 (ttp) REVERT: v 81 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7886 (mmtp) REVERT: w 45 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7094 (pp) REVERT: w 241 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.6547 (t80) outliers start: 132 outliers final: 103 residues processed: 1187 average time/residue: 0.6814 time to fit residues: 1363.4753 Evaluate side-chains 1204 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1082 time to evaluate : 5.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 90 TYR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 212 ARG Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 563 ASP Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 125 ARG Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 52 ARG Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 25 GLU Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain b residue 123 PHE Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 125 SER Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 113 CYS Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 22 SER Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain i residue 318 GLU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 453 SER Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 46 ASN Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 97 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 28 ASP Chi-restraints excluded: chain o residue 30 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 274 SER Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 285 LEU Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 153 GLU Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 81 LEU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 507 optimal weight: 0.0170 chunk 680 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 588 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 177 optimal weight: 6.9990 chunk 639 optimal weight: 4.9990 chunk 267 optimal weight: 3.9990 chunk 656 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 overall best weight: 1.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 76 ASN F 93 ASN H 37 GLN P 77 GLN T 122 HIS h 7 GLN u 77 HIS w 107 GLN ** w 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.115113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.094212 restraints weight = 99025.937| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.33 r_work: 0.2817 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 69949 Z= 0.224 Angle : 0.543 13.516 94552 Z= 0.271 Chirality : 0.042 0.327 10192 Planarity : 0.004 0.063 11778 Dihedral : 12.068 171.515 10860 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.79 % Rotamer: Outliers : 1.90 % Allowed : 17.78 % Favored : 80.32 % 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: 1.12 (0.09), residues: 8173 helix: 1.77 (0.08), residues: 4290 sheet: 0.13 (0.25), residues: 456 loop : -0.46 (0.11), residues: 3427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS A 133 PHE 0.033 0.001 PHE i 292 TYR 0.023 0.001 TYR l 422 ARG 0.011 0.000 ARG S 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20307.80 seconds wall clock time: 354 minutes 53.85 seconds (21293.85 seconds total)