Starting phenix.real_space_refine on Fri Mar 15 00:26:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzv_32230/03_2024/7vzv_32230_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzv_32230/03_2024/7vzv_32230.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzv_32230/03_2024/7vzv_32230_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzv_32230/03_2024/7vzv_32230_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzv_32230/03_2024/7vzv_32230_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzv_32230/03_2024/7vzv_32230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzv_32230/03_2024/7vzv_32230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzv_32230/03_2024/7vzv_32230_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzv_32230/03_2024/7vzv_32230_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 45 5.49 5 Mg 1 5.21 5 S 482 5.16 5 C 44174 2.51 5 N 11233 2.21 5 O 12219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 132": "OE1" <-> "OE2" Residue "M GLU 211": "OE1" <-> "OE2" Residue "M GLU 284": "OE1" <-> "OE2" Residue "M GLU 310": "OE1" <-> "OE2" Residue "M GLU 396": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "M GLU 660": "OE1" <-> "OE2" Residue "N GLU 50": "OE1" <-> "OE2" Residue "O GLU 236": "OE1" <-> "OE2" Residue "P GLU 167": "OE1" <-> "OE2" Residue "P GLU 225": "OE1" <-> "OE2" Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 148": "OE1" <-> "OE2" Residue "Q GLU 156": "OE1" <-> "OE2" Residue "Q GLU 259": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "T GLU 64": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "T GLU 105": "OE1" <-> "OE2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 129": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Y GLU 95": "OE1" <-> "OE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "b TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "b GLU 122": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 179": "OE1" <-> "OE2" Residue "d GLU 53": "OE1" <-> "OE2" Residue "d GLU 67": "OE1" <-> "OE2" Residue "d GLU 172": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "e GLU 151": "OE1" <-> "OE2" Residue "f GLU 64": "OE1" <-> "OE2" Residue "g GLU 19": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "i GLU 269": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "j GLU 32": "OE1" <-> "OE2" Residue "j GLU 105": "OE1" <-> "OE2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 238": "OE1" <-> "OE2" Residue "l TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 503": "OE1" <-> "OE2" Residue "m PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 77": "OE1" <-> "OE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "n GLU 48": "OE1" <-> "OE2" Residue "n GLU 54": "OE1" <-> "OE2" Residue "o GLU 46": "OE1" <-> "OE2" Residue "o TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 95": "OE1" <-> "OE2" Residue "p GLU 160": "OE1" <-> "OE2" Residue "p GLU 176": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "r GLU 222": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s GLU 143": "OE1" <-> "OE2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "s GLU 214": "OE1" <-> "OE2" Residue "u GLU 11": "OE1" <-> "OE2" Residue "u ASP 12": "OD1" <-> "OD2" Residue "u PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 109": "OE1" <-> "OE2" Residue "u ARG 135": "NH1" <-> "NH2" Residue "u GLU 149": "OE1" <-> "OE2" Residue "v GLU 45": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "w GLU 251": "OE1" <-> "OE2" Residue "w GLU 303": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 68183 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: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 690 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 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: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1161 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "X" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 694 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 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: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 863 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "i" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2706 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 4812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4812 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 577} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "m" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1291 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 34 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: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2590 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 170 Unusual residues: {' UQ': 1, 'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 133 Unusual residues: {' UQ': 1, 'NDP': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'PEE': 2} 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: "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: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "g" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'PEE': 2, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "l" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 290 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "m" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "r" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 203 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 89 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2718 SG CYS A 382 48.446 49.323 175.026 1.00 67.08 S ATOM 3060 SG CYS A 425 47.698 46.098 180.820 1.00 72.63 S ATOM 2738 SG CYS A 385 45.063 45.011 175.065 1.00 68.95 S ATOM 2699 SG CYS A 379 43.223 50.174 178.892 1.00 55.15 S ATOM 3961 SG CYS B 113 37.108 64.035 139.646 1.00 64.97 S ATOM 3980 SG CYS B 116 42.259 61.678 143.411 1.00 46.05 S ATOM 4003 SG CYS B 119 43.287 64.262 137.906 1.00 44.53 S ATOM 4332 SG CYS B 162 40.612 58.493 138.766 1.00 49.09 S ATOM 4030 SG CYS B 123 49.413 66.788 133.143 1.00 55.53 S ATOM 4256 SG CYS B 152 47.585 64.941 127.356 1.00 50.01 S ATOM 4303 SG CYS B 158 45.556 61.251 132.237 1.00 56.23 S ATOM 4282 SG CYS B 155 51.611 61.450 130.899 1.00 55.49 S ATOM 5724 SG CYS C 166 54.096 64.593 123.055 1.00 51.32 S ATOM 4996 SG CYS C 72 54.520 65.782 116.806 1.00 63.87 S ATOM 4990 SG CYS C 71 59.871 64.258 119.911 1.00 59.56 S ATOM 5494 SG CYS C 136 56.700 69.666 121.798 1.00 53.11 S ATOM 14946 SG CYS M 131 41.714 62.395 155.544 1.00 52.32 S ATOM 14925 SG CYS M 128 45.131 57.638 152.544 1.00 47.04 S ATOM 14986 SG CYS M 137 47.176 61.085 157.812 1.00 54.42 S ATOM 15318 SG CYS M 179 45.628 61.678 168.826 1.00 53.19 S ATOM 15672 SG CYS M 226 42.561 64.277 164.423 1.00 66.60 S ATOM 15342 SG CYS M 182 40.157 64.548 170.552 1.00 47.63 S ATOM 15295 SG CYS M 176 39.926 59.014 167.253 1.00 49.57 S ATOM 14543 SG CYS M 78 57.332 57.216 172.542 1.00 55.79 S ATOM 14644 SG CYS M 92 55.456 59.259 174.963 1.00 67.89 S ATOM 14432 SG CYS M 64 51.099 59.202 172.630 1.00 62.74 S ATOM 14518 SG CYS M 75 52.097 57.256 169.777 1.00 55.69 S ATOM 21481 SG CYS O 135 32.180 32.379 183.660 1.00 75.73 S ATOM 21515 SG CYS O 140 32.105 29.057 184.885 1.00 79.59 S ATOM 21795 SG CYS O 176 36.527 33.873 186.422 1.00 87.04 S ATOM 21818 SG CYS O 180 37.105 30.624 187.502 1.00 81.10 S ATOM 28557 SG CYS T 86 29.725 51.088 148.060 1.00 60.13 S ATOM 28735 SG CYS T 111 30.840 54.346 148.958 1.00 62.83 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.65 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.65 Time building chain proxies: 29.09, per 1000 atoms: 0.43 Number of scatterers: 68183 At special positions: 0 Unit cell: (216.988, 214.84, 232.027, 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 45 15.00 Mg 1 11.99 O 12219 8.00 N 11233 7.00 C 44174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, 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=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 36 " - pdb=" SG CYS u 66 " distance=3.00 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=1.60 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: 19.14 Conformation dependent library (CDL) restraints added in 8.6 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="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="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15530 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 342 helices and 30 sheets defined 51.8% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.66 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 59 removed outlier: 3.727A pdb=" N SER A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) 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: 4.490A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 259 through 263 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 339 through 344 Processing helix chain 'A' and resid 363 through 376 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.309A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 Processing helix chain 'A' and resid 427 through 456 Proline residue: A 434 - end of helix removed outlier: 3.633A 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 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: 5.405A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'C' and resid 43 through 60 Processing helix chain 'C' and resid 71 through 80 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 111 through 122 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 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 190 through 194 Processing helix chain 'E' and resid 25 through 50 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.406A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 40 removed outlier: 4.723A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS F 39 " --> pdb=" O PHE F 36 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG F 40 " --> pdb=" O ILE F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 95 Processing helix chain 'G' and resid 76 through 88 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 4.056A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 78 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 75 removed outlier: 4.033A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.779A 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 158 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 223 removed outlier: 3.611A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N PHE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.849A 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 350 through 356 removed outlier: 5.399A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 80 removed outlier: 3.685A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 77 through 80' Processing helix chain 'K' and resid 85 through 95 removed outlier: 4.452A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' 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: 3.967A 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 138 through 145 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 219 through 225 removed outlier: 3.826A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 292 Processing helix chain 'M' and resid 294 through 298 Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.612A pdb=" N SER M 332 " --> pdb=" O GLY M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 361 removed outlier: 3.801A pdb=" N VAL M 361 " --> pdb=" O LEU M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 384 No H-bonds generated for 'chain 'M' and resid 382 through 384' Processing helix chain 'M' and resid 392 through 395 removed outlier: 3.702A pdb=" N GLU M 395 " --> pdb=" O ALA M 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 392 through 395' Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 Processing helix chain 'M' and resid 461 through 468 Processing helix chain 'M' and resid 478 through 481 Processing helix chain 'M' and resid 486 through 503 Processing helix chain 'M' and resid 522 through 528 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 557 through 559 No H-bonds generated for 'chain 'M' and resid 557 through 559' Processing helix chain 'M' and resid 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 673 removed outlier: 3.596A pdb=" N LYS M 673 " --> pdb=" O ASN M 669 " (cutoff:3.500A) Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 4 through 17 removed outlier: 3.642A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 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: 3.588A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.273A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 141 No H-bonds generated for 'chain 'O' and resid 138 through 141' Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 210 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.594A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 4.633A 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 173 removed outlier: 3.744A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (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: 4.282A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 60 removed outlier: 4.105A pdb=" N HIS Q 60 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 57 through 60' Processing helix chain 'Q' and resid 120 through 126 Processing helix chain 'Q' and resid 133 through 139 removed outlier: 3.899A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 3.916A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 262 removed outlier: 3.705A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.870A 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: 4.458A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 371 No H-bonds generated for 'chain 'Q' and resid 368 through 371' Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 439 removed outlier: 4.467A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 453 Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'S' and resid 2 through 30 removed outlier: 3.586A 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 Processing helix chain 'S' and resid 42 through 55 Processing helix chain 'S' and resid 66 through 69 Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'U' and resid 4 through 15 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 Processing helix chain 'U' and resid 79 through 82 No H-bonds generated for 'chain 'U' and resid 79 through 82' Processing helix chain 'V' and resid 3 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 32 through 99 removed outlier: 3.634A pdb=" N LEU W 43 " --> pdb=" O GLY W 39 " (cutoff:3.500A) Proline residue: W 73 - end of helix removed outlier: 3.724A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 137 Processing helix chain 'X' and resid 76 through 89 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 through 81 Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Y' and resid 94 through 97 No H-bonds generated for 'chain 'Y' and resid 94 through 97' Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 39 removed outlier: 3.695A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 54 removed outlier: 3.844A pdb=" N SER Z 54 " --> pdb=" O TRP Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 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 removed outlier: 4.117A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 109 through 112' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 26 Processing helix chain 'b' and resid 69 through 74 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 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 57 removed outlier: 4.945A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 82 through 116 Processing helix chain 'd' and resid 118 through 124 removed outlier: 3.653A pdb=" N TYR d 121 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ARG d 122 " --> pdb=" O GLU d 119 " (cutoff:3.500A) removed outlier: 3.978A 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 174 Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 Processing helix chain 'e' and resid 116 through 132 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: 3.856A 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 53 removed outlier: 3.594A pdb=" N GLU h 53 " --> pdb=" O GLY h 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 49 through 53' Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'h' and resid 96 through 99 No H-bonds generated for 'chain 'h' and resid 96 through 99' Processing helix chain 'i' and resid 3 through 21 Processing helix chain 'i' and resid 26 through 44 Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.347A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.831A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.985A 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 169 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: 3.666A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.673A 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 271 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.487A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 23 Processing helix chain 'j' and resid 56 through 80 removed outlier: 4.342A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU j 68 " --> pdb=" O LEU j 64 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.607A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.495A 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 21 Processing helix chain 'k' and resid 27 through 51 Processing helix chain 'k' and resid 55 through 85 removed outlier: 3.943A pdb=" N MET k 58 " --> pdb=" O LEU k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix Processing helix chain 'k' and resid 90 through 92 No H-bonds generated for 'chain 'k' and resid 90 through 92' Processing helix chain 'l' and resid 3 through 23 removed outlier: 3.840A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.975A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.583A 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: 3.876A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 132 Processing helix chain 'l' and resid 137 through 155 Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.869A 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: 4.106A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 246 Processing helix chain 'l' and resid 252 through 262 removed outlier: 4.326A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.086A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.413A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 319 Processing helix chain 'l' and resid 322 through 349 removed outlier: 4.040A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 381 Processing helix chain 'l' and resid 389 through 400 removed outlier: 4.757A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.632A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 469 removed outlier: 5.693A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.346A 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: 3.899A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.510A 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: 4.167A 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 577 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 25 through 46 removed outlier: 3.948A pdb=" N GLY m 29 " --> pdb=" O SER m 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 74 Processing helix chain 'm' and resid 87 through 109 Processing helix chain 'm' and resid 125 through 127 No H-bonds generated for 'chain 'm' and resid 125 through 127' Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.262A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 4 through 34 removed outlier: 6.463A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.774A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 23 No H-bonds generated for 'chain 'o' and resid 20 through 23' Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.600A 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: 4.526A 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 96 removed outlier: 4.360A pdb=" N CYS p 96 " --> pdb=" O ARG p 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 93 through 96' Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 142 removed outlier: 4.690A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 4.724A 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: 4.290A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 80 Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 89 through 110 Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.751A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.511A 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: 4.189A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.847A 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 205 removed outlier: 4.468A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.244A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 237 through 246 Processing helix chain 'r' and resid 253 through 257 Processing helix chain 'r' and resid 259 through 277 removed outlier: 3.750A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 283 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.529A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 350 No H-bonds generated for 'chain 'r' and resid 348 through 350' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 392 through 415 Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 31 Proline residue: s 12 - end of helix removed outlier: 3.602A 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: 4.416A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 3.696A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.063A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.723A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 176 No H-bonds generated for 'chain 's' and resid 174 through 176' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 204 through 207 No H-bonds generated for 'chain 's' and resid 204 through 207' Processing helix chain 's' and resid 210 through 214 removed outlier: 4.607A pdb=" N GLU s 214 " --> pdb=" O PHE s 211 " (cutoff:3.500A) Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 284 through 291 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 No H-bonds generated for '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 114 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 82 through 124 Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 94 through 96 No H-bonds generated for 'chain 'w' and resid 94 through 96' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 163 through 165 No H-bonds generated for 'chain 'w' and resid 163 through 165' Processing helix chain 'w' and resid 167 through 175 Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.170A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.816A 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 251 removed outlier: 5.451A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix removed outlier: 3.950A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 261 through 263 No H-bonds generated for 'chain 'w' and resid 261 through 263' Processing helix chain 'w' and resid 266 through 274 Processing helix chain 'w' and resid 283 through 285 No H-bonds generated for 'chain 'w' and resid 283 through 285' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 309 removed outlier: 4.815A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 239 through 244 removed outlier: 3.694A pdb=" N THR A 241 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 5.917A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.184A 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: 6.614A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.427A 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: 6.910A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.607A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.774A 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 229 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 200 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= O, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 365 through 368 removed outlier: 4.494A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.217A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.457A 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: 6.494A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.494A 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: 6.621A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.765A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU P 83 " --> pdb=" O SER P 79 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.516A pdb=" N LEU Q 101 " --> pdb=" O LEU Q 80 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 77 through 79 Processing sheet with id= Z, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= AA, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= AB, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.327A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.793A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'w' and resid 84 through 86 2918 hydrogen bonds defined for protein. 8169 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.83 Time building geometry restraints manager: 21.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27743 1.40 - 1.62: 41169 1.62 - 1.84: 874 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 69866 Sorted by residual: 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 1.27e+02 bond pdb=" C18 UQ C 304 " pdb=" C19 UQ C 304 " ideal model delta sigma weight residual 1.336 1.557 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C18 UQ J 402 " pdb=" C19 UQ J 402 " ideal model delta sigma weight residual 1.336 1.556 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C13 UQ C 304 " pdb=" C14 UQ C 304 " ideal model delta sigma weight residual 1.335 1.550 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C13 UQ J 402 " pdb=" C14 UQ J 402 " ideal model delta sigma weight residual 1.335 1.547 -0.212 2.00e-02 2.50e+03 1.12e+02 ... (remaining 69861 not shown) Histogram of bond angle deviations from ideal: 73.64 - 85.82: 76 85.82 - 98.00: 0 98.00 - 110.18: 13385 110.18 - 122.36: 72749 122.36 - 134.55: 8216 Bond angle restraints: 94426 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 107.74 122.84 -15.10 1.95e+00 2.62e-01 5.97e+01 angle pdb=" C ASP h 103 " pdb=" N PRO h 104 " pdb=" CA PRO h 104 " ideal model delta sigma weight residual 120.31 127.82 -7.51 9.80e-01 1.04e+00 5.88e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 117.49 -13.65 1.91e+00 2.73e-01 5.08e+01 angle pdb=" C PRO h 94 " pdb=" N PRO h 95 " pdb=" CA PRO h 95 " ideal model delta sigma weight residual 120.38 127.42 -7.04 1.03e+00 9.43e-01 4.67e+01 angle pdb=" C51 CDL l 702 " pdb=" CB5 CDL l 702 " pdb=" OB6 CDL l 702 " ideal model delta sigma weight residual 111.33 120.31 -8.98 1.32e+00 5.72e-01 4.61e+01 ... (remaining 94421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 40703 35.31 - 70.62: 1566 70.62 - 105.94: 105 105.94 - 141.25: 19 141.25 - 176.56: 13 Dihedral angle restraints: 42406 sinusoidal: 18315 harmonic: 24091 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 257.59 81.03 176.56 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 101.70 -161.70 1 2.00e+01 2.50e-03 4.68e+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 -140.83 54.83 1 1.00e+01 1.00e-02 4.07e+01 ... (remaining 42403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 9448 0.080 - 0.160: 719 0.160 - 0.240: 34 0.240 - 0.320: 4 0.320 - 0.400: 2 Chirality restraints: 10207 Sorted by residual: chirality pdb=" CA LYS s 291 " pdb=" N LYS s 291 " pdb=" C LYS s 291 " pdb=" CB LYS s 291 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" C3B NDP J 401 " pdb=" C2B NDP J 401 " pdb=" C4B NDP J 401 " pdb=" O3B NDP J 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.38 -0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" C3D NDP J 401 " pdb=" C2D NDP J 401 " pdb=" C4D NDP J 401 " pdb=" O3D NDP J 401 " both_signs ideal model delta sigma weight residual False -2.71 -2.41 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 10204 not shown) Planarity restraints: 11770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ J 402 " -0.474 2.00e-02 2.50e+03 4.14e-01 2.14e+03 pdb=" C18 UQ J 402 " 0.525 2.00e-02 2.50e+03 pdb=" C19 UQ J 402 " 0.413 2.00e-02 2.50e+03 pdb=" C20 UQ J 402 " -0.036 2.00e-02 2.50e+03 pdb=" C21 UQ J 402 " -0.428 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ J 402 " 0.024 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C11 UQ J 402 " -0.065 2.00e-02 2.50e+03 pdb=" C7 UQ J 402 " -0.307 2.00e-02 2.50e+03 pdb=" C8 UQ J 402 " 0.564 2.00e-02 2.50e+03 pdb=" C9 UQ J 402 " -0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C42 UQ C 304 " -0.301 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C43 UQ C 304 " 0.560 2.00e-02 2.50e+03 pdb=" C44 UQ C 304 " -0.228 2.00e-02 2.50e+03 pdb=" C45 UQ C 304 " -0.060 2.00e-02 2.50e+03 pdb=" C46 UQ C 304 " 0.029 2.00e-02 2.50e+03 ... (remaining 11767 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5169 2.74 - 3.28: 67259 3.28 - 3.82: 114136 3.82 - 4.36: 139866 4.36 - 4.90: 243065 Nonbonded interactions: 569495 Sorted by model distance: nonbonded pdb=" OE2 GLU Q 176 " pdb=" OH TYR Q 311 " model vdw 2.195 2.440 nonbonded pdb=" OE1 GLN W 85 " pdb=" NH1 ARG h 105 " model vdw 2.195 2.520 nonbonded pdb=" OH TYR c 62 " pdb=" OD1 ASP c 74 " model vdw 2.200 2.440 nonbonded pdb=" OE1 GLU C 126 " pdb=" OH TYR J 89 " model vdw 2.205 2.440 nonbonded pdb=" OG1 THR j 61 " pdb=" OE2 GLU j 105 " model vdw 2.207 2.440 ... (remaining 569490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 69 through 93 or (resid 94 through 97 and (name N or name \ CA or name C or name O or name CB )) or resid 98 through 156 or resid 201)) selection = (chain 'X' and (resid 69 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB )) or resid 108 through 149 or (resid 150 through 153 a \ nd (name N or name 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=0.65 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 8.980 Check model and map are aligned: 0.750 Set scattering table: 0.460 Process input model: 153.980 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 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 69866 Z= 0.502 Angle : 0.798 17.425 94426 Z= 0.402 Chirality : 0.043 0.400 10207 Planarity : 0.011 0.414 11770 Dihedral : 17.959 176.561 26846 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 0.29 % Allowed : 15.12 % Favored : 84.59 % 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: 1.16 (0.10), residues: 8172 helix: 1.89 (0.08), residues: 4288 sheet: -0.01 (0.24), residues: 453 loop : -0.56 (0.11), residues: 3431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS r 220 PHE 0.031 0.001 PHE i 292 TYR 0.024 0.001 TYR d 63 ARG 0.017 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1137 time to evaluate : 5.783 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 66 MET cc_start: 0.9310 (mmm) cc_final: 0.9086 (mmp) REVERT: J 303 ARG cc_start: 0.8464 (tpt170) cc_final: 0.7652 (ttt90) REVERT: N 133 LYS cc_start: 0.8989 (mmtm) cc_final: 0.8744 (mmtm) REVERT: W 80 ASP cc_start: 0.8809 (m-30) cc_final: 0.8526 (m-30) REVERT: a 114 LYS cc_start: 0.9007 (ptmt) cc_final: 0.8418 (ttpp) REVERT: a 186 THR cc_start: 0.9039 (m) cc_final: 0.8354 (p) REVERT: g 3 MET cc_start: 0.8504 (ptt) cc_final: 0.8284 (ptt) REVERT: m 125 TRP cc_start: 0.8547 (p-90) cc_final: 0.8335 (p-90) REVERT: o 111 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8516 (mtmt) REVERT: s 235 ASN cc_start: 0.9096 (m-40) cc_final: 0.8834 (m-40) outliers start: 21 outliers final: 9 residues processed: 1145 average time/residue: 0.7010 time to fit residues: 1361.8238 Evaluate side-chains 1120 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1111 time to evaluate : 5.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain c residue 122 THR Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain u residue 46 CYS Chi-restraints excluded: chain u residue 121 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 679 optimal weight: 4.9990 chunk 610 optimal weight: 0.9980 chunk 338 optimal weight: 0.5980 chunk 208 optimal weight: 0.3980 chunk 411 optimal weight: 2.9990 chunk 325 optimal weight: 6.9990 chunk 630 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 383 optimal weight: 0.7980 chunk 469 optimal weight: 10.0000 chunk 731 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 99 GLN F 93 ASN G 101 ASN I 21 GLN M 540 ASN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 663 ASN Q 233 HIS V 129 GLN W 76 GLN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 132 ASN ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 580 GLN r 51 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.0358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 69866 Z= 0.177 Angle : 0.502 10.751 94426 Z= 0.250 Chirality : 0.040 0.197 10207 Planarity : 0.004 0.063 11770 Dihedral : 14.671 176.147 10671 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.74 % Favored : 96.21 % Rotamer: Outliers : 1.38 % Allowed : 14.41 % Favored : 84.21 % 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 (0.10), residues: 8172 helix: 1.93 (0.08), residues: 4269 sheet: 0.02 (0.24), residues: 455 loop : -0.55 (0.11), residues: 3448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.008 0.001 HIS E 108 PHE 0.030 0.001 PHE i 292 TYR 0.020 0.001 TYR s 114 ARG 0.007 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1255 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1156 time to evaluate : 6.379 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: F 95 LEU cc_start: 0.8406 (mp) cc_final: 0.8138 (mp) REVERT: G 146 ASP cc_start: 0.8074 (m-30) cc_final: 0.7842 (m-30) REVERT: M 434 SER cc_start: 0.9103 (OUTLIER) cc_final: 0.8658 (p) REVERT: N 76 ASP cc_start: 0.8084 (p0) cc_final: 0.7503 (p0) REVERT: O 215 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8600 (ptmt) REVERT: V 8 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8642 (mtpp) REVERT: X 77 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7110 (tm-30) REVERT: Z 71 PHE cc_start: 0.8760 (t80) cc_final: 0.8483 (t80) REVERT: a 186 THR cc_start: 0.8874 (m) cc_final: 0.8151 (p) REVERT: d 43 ARG cc_start: 0.8094 (tpp80) cc_final: 0.7698 (tpp80) REVERT: d 73 ASP cc_start: 0.8604 (p0) cc_final: 0.8399 (p0) REVERT: f 65 ASP cc_start: 0.8535 (m-30) cc_final: 0.8273 (m-30) REVERT: g 3 MET cc_start: 0.8500 (ptt) cc_final: 0.8253 (ptt) REVERT: j 98 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8857 (tp) REVERT: j 101 SER cc_start: 0.9237 (p) cc_final: 0.8951 (p) REVERT: k 10 MET cc_start: 0.8815 (ttp) cc_final: 0.8588 (ttm) REVERT: r 204 MET cc_start: 0.9240 (mmm) cc_final: 0.8913 (mmm) REVERT: r 420 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8467 (m) REVERT: s 234 MET cc_start: 0.8964 (tpp) cc_final: 0.8623 (mmm) REVERT: s 235 ASN cc_start: 0.9122 (m-40) cc_final: 0.8883 (m-40) REVERT: u 6 GLU cc_start: 0.8164 (tp30) cc_final: 0.7951 (tt0) REVERT: v 52 MET cc_start: 0.8243 (mmt) cc_final: 0.7980 (mmm) outliers start: 99 outliers final: 55 residues processed: 1206 average time/residue: 0.6557 time to fit residues: 1336.3496 Evaluate side-chains 1169 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1110 time to evaluate : 5.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 76 MET Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 434 SER Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 663 ASN Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 215 LYS Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain c residue 122 THR Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 54 GLU Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 442 LEU Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 56 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 406 optimal weight: 0.0270 chunk 226 optimal weight: 6.9990 chunk 608 optimal weight: 6.9990 chunk 497 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 732 optimal weight: 0.6980 chunk 791 optimal weight: 2.9990 chunk 652 optimal weight: 7.9990 chunk 726 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 587 optimal weight: 3.9990 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN E 45 ASN F 93 ASN G 101 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN I 21 GLN I 47 HIS K 75 ASN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 663 ASN V 129 GLN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.0493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 69866 Z= 0.227 Angle : 0.505 10.752 94426 Z= 0.253 Chirality : 0.041 0.194 10207 Planarity : 0.004 0.059 11770 Dihedral : 13.924 177.925 10657 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 1.93 % Allowed : 14.66 % Favored : 83.41 % 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: 1.15 (0.10), residues: 8172 helix: 1.88 (0.08), residues: 4284 sheet: -0.06 (0.24), residues: 452 loop : -0.55 (0.11), residues: 3436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.004 0.001 HIS E 108 PHE 0.032 0.001 PHE i 292 TYR 0.022 0.001 TYR l 587 ARG 0.009 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1138 time to evaluate : 5.787 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: G 146 ASP cc_start: 0.8097 (m-30) cc_final: 0.7763 (m-30) REVERT: J 87 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8685 (tm-30) REVERT: K 74 ARG cc_start: 0.7759 (mtt-85) cc_final: 0.7535 (mtt-85) REVERT: K 75 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8506 (t0) REVERT: M 680 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8273 (pp) REVERT: N 76 ASP cc_start: 0.8149 (p0) cc_final: 0.7501 (p0) REVERT: O 215 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8618 (ptmt) REVERT: P 81 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8693 (p90) REVERT: V 8 LYS cc_start: 0.8813 (mtpt) cc_final: 0.8556 (mtpp) REVERT: V 100 THR cc_start: 0.9436 (m) cc_final: 0.9168 (p) REVERT: W 7 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8403 (tptp) REVERT: W 50 MET cc_start: 0.9121 (tpp) cc_final: 0.8775 (tpp) REVERT: X 77 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7058 (tm-30) REVERT: Z 71 PHE cc_start: 0.8846 (t80) cc_final: 0.8558 (t80) REVERT: a 186 THR cc_start: 0.8756 (m) cc_final: 0.7995 (p) REVERT: d 43 ARG cc_start: 0.8097 (tpp80) cc_final: 0.7718 (tpp80) REVERT: d 73 ASP cc_start: 0.8667 (p0) cc_final: 0.8388 (p0) REVERT: f 65 ASP cc_start: 0.8625 (m-30) cc_final: 0.8407 (m-30) REVERT: f 70 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8643 (mttm) REVERT: j 98 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8859 (tp) REVERT: j 101 SER cc_start: 0.9236 (p) cc_final: 0.8941 (p) REVERT: k 10 MET cc_start: 0.8801 (ttp) cc_final: 0.8553 (ttm) REVERT: l 70 THR cc_start: 0.9289 (OUTLIER) cc_final: 0.8979 (m) REVERT: l 140 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8906 (tt) REVERT: m 33 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8751 (tp) REVERT: m 64 MET cc_start: 0.9484 (OUTLIER) cc_final: 0.9176 (mmm) REVERT: m 86 ASN cc_start: 0.9206 (t0) cc_final: 0.8901 (t0) REVERT: r 186 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8990 (mp) REVERT: r 204 MET cc_start: 0.9264 (mmm) cc_final: 0.8843 (mmm) REVERT: r 222 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8198 (mt-10) REVERT: r 420 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8517 (m) REVERT: s 235 ASN cc_start: 0.9168 (m-40) cc_final: 0.8935 (m-40) outliers start: 138 outliers final: 82 residues processed: 1211 average time/residue: 0.6949 time to fit residues: 1439.0855 Evaluate side-chains 1212 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1115 time to evaluate : 5.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 215 LYS Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 447 VAL Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain Y residue 62 SER Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain c residue 122 THR Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 70 LYS Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 54 GLU Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 109 SER Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 226 THR Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 442 LEU Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 64 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 222 GLU Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 121 ASP Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 56 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 0.6980 chunk 550 optimal weight: 7.9990 chunk 380 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 349 optimal weight: 0.7980 chunk 491 optimal weight: 0.9990 chunk 734 optimal weight: 7.9990 chunk 778 optimal weight: 6.9990 chunk 383 optimal weight: 6.9990 chunk 696 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 HIS A 452 GLN E 45 ASN F 93 ASN G 101 ASN G 103 HIS I 21 GLN K 106 GLN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 GLN a 90 ASN b 13 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.0602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 69866 Z= 0.199 Angle : 0.496 10.731 94426 Z= 0.248 Chirality : 0.040 0.188 10207 Planarity : 0.004 0.059 11770 Dihedral : 13.424 176.503 10657 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 2.21 % Allowed : 14.98 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.10), residues: 8172 helix: 1.92 (0.08), residues: 4267 sheet: 0.01 (0.24), residues: 457 loop : -0.54 (0.11), residues: 3448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.004 0.001 HIS i 112 PHE 0.031 0.001 PHE i 292 TYR 0.020 0.001 TYR l 587 ARG 0.011 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1152 time to evaluate : 6.921 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 72 MET cc_start: 0.9239 (tpp) cc_final: 0.9034 (tpp) REVERT: G 143 GLU cc_start: 0.7768 (mp0) cc_final: 0.7268 (mp0) REVERT: G 146 ASP cc_start: 0.8120 (m-30) cc_final: 0.7727 (m-30) REVERT: I 67 SER cc_start: 0.9203 (m) cc_final: 0.8934 (p) REVERT: J 87 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8682 (tm-30) REVERT: J 303 ARG cc_start: 0.8420 (tpt170) cc_final: 0.7726 (ttt90) REVERT: K 74 ARG cc_start: 0.7775 (mtt-85) cc_final: 0.7471 (mtt-85) REVERT: M 680 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8272 (pp) REVERT: O 215 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8619 (ptmt) REVERT: P 81 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8632 (p90) REVERT: V 8 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8548 (mtpp) REVERT: V 100 THR cc_start: 0.9418 (m) cc_final: 0.9140 (p) REVERT: W 7 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8412 (tptp) REVERT: W 50 MET cc_start: 0.9113 (tpp) cc_final: 0.8816 (tpp) REVERT: X 77 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7073 (tm-30) REVERT: Z 71 PHE cc_start: 0.8901 (t80) cc_final: 0.8640 (t80) REVERT: a 186 THR cc_start: 0.8711 (m) cc_final: 0.7934 (p) REVERT: d 73 ASP cc_start: 0.8683 (p0) cc_final: 0.8357 (p0) REVERT: f 65 ASP cc_start: 0.8725 (m-30) cc_final: 0.8498 (m-30) REVERT: f 70 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8667 (mttm) REVERT: f 73 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8652 (m-40) REVERT: i 48 PHE cc_start: 0.8224 (t80) cc_final: 0.7957 (t80) REVERT: i 54 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8664 (tt0) REVERT: i 171 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8822 (t160) REVERT: i 339 MET cc_start: 0.9196 (mmm) cc_final: 0.8917 (mmm) REVERT: j 98 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8847 (tp) REVERT: j 101 SER cc_start: 0.9249 (p) cc_final: 0.8953 (p) REVERT: k 10 MET cc_start: 0.8783 (ttp) cc_final: 0.8538 (ttm) REVERT: k 34 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8231 (mt-10) REVERT: l 140 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8897 (tt) REVERT: m 33 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8708 (tp) REVERT: m 86 ASN cc_start: 0.9205 (t0) cc_final: 0.8903 (t0) REVERT: r 44 GLN cc_start: 0.8980 (mm110) cc_final: 0.8746 (mm-40) REVERT: r 114 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: r 186 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8993 (mp) REVERT: r 204 MET cc_start: 0.9296 (mmm) cc_final: 0.8802 (mmm) REVERT: r 222 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8226 (mt-10) REVERT: r 420 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8492 (m) REVERT: s 192 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8457 (tm-30) REVERT: s 235 ASN cc_start: 0.9203 (m-40) cc_final: 0.9001 (m-40) REVERT: v 52 MET cc_start: 0.8287 (mmt) cc_final: 0.8018 (mmm) outliers start: 158 outliers final: 94 residues processed: 1235 average time/residue: 0.6615 time to fit residues: 1375.0696 Evaluate side-chains 1232 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1122 time to evaluate : 5.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 76 MET Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 208 LEU Chi-restraints excluded: chain O residue 215 LYS Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 447 VAL Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain c residue 122 THR Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 70 LYS Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 54 GLU Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain i residue 171 ASN Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 442 LEU Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 222 GLU Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain s residue 168 THR Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 121 ASP Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 56 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 5.9990 chunk 441 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 579 optimal weight: 7.9990 chunk 321 optimal weight: 2.9990 chunk 664 optimal weight: 0.9990 chunk 537 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 397 optimal weight: 0.0980 chunk 698 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN F 93 ASN G 101 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 GLN K 106 GLN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 663 ASN M 677 GLN V 129 GLN b 13 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 400 ASN ** w 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 69866 Z= 0.233 Angle : 0.508 11.328 94426 Z= 0.254 Chirality : 0.041 0.197 10207 Planarity : 0.004 0.059 11770 Dihedral : 13.121 176.710 10657 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.03 % Favored : 95.93 % Rotamer: Outliers : 2.15 % Allowed : 15.50 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.10), residues: 8172 helix: 1.90 (0.08), residues: 4269 sheet: -0.05 (0.24), residues: 452 loop : -0.54 (0.11), residues: 3451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.006 0.001 HIS G 103 PHE 0.032 0.001 PHE i 292 TYR 0.022 0.001 TYR l 587 ARG 0.012 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1144 time to evaluate : 5.868 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 72 MET cc_start: 0.9269 (tpp) cc_final: 0.9041 (tpp) REVERT: C 59 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8741 (ttp-110) REVERT: E 66 MET cc_start: 0.9269 (mmm) cc_final: 0.9050 (mmt) REVERT: G 143 GLU cc_start: 0.7483 (mp0) cc_final: 0.7153 (mp0) REVERT: G 146 ASP cc_start: 0.8167 (m-30) cc_final: 0.7941 (m-30) REVERT: I 67 SER cc_start: 0.9189 (m) cc_final: 0.8931 (p) REVERT: J 87 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8678 (tm-30) REVERT: J 303 ARG cc_start: 0.8442 (tpt170) cc_final: 0.7738 (ttt90) REVERT: K 74 ARG cc_start: 0.7725 (mtt-85) cc_final: 0.7363 (mtt-85) REVERT: M 75 CYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8738 (p) REVERT: M 680 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8310 (pp) REVERT: O 215 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8616 (ptmt) REVERT: P 81 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8691 (p90) REVERT: V 8 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8552 (mtpp) REVERT: V 100 THR cc_start: 0.9408 (m) cc_final: 0.9129 (p) REVERT: V 106 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6611 (tpm170) REVERT: W 7 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8423 (tptp) REVERT: W 50 MET cc_start: 0.9135 (tpp) cc_final: 0.8851 (tpp) REVERT: X 77 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7054 (tm-30) REVERT: Z 71 PHE cc_start: 0.8931 (t80) cc_final: 0.8688 (t80) REVERT: a 114 LYS cc_start: 0.9061 (ptmt) cc_final: 0.8505 (ttpp) REVERT: a 186 THR cc_start: 0.8730 (m) cc_final: 0.7949 (p) REVERT: b 88 TYR cc_start: 0.9342 (m-80) cc_final: 0.9031 (m-10) REVERT: d 73 ASP cc_start: 0.8782 (p0) cc_final: 0.8412 (p0) REVERT: f 65 ASP cc_start: 0.8761 (m-30) cc_final: 0.8546 (m-30) REVERT: f 70 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8667 (mttm) REVERT: f 73 ASN cc_start: 0.9024 (OUTLIER) cc_final: 0.8682 (m-40) REVERT: i 54 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8684 (tt0) REVERT: i 171 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8831 (t160) REVERT: i 339 MET cc_start: 0.9201 (mmm) cc_final: 0.8930 (mmm) REVERT: j 98 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8864 (tp) REVERT: j 101 SER cc_start: 0.9259 (p) cc_final: 0.8948 (p) REVERT: k 10 MET cc_start: 0.8795 (ttp) cc_final: 0.8547 (ttm) REVERT: k 34 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8283 (mt-10) REVERT: l 70 THR cc_start: 0.9321 (OUTLIER) cc_final: 0.9012 (m) REVERT: l 140 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8913 (tt) REVERT: m 33 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8767 (tp) REVERT: m 64 MET cc_start: 0.9539 (OUTLIER) cc_final: 0.9312 (mmm) REVERT: m 86 ASN cc_start: 0.9209 (t0) cc_final: 0.8931 (t0) REVERT: m 122 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6461 (pt) REVERT: r 44 GLN cc_start: 0.9004 (mm110) cc_final: 0.8801 (mm110) REVERT: r 114 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: r 186 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9004 (mp) REVERT: r 204 MET cc_start: 0.9309 (mmm) cc_final: 0.8784 (mmm) REVERT: r 420 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8557 (m) REVERT: s 192 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8467 (tm-30) REVERT: s 235 ASN cc_start: 0.9258 (m-40) cc_final: 0.9047 (m-40) REVERT: w 72 ARG cc_start: 0.8278 (ttp-110) cc_final: 0.7859 (ttp80) outliers start: 154 outliers final: 98 residues processed: 1229 average time/residue: 0.6656 time to fit residues: 1382.7217 Evaluate side-chains 1249 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1130 time to evaluate : 5.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain M residue 663 ASN Chi-restraints excluded: chain M residue 677 GLN Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 215 LYS Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 447 VAL Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 140 LYS Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain Y residue 62 SER Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain c residue 122 THR Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 70 LYS Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 54 GLU Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain i residue 171 ASN Chi-restraints excluded: chain i residue 226 THR Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 442 LEU Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 64 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 122 LEU Chi-restraints excluded: chain m residue 126 VAL Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain s residue 168 THR Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 121 ASP Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 184 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 2.9990 chunk 700 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 456 optimal weight: 0.0170 chunk 192 optimal weight: 2.9990 chunk 778 optimal weight: 0.5980 chunk 646 optimal weight: 5.9990 chunk 360 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 257 optimal weight: 3.9990 chunk 408 optimal weight: 6.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN E 45 ASN F 93 ASN G 101 ASN G 103 HIS I 21 GLN K 106 GLN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 663 ASN V 129 GLN b 13 GLN e 86 ASN i 49 ASN ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 300 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 69866 Z= 0.184 Angle : 0.498 17.654 94426 Z= 0.248 Chirality : 0.040 0.215 10207 Planarity : 0.004 0.058 11770 Dihedral : 12.791 176.325 10657 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.78 % Favored : 96.17 % Rotamer: Outliers : 2.15 % Allowed : 16.13 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.10), residues: 8172 helix: 1.92 (0.08), residues: 4274 sheet: -0.02 (0.24), residues: 452 loop : -0.52 (0.11), residues: 3446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.004 0.001 HIS G 103 PHE 0.030 0.001 PHE i 292 TYR 0.020 0.001 TYR l 587 ARG 0.013 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1151 time to evaluate : 5.810 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.9227 (tpp) cc_final: 0.8997 (tpp) REVERT: C 59 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8719 (ttp-110) REVERT: G 143 GLU cc_start: 0.7381 (mp0) cc_final: 0.7063 (mp0) REVERT: G 146 ASP cc_start: 0.8155 (m-30) cc_final: 0.7930 (m-30) REVERT: I 67 SER cc_start: 0.9184 (m) cc_final: 0.8933 (p) REVERT: J 87 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8696 (tm-30) REVERT: J 303 ARG cc_start: 0.8528 (tpt170) cc_final: 0.7802 (ttt90) REVERT: M 75 CYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8725 (p) REVERT: M 678 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7698 (mm-40) REVERT: O 215 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8652 (ptmt) REVERT: P 81 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8645 (p90) REVERT: U 16 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7852 (tp30) REVERT: V 8 LYS cc_start: 0.8792 (mtpt) cc_final: 0.8567 (mtpp) REVERT: V 100 THR cc_start: 0.9396 (m) cc_final: 0.9175 (p) REVERT: V 106 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6613 (tpm170) REVERT: W 7 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8421 (tptp) REVERT: W 50 MET cc_start: 0.9080 (tpp) cc_final: 0.8808 (tpp) REVERT: X 77 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7089 (tm-30) REVERT: Z 18 ASP cc_start: 0.8412 (t0) cc_final: 0.8165 (t70) REVERT: Z 71 PHE cc_start: 0.8932 (t80) cc_final: 0.8706 (t80) REVERT: a 114 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8509 (ttpp) REVERT: a 186 THR cc_start: 0.8703 (m) cc_final: 0.7938 (p) REVERT: b 88 TYR cc_start: 0.9358 (m-80) cc_final: 0.9030 (m-10) REVERT: d 73 ASP cc_start: 0.8778 (p0) cc_final: 0.8397 (p0) REVERT: f 65 ASP cc_start: 0.8767 (m-30) cc_final: 0.8547 (m-30) REVERT: f 73 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8603 (m-40) REVERT: i 171 ASN cc_start: 0.9216 (OUTLIER) cc_final: 0.8812 (t160) REVERT: i 284 MET cc_start: 0.9139 (mmm) cc_final: 0.8856 (mmm) REVERT: i 339 MET cc_start: 0.9199 (mmm) cc_final: 0.8931 (mmm) REVERT: j 83 ASN cc_start: 0.9073 (p0) cc_final: 0.8682 (p0) REVERT: j 98 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8857 (tp) REVERT: j 101 SER cc_start: 0.9258 (p) cc_final: 0.8948 (p) REVERT: k 10 MET cc_start: 0.8811 (ttp) cc_final: 0.8575 (ttm) REVERT: k 34 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8303 (mt-10) REVERT: l 70 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.9032 (m) REVERT: l 140 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8919 (tt) REVERT: m 33 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8723 (tp) REVERT: m 64 MET cc_start: 0.9536 (OUTLIER) cc_final: 0.9287 (mmm) REVERT: m 86 ASN cc_start: 0.9202 (t0) cc_final: 0.8887 (t0) REVERT: m 122 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6538 (pt) REVERT: m 125 TRP cc_start: 0.8658 (p-90) cc_final: 0.8441 (p-90) REVERT: r 44 GLN cc_start: 0.9006 (mm110) cc_final: 0.8748 (mm-40) REVERT: r 114 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: r 186 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9000 (mp) REVERT: r 204 MET cc_start: 0.9304 (mmm) cc_final: 0.8743 (mmm) REVERT: r 420 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8482 (m) REVERT: s 192 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8469 (tm-30) REVERT: s 235 ASN cc_start: 0.9253 (m-40) cc_final: 0.9029 (m-40) REVERT: v 38 GLU cc_start: 0.7983 (tp30) cc_final: 0.7622 (tm-30) REVERT: v 52 MET cc_start: 0.8281 (mmt) cc_final: 0.7992 (mmm) outliers start: 154 outliers final: 106 residues processed: 1232 average time/residue: 0.6579 time to fit residues: 1372.9231 Evaluate side-chains 1251 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1125 time to evaluate : 5.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 76 MET Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 215 LYS Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 447 VAL Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain c residue 122 THR Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 54 GLU Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain i residue 171 ASN Chi-restraints excluded: chain i residue 226 THR Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 442 LEU Chi-restraints excluded: chain l residue 450 LEU Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 64 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 122 LEU Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 121 ASP Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 203 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 443 optimal weight: 6.9990 chunk 568 optimal weight: 5.9990 chunk 440 optimal weight: 4.9990 chunk 655 optimal weight: 4.9990 chunk 434 optimal weight: 9.9990 chunk 775 optimal weight: 2.9990 chunk 485 optimal weight: 4.9990 chunk 473 optimal weight: 8.9990 chunk 358 optimal weight: 0.0370 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN F 93 ASN G 101 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 GLN K 75 ASN K 78 HIS K 79 HIS K 106 GLN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 GLN a 90 ASN b 13 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 ASN h 21 GLN ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 69866 Z= 0.389 Angle : 0.582 16.428 94426 Z= 0.291 Chirality : 0.044 0.207 10207 Planarity : 0.004 0.059 11770 Dihedral : 12.833 177.705 10657 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 2.10 % Allowed : 16.35 % Favored : 81.55 % 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: 0.93 (0.09), residues: 8172 helix: 1.68 (0.08), residues: 4288 sheet: -0.08 (0.24), residues: 451 loop : -0.63 (0.11), residues: 3433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP u 86 HIS 0.006 0.001 HIS r 422 PHE 0.033 0.002 PHE i 292 TYR 0.031 0.002 TYR l 587 ARG 0.013 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1258 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1108 time to evaluate : 5.890 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8741 (ttp-110) REVERT: G 110 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7430 (mt) REVERT: G 146 ASP cc_start: 0.8162 (m-30) cc_final: 0.7921 (m-30) REVERT: I 25 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7723 (pm20) REVERT: J 87 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8683 (tm-30) REVERT: M 75 CYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8791 (p) REVERT: M 678 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7584 (mm110) REVERT: N 133 LYS cc_start: 0.8945 (mmtm) cc_final: 0.8697 (mmtm) REVERT: O 215 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8648 (ptmt) REVERT: P 81 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8798 (p90) REVERT: V 100 THR cc_start: 0.9457 (m) cc_final: 0.9097 (p) REVERT: V 106 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6672 (tpm170) REVERT: W 7 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8391 (tptp) REVERT: X 77 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7110 (tm-30) REVERT: Z 18 ASP cc_start: 0.8456 (t0) cc_final: 0.8223 (t70) REVERT: a 114 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8587 (ttpp) REVERT: a 186 THR cc_start: 0.8814 (m) cc_final: 0.7983 (p) REVERT: d 73 ASP cc_start: 0.8853 (p0) cc_final: 0.8575 (p0) REVERT: e 111 ASP cc_start: 0.8408 (t0) cc_final: 0.8074 (t0) REVERT: i 171 ASN cc_start: 0.9225 (OUTLIER) cc_final: 0.8839 (t160) REVERT: i 339 MET cc_start: 0.9217 (mmm) cc_final: 0.8934 (mmm) REVERT: k 10 MET cc_start: 0.8888 (ttp) cc_final: 0.8655 (ttm) REVERT: k 34 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8350 (mt-10) REVERT: l 70 THR cc_start: 0.9316 (OUTLIER) cc_final: 0.8947 (m) REVERT: l 140 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.8961 (tt) REVERT: m 33 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8815 (tp) REVERT: m 64 MET cc_start: 0.9538 (OUTLIER) cc_final: 0.9301 (mmm) REVERT: m 77 GLU cc_start: 0.8581 (pm20) cc_final: 0.8359 (pm20) REVERT: m 86 ASN cc_start: 0.9316 (t0) cc_final: 0.9021 (t0) REVERT: m 122 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6469 (pt) REVERT: m 141 MET cc_start: 0.9084 (mmp) cc_final: 0.8868 (mmt) REVERT: o 7 LYS cc_start: 0.9210 (ptmm) cc_final: 0.8904 (ptmm) REVERT: r 44 GLN cc_start: 0.9071 (mm110) cc_final: 0.8825 (mm110) REVERT: r 114 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: r 186 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9024 (mp) REVERT: r 204 MET cc_start: 0.9332 (mmm) cc_final: 0.8829 (mmm) REVERT: s 192 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8492 (tm-30) REVERT: v 38 GLU cc_start: 0.7936 (tp30) cc_final: 0.7594 (tm-30) REVERT: v 46 MET cc_start: 0.9238 (mtm) cc_final: 0.8959 (mtp) REVERT: v 103 GLU cc_start: 0.8321 (tp30) cc_final: 0.7921 (tp30) REVERT: w 72 ARG cc_start: 0.8354 (ttp-110) cc_final: 0.7919 (ttp80) outliers start: 150 outliers final: 102 residues processed: 1195 average time/residue: 0.6697 time to fit residues: 1353.7950 Evaluate side-chains 1219 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1099 time to evaluate : 5.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 215 LYS Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 447 VAL Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 140 LYS Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain c residue 122 THR Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain e residue 58 ASP Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 54 GLU Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain i residue 171 ASN Chi-restraints excluded: chain i residue 226 THR Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 172 ILE Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 391 SER Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 442 LEU Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 64 MET Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 122 LEU Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain s residue 168 THR Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 121 ASP Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 184 VAL 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: 0.0370 chunk 463 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 493 optimal weight: 0.3980 chunk 528 optimal weight: 0.9980 chunk 383 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 609 optimal weight: 4.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN F 93 ASN G 101 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 GLN J 124 ASN K 79 HIS K 106 GLN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN V 129 GLN a 90 ASN b 13 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 ASN e 86 ASN h 21 GLN j 10 ASN ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 69866 Z= 0.141 Angle : 0.499 16.699 94426 Z= 0.249 Chirality : 0.039 0.215 10207 Planarity : 0.004 0.059 11770 Dihedral : 12.228 176.148 10657 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.34 % Rotamer: Outliers : 1.57 % Allowed : 17.08 % Favored : 81.36 % 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: 1.17 (0.10), residues: 8172 helix: 1.88 (0.08), residues: 4278 sheet: -0.05 (0.24), residues: 452 loop : -0.51 (0.11), residues: 3442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.005 0.001 HIS i 112 PHE 0.029 0.001 PHE i 292 TYR 0.021 0.001 TYR l 422 ARG 0.013 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1155 time to evaluate : 5.808 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 110 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7290 (mt) REVERT: G 146 ASP cc_start: 0.8185 (m-30) cc_final: 0.7975 (m-30) REVERT: I 67 SER cc_start: 0.9169 (m) cc_final: 0.8904 (p) REVERT: J 87 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8723 (tm-30) REVERT: J 303 ARG cc_start: 0.8407 (tpt170) cc_final: 0.7680 (ttt90) REVERT: L 148 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8661 (mt-10) REVERT: M 75 CYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8715 (p) REVERT: M 678 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7591 (mm110) REVERT: N 76 ASP cc_start: 0.8252 (p0) cc_final: 0.7555 (p0) REVERT: P 81 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8689 (p90) REVERT: U 16 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7881 (tp30) REVERT: V 100 THR cc_start: 0.9404 (m) cc_final: 0.9187 (p) REVERT: V 106 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6640 (tpm170) REVERT: W 98 MET cc_start: 0.8361 (mmt) cc_final: 0.7844 (mmm) REVERT: X 77 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7054 (tm-30) REVERT: Z 18 ASP cc_start: 0.8371 (t0) cc_final: 0.8152 (t70) REVERT: a 114 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8508 (ttpp) REVERT: a 186 THR cc_start: 0.8760 (m) cc_final: 0.7932 (p) REVERT: e 111 ASP cc_start: 0.8358 (t0) cc_final: 0.8044 (t0) REVERT: f 68 GLU cc_start: 0.8989 (tp30) cc_final: 0.8526 (tp30) REVERT: f 73 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8637 (m-40) REVERT: i 54 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8622 (tt0) REVERT: i 89 MET cc_start: 0.9254 (ttm) cc_final: 0.8976 (ttt) REVERT: i 171 ASN cc_start: 0.9208 (OUTLIER) cc_final: 0.8785 (t160) REVERT: j 83 ASN cc_start: 0.9039 (p0) cc_final: 0.8608 (p0) REVERT: j 101 SER cc_start: 0.9241 (p) cc_final: 0.8933 (p) REVERT: k 10 MET cc_start: 0.8823 (ttp) cc_final: 0.8615 (ttm) REVERT: l 70 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.9052 (m) REVERT: l 140 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8906 (tt) REVERT: l 331 MET cc_start: 0.9242 (mmt) cc_final: 0.9040 (mmt) REVERT: m 33 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8716 (tp) REVERT: m 64 MET cc_start: 0.9512 (OUTLIER) cc_final: 0.9139 (mmm) REVERT: m 86 ASN cc_start: 0.9210 (t0) cc_final: 0.8911 (t0) REVERT: m 122 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6561 (pt) REVERT: o 7 LYS cc_start: 0.9145 (ptmm) cc_final: 0.8852 (ptmm) REVERT: r 44 GLN cc_start: 0.9025 (mm110) cc_final: 0.8766 (mm-40) REVERT: r 114 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: r 186 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8990 (mp) REVERT: r 204 MET cc_start: 0.9294 (mmm) cc_final: 0.8732 (mmm) REVERT: s 192 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8463 (tm-30) REVERT: s 224 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8241 (m-80) REVERT: v 38 GLU cc_start: 0.7913 (tp30) cc_final: 0.7571 (tm-30) REVERT: v 52 MET cc_start: 0.8211 (mmt) cc_final: 0.7946 (mmm) REVERT: v 103 GLU cc_start: 0.8291 (tp30) cc_final: 0.7894 (tp30) REVERT: w 72 ARG cc_start: 0.8250 (ttp-110) cc_final: 0.7821 (ttp80) outliers start: 112 outliers final: 75 residues processed: 1211 average time/residue: 0.6480 time to fit residues: 1330.8836 Evaluate side-chains 1219 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1126 time to evaluate : 7.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 447 VAL Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain c residue 122 THR Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 54 GLU Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain i residue 171 ASN Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 391 SER Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 442 LEU Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 64 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 122 LEU Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 283 ASP Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 184 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 0.0370 chunk 743 optimal weight: 2.9990 chunk 678 optimal weight: 4.9990 chunk 723 optimal weight: 1.9990 chunk 435 optimal weight: 1.9990 chunk 314 optimal weight: 2.9990 chunk 567 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 653 optimal weight: 8.9990 chunk 683 optimal weight: 0.0980 chunk 720 optimal weight: 4.9990 overall best weight: 1.4264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN E 45 ASN F 93 ASN G 101 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 GLN K 79 HIS K 106 GLN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 GLN b 13 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 ASN h 21 GLN h 27 HIS ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 69866 Z= 0.203 Angle : 0.516 14.112 94426 Z= 0.257 Chirality : 0.041 0.205 10207 Planarity : 0.004 0.060 11770 Dihedral : 11.945 176.309 10657 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.95 % Rotamer: Outliers : 1.50 % Allowed : 17.24 % Favored : 81.26 % 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: 1.17 (0.10), residues: 8172 helix: 1.87 (0.08), residues: 4284 sheet: -0.03 (0.24), residues: 452 loop : -0.49 (0.11), residues: 3436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.005 0.001 HIS r 422 PHE 0.031 0.001 PHE i 292 TYR 0.021 0.001 TYR d 63 ARG 0.016 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1126 time to evaluate : 5.774 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: G 146 ASP cc_start: 0.8186 (m-30) cc_final: 0.7971 (m-30) REVERT: J 87 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8714 (tm-30) REVERT: J 303 ARG cc_start: 0.8502 (tpt170) cc_final: 0.7733 (ttt90) REVERT: L 148 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8665 (mt-10) REVERT: M 75 CYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8711 (p) REVERT: M 678 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7631 (mm110) REVERT: N 76 ASP cc_start: 0.8162 (p0) cc_final: 0.7546 (p0) REVERT: P 81 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8715 (p90) REVERT: U 16 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7859 (tp30) REVERT: V 8 LYS cc_start: 0.8934 (mtpp) cc_final: 0.8347 (mttt) REVERT: V 100 THR cc_start: 0.9399 (m) cc_final: 0.9175 (p) REVERT: V 106 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6654 (tpm170) REVERT: W 7 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8425 (tptp) REVERT: X 77 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7087 (tm-30) REVERT: Z 18 ASP cc_start: 0.8376 (t0) cc_final: 0.8150 (t70) REVERT: a 114 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8543 (ttpp) REVERT: a 186 THR cc_start: 0.8709 (m) cc_final: 0.7943 (p) REVERT: b 121 LYS cc_start: 0.8889 (tmtt) cc_final: 0.8105 (tmtt) REVERT: e 111 ASP cc_start: 0.8400 (t0) cc_final: 0.8081 (t0) REVERT: f 68 GLU cc_start: 0.9014 (tp30) cc_final: 0.8552 (tp30) REVERT: i 171 ASN cc_start: 0.9216 (OUTLIER) cc_final: 0.8815 (t160) REVERT: j 83 ASN cc_start: 0.9046 (p0) cc_final: 0.8609 (p0) REVERT: j 101 SER cc_start: 0.9245 (p) cc_final: 0.8932 (p) REVERT: k 10 MET cc_start: 0.8844 (ttp) cc_final: 0.8624 (ttm) REVERT: l 70 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.9062 (m) REVERT: l 140 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8933 (tt) REVERT: l 331 MET cc_start: 0.9261 (mmt) cc_final: 0.9059 (mmt) REVERT: m 33 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8785 (tp) REVERT: m 64 MET cc_start: 0.9432 (OUTLIER) cc_final: 0.9192 (mmm) REVERT: m 86 ASN cc_start: 0.9225 (t0) cc_final: 0.8925 (t0) REVERT: m 122 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6558 (pt) REVERT: r 44 GLN cc_start: 0.9027 (mm110) cc_final: 0.8765 (mm-40) REVERT: r 114 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: r 186 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8999 (mp) REVERT: r 204 MET cc_start: 0.9297 (mmm) cc_final: 0.8723 (mmm) REVERT: s 192 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8439 (tm-30) REVERT: s 224 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: v 52 MET cc_start: 0.8257 (mmt) cc_final: 0.8033 (mmm) REVERT: v 95 TYR cc_start: 0.9338 (t80) cc_final: 0.8897 (t80) REVERT: v 103 GLU cc_start: 0.8310 (tp30) cc_final: 0.7917 (tp30) outliers start: 107 outliers final: 81 residues processed: 1180 average time/residue: 0.6584 time to fit residues: 1316.8282 Evaluate side-chains 1215 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1118 time to evaluate : 5.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain J residue 76 MET Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 447 VAL Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain c residue 122 THR Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 54 GLU Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain i residue 171 ASN Chi-restraints excluded: chain i residue 226 THR Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 391 SER Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 442 LEU Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 64 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 122 LEU Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 283 ASP Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 184 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 474 optimal weight: 7.9990 chunk 764 optimal weight: 4.9990 chunk 466 optimal weight: 1.9990 chunk 362 optimal weight: 5.9990 chunk 531 optimal weight: 5.9990 chunk 801 optimal weight: 0.9990 chunk 738 optimal weight: 5.9990 chunk 638 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 493 optimal weight: 0.0050 chunk 391 optimal weight: 5.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN F 93 ASN G 101 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 GLN K 106 GLN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 GLN Y 49 GLN b 13 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 69866 Z= 0.273 Angle : 0.547 17.534 94426 Z= 0.272 Chirality : 0.042 0.208 10207 Planarity : 0.004 0.070 11770 Dihedral : 11.857 177.226 10657 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.05 % Favored : 95.89 % Rotamer: Outliers : 1.55 % Allowed : 17.27 % Favored : 81.18 % 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: 1.11 (0.10), residues: 8172 helix: 1.82 (0.08), residues: 4273 sheet: -0.07 (0.24), residues: 452 loop : -0.51 (0.11), residues: 3447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP u 86 HIS 0.005 0.001 HIS r 422 PHE 0.033 0.001 PHE i 292 TYR 0.024 0.001 TYR l 587 ARG 0.018 0.000 ARG h 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1230 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1119 time to evaluate : 5.944 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8748 (ttp-110) REVERT: G 110 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7277 (mt) REVERT: G 146 ASP cc_start: 0.8192 (m-30) cc_final: 0.7974 (m-30) REVERT: J 87 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8697 (tm-30) REVERT: J 303 ARG cc_start: 0.8525 (tpt170) cc_final: 0.7756 (ttt90) REVERT: M 75 CYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8744 (p) REVERT: N 76 ASP cc_start: 0.8259 (p0) cc_final: 0.7601 (p0) REVERT: P 81 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8738 (p90) REVERT: U 16 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7862 (tp30) REVERT: V 100 THR cc_start: 0.9416 (m) cc_final: 0.9148 (p) REVERT: V 106 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6650 (tpm170) REVERT: W 7 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8411 (tptp) REVERT: X 77 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7091 (tm-30) REVERT: Z 18 ASP cc_start: 0.8394 (t0) cc_final: 0.8170 (t70) REVERT: a 114 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8561 (ttpp) REVERT: a 186 THR cc_start: 0.8724 (m) cc_final: 0.7948 (p) REVERT: e 111 ASP cc_start: 0.8430 (t0) cc_final: 0.8131 (t0) REVERT: i 54 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8637 (tt0) REVERT: i 171 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8793 (t160) REVERT: j 73 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9083 (mp) REVERT: j 83 ASN cc_start: 0.9073 (p0) cc_final: 0.8640 (p0) REVERT: j 101 SER cc_start: 0.9235 (p) cc_final: 0.8916 (p) REVERT: k 10 MET cc_start: 0.8863 (ttp) cc_final: 0.8647 (ttm) REVERT: l 70 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9042 (m) REVERT: l 140 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8950 (tt) REVERT: m 33 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8820 (tp) REVERT: m 64 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.9130 (mmm) REVERT: m 86 ASN cc_start: 0.9262 (t0) cc_final: 0.8967 (t0) REVERT: m 122 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6527 (pt) REVERT: m 141 MET cc_start: 0.8967 (mmp) cc_final: 0.8755 (mmt) REVERT: o 7 LYS cc_start: 0.9174 (ptmm) cc_final: 0.8915 (ptmm) REVERT: o 120 LYS cc_start: 0.8392 (pttm) cc_final: 0.8055 (mttp) REVERT: r 44 GLN cc_start: 0.9052 (mm110) cc_final: 0.8834 (mm110) REVERT: r 114 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: r 186 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9009 (mp) REVERT: r 204 MET cc_start: 0.9300 (mmm) cc_final: 0.8739 (mmm) REVERT: s 192 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8476 (tm-30) REVERT: v 52 MET cc_start: 0.8269 (mmt) cc_final: 0.8025 (mmm) REVERT: v 103 GLU cc_start: 0.8347 (tp30) cc_final: 0.7935 (tp30) REVERT: w 72 ARG cc_start: 0.8299 (ttp-110) cc_final: 0.7845 (ttp80) outliers start: 111 outliers final: 84 residues processed: 1178 average time/residue: 0.6543 time to fit residues: 1304.7065 Evaluate side-chains 1213 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1110 time to evaluate : 5.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain J residue 76 MET Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 447 VAL Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 140 LYS Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain c residue 122 THR Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 54 GLU Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain i residue 171 ASN Chi-restraints excluded: chain i residue 226 THR Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 172 ILE Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 254 VAL Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 391 SER Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 442 LEU Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 64 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 122 LEU Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 283 ASP Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 184 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 507 optimal weight: 0.2980 chunk 680 optimal weight: 0.0570 chunk 195 optimal weight: 5.9990 chunk 588 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 639 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 chunk 656 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN F 93 ASN G 101 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 GLN K 106 GLN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 GLN Y 49 GLN ** a 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN e 86 ASN h 21 GLN j 28 ASN ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.093847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.074541 restraints weight = 110440.102| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 1.90 r_work: 0.2666 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 69866 Z= 0.136 Angle : 0.506 16.789 94426 Z= 0.252 Chirality : 0.039 0.209 10207 Planarity : 0.004 0.069 11770 Dihedral : 11.360 175.363 10657 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 1.27 % Allowed : 17.62 % Favored : 81.11 % 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: 1.25 (0.10), residues: 8172 helix: 1.94 (0.08), residues: 4275 sheet: 0.05 (0.24), residues: 459 loop : -0.46 (0.11), residues: 3438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP u 86 HIS 0.004 0.000 HIS r 422 PHE 0.029 0.001 PHE i 292 TYR 0.022 0.001 TYR l 422 ARG 0.017 0.000 ARG h 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19828.53 seconds wall clock time: 347 minutes 12.92 seconds (20832.92 seconds total)