Starting phenix.real_space_refine on Sat Feb 17 06:47:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d09_30527/02_2024/7d09_30527_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d09_30527/02_2024/7d09_30527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d09_30527/02_2024/7d09_30527.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d09_30527/02_2024/7d09_30527.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d09_30527/02_2024/7d09_30527_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d09_30527/02_2024/7d09_30527_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 88 5.16 5 C 11342 2.51 5 N 2988 2.21 5 O 3378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 175": "OE1" <-> "OE2" Residue "E GLU 254": "OE1" <-> "OE2" Residue "F GLU 8": "OE1" <-> "OE2" Residue "G ARG 4": "NH1" <-> "NH2" Residue "G ASP 38": "OD1" <-> "OD2" Residue "G PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "G TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 4": "NH1" <-> "NH2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "I TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 78": "NH1" <-> "NH2" Residue "I GLU 96": "OE1" <-> "OE2" Residue "I GLU 186": "OE1" <-> "OE2" Residue "J ARG 4": "NH1" <-> "NH2" Residue "J GLU 7": "OE1" <-> "OE2" Residue "J GLU 186": "OE1" <-> "OE2" Residue "K ARG 4": "NH1" <-> "NH2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K ARG 78": "NH1" <-> "NH2" Residue "K GLU 100": "OE1" <-> "OE2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 186": "OE1" <-> "OE2" Residue "L PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17802 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1902 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "B" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2032 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain: "C" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 763 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1902 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "E" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2032 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain: "F" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 763 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "G" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "H" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "I" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "J" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "K" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "L" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.74, per 1000 atoms: 0.55 Number of scatterers: 17802 At special positions: 0 Unit cell: (131.527, 121.744, 148.919, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 6 15.00 O 3378 8.00 N 2988 7.00 C 11342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 6.95 Conformation dependent library (CDL) restraints added in 3.5 seconds 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4328 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 16 sheets defined 39.9% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 2 through 29 removed outlier: 3.609A pdb=" N GLU A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 28 " --> pdb=" O MET A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 48 removed outlier: 3.614A pdb=" N PHE A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 75 removed outlier: 4.211A pdb=" N LEU A 54 " --> pdb=" O MET A 51 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 55 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 56 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A 57 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 58 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 59 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 60 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 63 " --> pdb=" O GLY A 60 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 65 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 67 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY A 68 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN A 70 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY A 71 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR A 72 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 74 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 75 " --> pdb=" O TYR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 removed outlier: 3.534A pdb=" N SER A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 removed outlier: 3.824A pdb=" N ALA A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 108 No H-bonds generated for 'chain 'A' and resid 105 through 108' Processing helix chain 'A' and resid 110 through 122 removed outlier: 3.764A pdb=" N THR A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 removed outlier: 3.649A pdb=" N MET A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 139 No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 141 through 172 removed outlier: 3.568A pdb=" N VAL A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Proline residue: A 153 - end of helix removed outlier: 3.936A pdb=" N VAL A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 189 removed outlier: 3.670A pdb=" N MET A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 219 removed outlier: 3.633A pdb=" N LYS A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 214 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 254 removed outlier: 3.717A pdb=" N SER A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.643A pdb=" N LEU B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 91 removed outlier: 3.992A pdb=" N ALA B 90 " --> pdb=" O PHE B 86 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.632A pdb=" N HIS B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 137 removed outlier: 3.963A pdb=" N GLU B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 163 removed outlier: 3.977A pdb=" N ARG B 156 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 199 removed outlier: 3.814A pdb=" N ARG B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 216 removed outlier: 3.607A pdb=" N SER B 215 " --> pdb=" O PRO B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 239 No H-bonds generated for 'chain 'B' and resid 236 through 239' Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.563A pdb=" N THR B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 33 removed outlier: 3.677A pdb=" N GLY C 27 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 63 removed outlier: 3.511A pdb=" N LEU C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 85 Processing helix chain 'D' and resid 2 through 29 removed outlier: 3.541A pdb=" N GLU D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 18 " --> pdb=" O ARG D 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 28 " --> pdb=" O MET D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 48 removed outlier: 3.615A pdb=" N PHE D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR D 43 " --> pdb=" O GLY D 39 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS D 46 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 75 removed outlier: 4.210A pdb=" N LEU D 54 " --> pdb=" O MET D 51 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE D 55 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE D 56 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR D 57 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 58 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER D 59 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY D 60 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D 63 " --> pdb=" O GLY D 60 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU D 65 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 67 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY D 68 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN D 70 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY D 71 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR D 72 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE D 74 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 75 " --> pdb=" O TYR D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 94 removed outlier: 3.534A pdb=" N SER D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 93 " --> pdb=" O SER D 89 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 103 removed outlier: 3.824A pdb=" N ALA D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 108 No H-bonds generated for 'chain 'D' and resid 105 through 108' Processing helix chain 'D' and resid 110 through 122 removed outlier: 3.764A pdb=" N THR D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 132 removed outlier: 3.648A pdb=" N MET D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 141 through 172 removed outlier: 3.567A pdb=" N VAL D 150 " --> pdb=" O TRP D 146 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER D 151 " --> pdb=" O ALA D 147 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) Proline residue: D 153 - end of helix removed outlier: 3.935A pdb=" N VAL D 157 " --> pdb=" O PRO D 153 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 170 " --> pdb=" O GLY D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 189 removed outlier: 3.670A pdb=" N MET D 186 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN D 188 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN D 189 " --> pdb=" O GLY D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 219 removed outlier: 3.634A pdb=" N LYS D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER D 203 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 209 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA D 214 " --> pdb=" O CYS D 210 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 254 removed outlier: 3.717A pdb=" N SER D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 60 removed outlier: 3.643A pdb=" N LEU E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG E 57 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 91 removed outlier: 3.993A pdb=" N ALA E 90 " --> pdb=" O PHE E 86 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 111 Processing helix chain 'E' and resid 113 through 118 removed outlier: 3.633A pdb=" N HIS E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 137 removed outlier: 3.963A pdb=" N GLU E 128 " --> pdb=" O ASN E 124 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 163 removed outlier: 3.977A pdb=" N ARG E 156 " --> pdb=" O GLY E 152 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 199 removed outlier: 3.814A pdb=" N ARG E 190 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG E 193 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 216 removed outlier: 3.606A pdb=" N SER E 215 " --> pdb=" O PRO E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 239 No H-bonds generated for 'chain 'E' and resid 236 through 239' Processing helix chain 'E' and resid 245 through 250 removed outlier: 3.563A pdb=" N THR E 250 " --> pdb=" O LYS E 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 33 removed outlier: 3.678A pdb=" N GLY F 27 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE F 31 " --> pdb=" O GLY F 27 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS F 32 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS F 33 " --> pdb=" O ALA F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 62 removed outlier: 3.511A pdb=" N LEU F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 85 Processing helix chain 'G' and resid 4 through 25 removed outlier: 3.555A pdb=" N GLY G 11 " --> pdb=" O GLU G 7 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE G 16 " --> pdb=" O ILE G 12 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 108 removed outlier: 4.644A pdb=" N GLN G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS G 103 " --> pdb=" O LYS G 99 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 132 removed outlier: 3.576A pdb=" N GLN G 129 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU G 130 " --> pdb=" O MET G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 192 Processing helix chain 'H' and resid 5 through 19 removed outlier: 3.729A pdb=" N VAL H 10 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 29 removed outlier: 3.577A pdb=" N SER H 29 " --> pdb=" O ALA H 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 25 through 29' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 95 through 109 removed outlier: 3.949A pdb=" N LYS H 99 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS H 103 " --> pdb=" O LYS H 99 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA H 105 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU H 106 " --> pdb=" O GLN H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 125 through 131 removed outlier: 3.988A pdb=" N GLN H 129 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU H 130 " --> pdb=" O MET H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 192 removed outlier: 4.729A pdb=" N LYS H 191 " --> pdb=" O ASP H 187 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE H 192 " --> pdb=" O LEU H 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 187 through 192' Processing helix chain 'I' and resid 6 through 27 removed outlier: 3.731A pdb=" N VAL I 10 " --> pdb=" O SER I 6 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY I 11 " --> pdb=" O GLU I 7 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE I 17 " --> pdb=" O PHE I 13 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU I 21 " --> pdb=" O PHE I 17 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 100 removed outlier: 4.075A pdb=" N LYS I 99 " --> pdb=" O ALA I 95 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU I 100 " --> pdb=" O GLU I 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 95 through 100' Processing helix chain 'I' and resid 105 through 109 removed outlier: 4.061A pdb=" N LEU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 105 through 109' Processing helix chain 'I' and resid 116 through 118 No H-bonds generated for 'chain 'I' and resid 116 through 118' Processing helix chain 'I' and resid 125 through 131 removed outlier: 4.328A pdb=" N LEU I 130 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 191 removed outlier: 4.385A pdb=" N SER I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 8 Processing helix chain 'J' and resid 11 through 27 removed outlier: 3.620A pdb=" N ILE J 15 " --> pdb=" O GLY J 11 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 105 removed outlier: 3.661A pdb=" N LYS J 99 " --> pdb=" O GLU J 96 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL J 101 " --> pdb=" O LEU J 98 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS J 103 " --> pdb=" O GLU J 100 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN J 104 " --> pdb=" O VAL J 101 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA J 105 " --> pdb=" O GLN J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 117 removed outlier: 4.337A pdb=" N GLN J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 131 removed outlier: 4.495A pdb=" N LEU J 130 " --> pdb=" O MET J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 188 No H-bonds generated for 'chain 'J' and resid 185 through 188' Processing helix chain 'K' and resid 4 through 22 removed outlier: 4.378A pdb=" N VAL K 14 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 105 removed outlier: 4.303A pdb=" N LYS K 103 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN K 104 " --> pdb=" O GLU K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 133 removed outlier: 3.968A pdb=" N ILE K 131 " --> pdb=" O GLU K 127 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER K 132 " --> pdb=" O GLN K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 192 removed outlier: 3.506A pdb=" N ILE K 189 " --> pdb=" O LEU K 185 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER K 190 " --> pdb=" O GLU K 186 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS K 191 " --> pdb=" O ASP K 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 7 Processing helix chain 'L' and resid 10 through 27 removed outlier: 3.902A pdb=" N ILE L 15 " --> pdb=" O GLY L 11 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE L 17 " --> pdb=" O PHE L 13 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU L 21 " --> pdb=" O PHE L 17 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE L 22 " --> pdb=" O GLY L 18 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA L 25 " --> pdb=" O LEU L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 91 No H-bonds generated for 'chain 'L' and resid 88 through 91' Processing helix chain 'L' and resid 95 through 101 removed outlier: 3.646A pdb=" N GLU L 100 " --> pdb=" O GLU L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 109 removed outlier: 3.963A pdb=" N GLU L 108 " --> pdb=" O ASN L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 122 Processing helix chain 'L' and resid 124 through 134 removed outlier: 3.716A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLN L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU L 130 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE L 131 " --> pdb=" O GLU L 127 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER L 132 " --> pdb=" O GLN L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 191 Processing sheet with id= A, first strand: chain 'B' and resid 69 through 72 removed outlier: 3.829A pdb=" N GLU B 69 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 17 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 36 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU B 15 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 34 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 228 through 232 removed outlier: 6.787A pdb=" N VAL B 222 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU B 231 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 220 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE B 171 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N VAL B 206 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR B 173 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLY B 93 " --> pdb=" O MET B 172 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ASP B 174 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B 95 " --> pdb=" O ASP B 174 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 69 through 72 removed outlier: 3.830A pdb=" N GLU E 69 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS E 17 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE E 36 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU E 15 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU E 34 " --> pdb=" O GLU E 15 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 228 through 232 removed outlier: 6.787A pdb=" N VAL E 222 " --> pdb=" O GLN E 229 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU E 231 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE E 220 " --> pdb=" O GLU E 231 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE E 171 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N VAL E 206 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR E 173 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY E 93 " --> pdb=" O MET E 172 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ASP E 174 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU E 95 " --> pdb=" O ASP E 174 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 41 through 46 removed outlier: 3.825A pdb=" N THR G 83 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER G 70 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP G 85 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL G 68 " --> pdb=" O ASP G 85 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 145 through 150 removed outlier: 3.509A pdb=" N ALA G 149 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 39 through 44 removed outlier: 3.620A pdb=" N TYR H 40 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP H 85 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VAL H 68 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP H 87 " --> pdb=" O GLY H 66 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLY H 66 " --> pdb=" O ASP H 87 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL H 58 " --> pdb=" O ILE H 65 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 145 through 150 Processing sheet with id= I, first strand: chain 'I' and resid 41 through 46 removed outlier: 5.816A pdb=" N ASP I 85 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL I 68 " --> pdb=" O ASP I 85 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL I 58 " --> pdb=" O ILE I 65 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 145 through 149 Processing sheet with id= K, first strand: chain 'J' and resid 42 through 44 removed outlier: 3.519A pdb=" N LEU J 79 " --> pdb=" O ASP J 74 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER J 70 " --> pdb=" O THR J 83 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'J' and resid 145 through 150 removed outlier: 3.554A pdb=" N TYR J 145 " --> pdb=" O VAL J 162 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL J 162 " --> pdb=" O TYR J 145 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'K' and resid 40 through 46 removed outlier: 3.632A pdb=" N ALA K 44 " --> pdb=" O VAL K 82 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE K 46 " --> pdb=" O ALA K 80 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASP K 85 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL K 68 " --> pdb=" O ASP K 85 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'K' and resid 145 through 149 removed outlier: 3.619A pdb=" N TYR K 145 " --> pdb=" O VAL K 162 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR K 158 " --> pdb=" O ALA K 149 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'L' and resid 41 through 44 removed outlier: 3.645A pdb=" N PHE L 84 " --> pdb=" O MET L 42 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU L 79 " --> pdb=" O ASP L 74 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP L 85 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL L 68 " --> pdb=" O ASP L 85 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 145 through 149 490 hydrogen bonds defined for protein. 1374 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: 4.13 Time building geometry restraints manager: 7.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5574 1.33 - 1.46: 2726 1.46 - 1.58: 9566 1.58 - 1.70: 10 1.70 - 1.82: 168 Bond restraints: 18044 Sorted by residual: bond pdb=" C4 ATP E 301 " pdb=" C5 ATP E 301 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.40e+01 bond pdb=" C4 ATP B 301 " pdb=" C5 ATP B 301 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.38e+01 bond pdb=" C5 ATP B 301 " pdb=" C6 ATP B 301 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.04e+01 bond pdb=" C5 ATP E 301 " pdb=" C6 ATP E 301 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.87e+01 bond pdb=" C5 ATP B 301 " pdb=" N7 ATP B 301 " ideal model delta sigma weight residual 1.387 1.331 0.056 1.00e-02 1.00e+04 3.15e+01 ... (remaining 18039 not shown) Histogram of bond angle deviations from ideal: 98.88 - 106.25: 360 106.25 - 113.61: 10343 113.61 - 120.98: 8698 120.98 - 128.35: 4971 128.35 - 135.71: 78 Bond angle restraints: 24450 Sorted by residual: angle pdb=" PB ATP E 301 " pdb=" O3B ATP E 301 " pdb=" PG ATP E 301 " ideal model delta sigma weight residual 139.87 121.53 18.34 1.00e+00 1.00e+00 3.37e+02 angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 121.55 18.32 1.00e+00 1.00e+00 3.36e+02 angle pdb=" PA ATP B 301 " pdb=" O3A ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 136.83 121.95 14.88 1.00e+00 1.00e+00 2.21e+02 angle pdb=" PA ATP E 301 " pdb=" O3A ATP E 301 " pdb=" PB ATP E 301 " ideal model delta sigma weight residual 136.83 121.97 14.86 1.00e+00 1.00e+00 2.21e+02 angle pdb=" C ASP E 209 " pdb=" N VAL E 210 " pdb=" CA VAL E 210 " ideal model delta sigma weight residual 120.24 125.66 -5.42 6.30e-01 2.52e+00 7.41e+01 ... (remaining 24445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 9531 17.65 - 35.31: 963 35.31 - 52.96: 240 52.96 - 70.61: 110 70.61 - 88.26: 30 Dihedral angle restraints: 10874 sinusoidal: 4132 harmonic: 6742 Sorted by residual: dihedral pdb=" CA CYS D 221 " pdb=" C CYS D 221 " pdb=" N ASP D 222 " pdb=" CA ASP D 222 " ideal model delta harmonic sigma weight residual 180.00 152.49 27.51 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA CYS A 221 " pdb=" C CYS A 221 " pdb=" N ASP A 222 " pdb=" CA ASP A 222 " ideal model delta harmonic sigma weight residual 180.00 152.51 27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ALA G 144 " pdb=" C ALA G 144 " pdb=" N TYR G 145 " pdb=" CA TYR G 145 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 10871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2215 0.056 - 0.112: 575 0.112 - 0.168: 152 0.168 - 0.225: 18 0.225 - 0.281: 6 Chirality restraints: 2966 Sorted by residual: chirality pdb=" CB THR E 142 " pdb=" CA THR E 142 " pdb=" OG1 THR E 142 " pdb=" CG2 THR E 142 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB THR B 142 " pdb=" CA THR B 142 " pdb=" OG1 THR B 142 " pdb=" CG2 THR B 142 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA ARG E 140 " pdb=" N ARG E 140 " pdb=" C ARG E 140 " pdb=" CB ARG E 140 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 2963 not shown) Planarity restraints: 3102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 51 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C THR C 51 " 0.051 2.00e-02 2.50e+03 pdb=" O THR C 51 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU C 52 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 51 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.54e+00 pdb=" C THR F 51 " 0.051 2.00e-02 2.50e+03 pdb=" O THR F 51 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU F 52 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 97 " -0.048 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO A 98 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " -0.041 5.00e-02 4.00e+02 ... (remaining 3099 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1685 2.72 - 3.27: 16871 3.27 - 3.81: 27711 3.81 - 4.36: 33189 4.36 - 4.90: 56767 Nonbonded interactions: 136223 Sorted by model distance: nonbonded pdb=" N MET G 26 " pdb=" SD MET G 26 " model vdw 2.181 2.880 nonbonded pdb=" CG2 VAL K 76 " pdb=" OE1 GLN L 97 " model vdw 2.222 3.460 nonbonded pdb=" OE2 GLU G 186 " pdb=" OG1 THR H 150 " model vdw 2.234 2.440 nonbonded pdb=" CD1 LEU H 185 " pdb=" CG2 THR I 150 " model vdw 2.241 3.880 nonbonded pdb=" CG1 VAL G 63 " pdb=" CD1 LEU L 73 " model vdw 2.242 3.880 ... (remaining 136218 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 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 0.010 Extract box with map and model: 2.690 Check model and map are aligned: 0.280 Set scattering table: 0.140 Process input model: 47.400 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 0.080 18044 Z= 0.486 Angle : 1.112 18.344 24450 Z= 0.705 Chirality : 0.056 0.281 2966 Planarity : 0.006 0.072 3102 Dihedral : 17.110 88.263 6546 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 1.23 % Allowed : 9.28 % Favored : 89.49 % Rotamer: Outliers : 8.59 % Allowed : 10.41 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -6.00 (0.12), residues: 2350 helix: -4.77 (0.05), residues: 986 sheet: -2.72 (0.27), residues: 301 loop : -3.45 (0.15), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 212 HIS 0.005 0.001 HIS F 48 PHE 0.021 0.002 PHE I 13 TYR 0.019 0.002 TYR G 40 ARG 0.008 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 420 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.5596 (OUTLIER) cc_final: 0.4283 (m) REVERT: A 95 GLU cc_start: 0.8324 (tp30) cc_final: 0.7020 (tt0) REVERT: A 116 GLU cc_start: 0.7629 (tt0) cc_final: 0.7349 (mt-10) REVERT: A 154 MET cc_start: 0.8549 (mtp) cc_final: 0.8347 (mtp) REVERT: A 168 LYS cc_start: 0.9077 (tmtt) cc_final: 0.8838 (tttm) REVERT: B 227 LYS cc_start: 0.8484 (pttp) cc_final: 0.8202 (mptt) REVERT: B 229 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8410 (mp10) REVERT: C 18 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7777 (pm20) REVERT: C 19 ASN cc_start: 0.8261 (p0) cc_final: 0.7977 (p0) REVERT: C 80 LEU cc_start: 0.8879 (pt) cc_final: 0.8275 (pt) REVERT: D 24 MET cc_start: 0.9159 (ttp) cc_final: 0.8881 (ttm) REVERT: D 116 GLU cc_start: 0.7439 (tt0) cc_final: 0.7229 (mt-10) REVERT: D 138 LYS cc_start: 0.8834 (tppt) cc_final: 0.8431 (tttt) REVERT: D 230 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8940 (m) REVERT: D 232 MET cc_start: 0.9008 (mtp) cc_final: 0.8719 (mtm) REVERT: E 135 GLU cc_start: 0.8014 (tp30) cc_final: 0.7629 (tm-30) REVERT: E 169 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7811 (m-30) REVERT: E 229 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8860 (mm110) REVERT: E 246 LYS cc_start: 0.9192 (tttp) cc_final: 0.8350 (pttp) REVERT: F 42 ASP cc_start: 0.7496 (m-30) cc_final: 0.7233 (t0) REVERT: F 43 LEU cc_start: 0.8538 (pt) cc_final: 0.8238 (pp) REVERT: F 73 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7966 (tppt) REVERT: F 78 LYS cc_start: 0.8918 (tmtt) cc_final: 0.8458 (ttpt) REVERT: G 129 GLN cc_start: 0.2527 (tt0) cc_final: 0.1959 (tt0) REVERT: G 168 ASN cc_start: 0.7879 (m110) cc_final: 0.7650 (m110) REVERT: G 192 PHE cc_start: 0.6591 (t80) cc_final: 0.6198 (t80) REVERT: H 85 ASP cc_start: 0.8729 (p0) cc_final: 0.8523 (p0) REVERT: H 143 ASP cc_start: 0.8067 (p0) cc_final: 0.7772 (p0) REVERT: H 183 MET cc_start: 0.5919 (ttp) cc_final: 0.5702 (ttm) REVERT: H 192 PHE cc_start: 0.5639 (t80) cc_final: 0.4963 (t80) REVERT: I 50 ASN cc_start: 0.8622 (m-40) cc_final: 0.7866 (m110) REVERT: J 87 ASP cc_start: 0.7350 (m-30) cc_final: 0.6993 (t70) REVERT: J 180 GLN cc_start: 0.6512 (pt0) cc_final: 0.6090 (pt0) REVERT: K 97 GLN cc_start: 0.6105 (tt0) cc_final: 0.5393 (mm110) REVERT: L 189 ILE cc_start: 0.6279 (OUTLIER) cc_final: 0.6072 (mm) REVERT: L 191 LYS cc_start: 0.5508 (OUTLIER) cc_final: 0.4781 (ptmm) outliers start: 161 outliers final: 37 residues processed: 524 average time/residue: 0.3164 time to fit residues: 241.3679 Evaluate side-chains 354 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 308 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 189 ILE Chi-restraints excluded: chain L residue 191 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.0470 chunk 177 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 70 GLN A 189 ASN A 198 ASN B 31 ASN B 229 GLN B 263 HIS C 34 GLN C 45 GLN C 66 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS D 46 HIS D 70 GLN E 31 ASN E 263 HIS F 45 GLN F 48 HIS G 128 GLN H 45 GLN H 102 GLN ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 ASN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 ASN ** K 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN L 180 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18044 Z= 0.194 Angle : 0.618 8.309 24450 Z= 0.322 Chirality : 0.042 0.166 2966 Planarity : 0.004 0.049 3102 Dihedral : 9.437 74.195 2663 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.98 % Favored : 92.72 % Rotamer: Outliers : 4.48 % Allowed : 16.33 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.63 (0.14), residues: 2350 helix: -3.22 (0.11), residues: 982 sheet: -2.29 (0.27), residues: 296 loop : -3.07 (0.16), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 212 HIS 0.003 0.001 HIS C 71 PHE 0.037 0.001 PHE C 37 TYR 0.018 0.001 TYR E 259 ARG 0.006 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 337 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 THR cc_start: 0.7415 (OUTLIER) cc_final: 0.7175 (m) REVERT: A 27 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: A 87 MET cc_start: 0.8054 (tmm) cc_final: 0.7755 (tmm) REVERT: A 95 GLU cc_start: 0.8140 (tp30) cc_final: 0.7911 (tp30) REVERT: C 18 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: C 19 ASN cc_start: 0.8318 (p0) cc_final: 0.7949 (p0) REVERT: D 24 MET cc_start: 0.9132 (ttp) cc_final: 0.8777 (ttm) REVERT: D 116 GLU cc_start: 0.7427 (tt0) cc_final: 0.6973 (mt-10) REVERT: D 234 ARG cc_start: 0.6297 (ttt180) cc_final: 0.5864 (mtm-85) REVERT: E 246 LYS cc_start: 0.9237 (tttp) cc_final: 0.8333 (pttp) REVERT: F 43 LEU cc_start: 0.8340 (pt) cc_final: 0.8010 (pp) REVERT: F 73 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7829 (tppt) REVERT: F 78 LYS cc_start: 0.8860 (tmtt) cc_final: 0.8636 (tptp) REVERT: F 84 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8158 (mp10) REVERT: G 64 THR cc_start: 0.8355 (m) cc_final: 0.8108 (p) REVERT: H 96 GLU cc_start: 0.7553 (pm20) cc_final: 0.7053 (pm20) REVERT: H 143 ASP cc_start: 0.7955 (p0) cc_final: 0.7633 (p0) REVERT: I 48 ASN cc_start: 0.7923 (t0) cc_final: 0.7268 (t0) REVERT: I 50 ASN cc_start: 0.8242 (m-40) cc_final: 0.7782 (m110) REVERT: I 141 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6900 (m-30) REVERT: J 151 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.7428 (p0) REVERT: K 7 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7394 (mm-30) REVERT: K 97 GLN cc_start: 0.6004 (tt0) cc_final: 0.5220 (mm110) REVERT: L 134 MET cc_start: 0.6481 (tmm) cc_final: 0.6204 (tmm) REVERT: L 135 ASN cc_start: 0.7071 (OUTLIER) cc_final: 0.6833 (m110) REVERT: L 191 LYS cc_start: 0.5238 (OUTLIER) cc_final: 0.4687 (ptmm) outliers start: 84 outliers final: 41 residues processed: 393 average time/residue: 0.3010 time to fit residues: 177.4976 Evaluate side-chains 338 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 287 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 191 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 0.0070 chunk 65 optimal weight: 0.9980 chunk 176 optimal weight: 10.0000 chunk 144 optimal weight: 0.3980 chunk 58 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 229 optimal weight: 20.0000 chunk 189 optimal weight: 0.9990 chunk 211 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 170 optimal weight: 30.0000 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN C 66 GLN C 74 ASN C 89 GLN H 94 ASN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN K 180 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18044 Z= 0.137 Angle : 0.562 8.608 24450 Z= 0.289 Chirality : 0.041 0.150 2966 Planarity : 0.003 0.038 3102 Dihedral : 7.570 66.520 2598 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.51 % Favored : 93.36 % Rotamer: Outliers : 3.90 % Allowed : 18.25 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.70 (0.15), residues: 2350 helix: -2.20 (0.14), residues: 1000 sheet: -1.83 (0.29), residues: 295 loop : -2.84 (0.16), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 212 HIS 0.002 0.000 HIS C 71 PHE 0.012 0.001 PHE A 182 TYR 0.020 0.001 TYR E 259 ARG 0.005 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 324 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: A 80 SER cc_start: 0.5962 (OUTLIER) cc_final: 0.5656 (p) REVERT: A 95 GLU cc_start: 0.8079 (tp30) cc_final: 0.7807 (tp30) REVERT: C 19 ASN cc_start: 0.8240 (p0) cc_final: 0.7905 (p0) REVERT: C 91 ASP cc_start: 0.8455 (t0) cc_final: 0.8085 (t0) REVERT: D 24 MET cc_start: 0.9082 (ttp) cc_final: 0.8689 (ttm) REVERT: D 116 GLU cc_start: 0.7386 (tt0) cc_final: 0.7116 (mt-10) REVERT: D 230 THR cc_start: 0.9247 (t) cc_final: 0.8999 (m) REVERT: D 234 ARG cc_start: 0.6289 (ttt180) cc_final: 0.5925 (mtm-85) REVERT: E 75 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8405 (mmtm) REVERT: E 82 ARG cc_start: 0.8008 (tpp80) cc_final: 0.7770 (mmm160) REVERT: E 145 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8229 (pp) REVERT: E 246 LYS cc_start: 0.9253 (tttp) cc_final: 0.8342 (pttp) REVERT: F 43 LEU cc_start: 0.7998 (pt) cc_final: 0.7662 (pp) REVERT: F 78 LYS cc_start: 0.8863 (tmtt) cc_final: 0.8521 (ttpt) REVERT: F 84 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8087 (mp-120) REVERT: G 64 THR cc_start: 0.8317 (m) cc_final: 0.8103 (p) REVERT: G 168 ASN cc_start: 0.7986 (m110) cc_final: 0.7747 (m-40) REVERT: H 94 ASN cc_start: 0.6417 (OUTLIER) cc_final: 0.5714 (m-40) REVERT: H 134 MET cc_start: 0.6108 (mtt) cc_final: 0.5700 (ttp) REVERT: I 50 ASN cc_start: 0.8251 (m-40) cc_final: 0.7837 (m110) REVERT: I 141 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6737 (m-30) REVERT: I 154 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7523 (mp) REVERT: J 147 MET cc_start: 0.6606 (ptp) cc_final: 0.6391 (ptp) REVERT: K 7 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7248 (mm-30) REVERT: K 97 GLN cc_start: 0.6350 (tt0) cc_final: 0.5502 (mm110) REVERT: K 98 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6582 (mm) REVERT: L 191 LYS cc_start: 0.5207 (OUTLIER) cc_final: 0.4675 (ptmm) outliers start: 73 outliers final: 45 residues processed: 371 average time/residue: 0.3072 time to fit residues: 168.7861 Evaluate side-chains 339 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 284 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 191 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 23 optimal weight: 0.0770 chunk 101 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 213 optimal weight: 0.0060 chunk 226 optimal weight: 50.0000 chunk 111 optimal weight: 0.1980 chunk 202 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 overall best weight: 1.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN C 66 GLN C 93 HIS D 139 GLN F 74 ASN G 180 GLN H 94 ASN ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18044 Z= 0.165 Angle : 0.556 9.473 24450 Z= 0.285 Chirality : 0.041 0.141 2966 Planarity : 0.003 0.044 3102 Dihedral : 6.894 67.004 2581 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.38 % Favored : 93.49 % Rotamer: Outliers : 4.11 % Allowed : 19.42 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.13 (0.16), residues: 2350 helix: -1.56 (0.15), residues: 1003 sheet: -1.57 (0.30), residues: 293 loop : -2.71 (0.17), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 212 HIS 0.002 0.001 HIS B 208 PHE 0.038 0.001 PHE C 37 TYR 0.018 0.001 TYR E 259 ARG 0.005 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 309 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: A 95 GLU cc_start: 0.8151 (tp30) cc_final: 0.7821 (tp30) REVERT: B 19 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8631 (pt) REVERT: C 19 ASN cc_start: 0.8437 (p0) cc_final: 0.8051 (p0) REVERT: C 91 ASP cc_start: 0.8582 (t0) cc_final: 0.8096 (t0) REVERT: D 24 MET cc_start: 0.9088 (ttp) cc_final: 0.8724 (ttm) REVERT: D 95 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7660 (tp30) REVERT: D 116 GLU cc_start: 0.7422 (tt0) cc_final: 0.7163 (mt-10) REVERT: D 230 THR cc_start: 0.9270 (t) cc_final: 0.9018 (m) REVERT: D 234 ARG cc_start: 0.6444 (ttt180) cc_final: 0.5961 (mtm-85) REVERT: E 75 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8381 (mmtm) REVERT: E 205 ILE cc_start: 0.8858 (mt) cc_final: 0.8557 (tt) REVERT: E 246 LYS cc_start: 0.9273 (tttp) cc_final: 0.8379 (pttp) REVERT: F 78 LYS cc_start: 0.8873 (tmtt) cc_final: 0.8540 (ttmt) REVERT: G 64 THR cc_start: 0.8305 (m) cc_final: 0.8099 (p) REVERT: H 96 GLU cc_start: 0.8066 (pt0) cc_final: 0.7547 (pm20) REVERT: H 100 GLU cc_start: 0.7860 (pp20) cc_final: 0.7649 (tp30) REVERT: H 134 MET cc_start: 0.6360 (mtt) cc_final: 0.5890 (ttt) REVERT: I 50 ASN cc_start: 0.8257 (m-40) cc_final: 0.7858 (m110) REVERT: I 141 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6701 (m-30) REVERT: J 143 ASP cc_start: 0.8077 (m-30) cc_final: 0.7111 (t0) REVERT: J 151 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.7425 (p0) REVERT: J 189 ILE cc_start: 0.7599 (mm) cc_final: 0.7318 (tp) REVERT: K 97 GLN cc_start: 0.6289 (tt0) cc_final: 0.5480 (mm110) REVERT: K 98 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6612 (mm) REVERT: L 191 LYS cc_start: 0.5199 (OUTLIER) cc_final: 0.4666 (ptmm) outliers start: 77 outliers final: 57 residues processed: 363 average time/residue: 0.2796 time to fit residues: 153.2504 Evaluate side-chains 355 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 291 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 191 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 0.0970 chunk 128 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 overall best weight: 2.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 HIS C 66 GLN E 79 GLN H 94 ASN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18044 Z= 0.207 Angle : 0.570 10.440 24450 Z= 0.292 Chirality : 0.042 0.209 2966 Planarity : 0.003 0.051 3102 Dihedral : 6.787 67.278 2580 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.89 % Favored : 93.02 % Rotamer: Outliers : 4.86 % Allowed : 19.58 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.86 (0.16), residues: 2350 helix: -1.25 (0.16), residues: 1006 sheet: -1.50 (0.31), residues: 293 loop : -2.64 (0.17), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 212 HIS 0.003 0.001 HIS F 71 PHE 0.014 0.001 PHE F 72 TYR 0.015 0.001 TYR E 259 ARG 0.006 0.000 ARG E 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 301 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: A 95 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7856 (tp30) REVERT: B 19 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8608 (pt) REVERT: C 19 ASN cc_start: 0.8485 (p0) cc_final: 0.8098 (p0) REVERT: C 91 ASP cc_start: 0.8666 (t0) cc_final: 0.8309 (t0) REVERT: D 24 MET cc_start: 0.9139 (ttp) cc_final: 0.8771 (ttm) REVERT: D 95 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7681 (tp30) REVERT: D 116 GLU cc_start: 0.7452 (tt0) cc_final: 0.7205 (mt-10) REVERT: D 234 ARG cc_start: 0.6300 (ttt180) cc_final: 0.5950 (mtm-85) REVERT: E 75 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8476 (mmtm) REVERT: E 205 ILE cc_start: 0.8882 (mt) cc_final: 0.8586 (tt) REVERT: E 246 LYS cc_start: 0.9294 (tttp) cc_final: 0.8367 (pttp) REVERT: F 18 GLU cc_start: 0.7767 (pm20) cc_final: 0.7406 (pm20) REVERT: F 78 LYS cc_start: 0.8982 (tmtt) cc_final: 0.8578 (ttmt) REVERT: G 26 MET cc_start: 0.6997 (mpp) cc_final: 0.6775 (mpp) REVERT: G 27 LYS cc_start: 0.8111 (tppp) cc_final: 0.7720 (mmmm) REVERT: H 94 ASN cc_start: 0.6459 (OUTLIER) cc_final: 0.6210 (m-40) REVERT: H 96 GLU cc_start: 0.8030 (pt0) cc_final: 0.7644 (pm20) REVERT: H 100 GLU cc_start: 0.7896 (pp20) cc_final: 0.7640 (tp30) REVERT: H 134 MET cc_start: 0.6431 (mtt) cc_final: 0.5886 (ttt) REVERT: I 50 ASN cc_start: 0.8280 (m-40) cc_final: 0.7828 (m110) REVERT: I 134 MET cc_start: 0.6888 (mmt) cc_final: 0.6589 (mmm) REVERT: I 141 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6676 (m-30) REVERT: J 55 ARG cc_start: 0.6847 (ttm-80) cc_final: 0.6614 (ttm-80) REVERT: J 151 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.7439 (p0) REVERT: J 189 ILE cc_start: 0.7768 (mm) cc_final: 0.7526 (tp) REVERT: K 7 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: L 134 MET cc_start: 0.6882 (tmm) cc_final: 0.6170 (tmm) REVERT: L 191 LYS cc_start: 0.5042 (OUTLIER) cc_final: 0.4575 (ptmm) outliers start: 91 outliers final: 66 residues processed: 364 average time/residue: 0.2909 time to fit residues: 159.0314 Evaluate side-chains 359 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 284 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 191 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN E 97 GLN H 35 ASN ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18044 Z= 0.283 Angle : 0.605 11.162 24450 Z= 0.310 Chirality : 0.044 0.241 2966 Planarity : 0.003 0.052 3102 Dihedral : 6.934 69.006 2580 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.70 % Favored : 92.21 % Rotamer: Outliers : 5.28 % Allowed : 20.06 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.75 (0.16), residues: 2350 helix: -1.18 (0.16), residues: 1007 sheet: -1.47 (0.30), residues: 302 loop : -2.55 (0.17), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 212 HIS 0.003 0.001 HIS B 208 PHE 0.038 0.002 PHE C 37 TYR 0.018 0.002 TYR A 72 ARG 0.004 0.000 ARG J 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 292 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7934 (tp30) REVERT: B 19 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8591 (pt) REVERT: C 19 ASN cc_start: 0.8516 (p0) cc_final: 0.8158 (p0) REVERT: C 91 ASP cc_start: 0.8595 (t0) cc_final: 0.8299 (t0) REVERT: D 24 MET cc_start: 0.9151 (ttp) cc_final: 0.8816 (ttm) REVERT: D 95 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8040 (mm-30) REVERT: D 116 GLU cc_start: 0.7533 (tt0) cc_final: 0.7041 (mt-10) REVERT: D 234 ARG cc_start: 0.6458 (ttt180) cc_final: 0.6091 (mtm-85) REVERT: E 82 ARG cc_start: 0.8054 (tpp80) cc_final: 0.7768 (mmm160) REVERT: E 246 LYS cc_start: 0.9302 (tttp) cc_final: 0.8384 (pttp) REVERT: F 18 GLU cc_start: 0.7680 (pm20) cc_final: 0.7452 (pm20) REVERT: F 78 LYS cc_start: 0.8970 (tmtt) cc_final: 0.8728 (tptp) REVERT: F 79 MET cc_start: 0.8315 (mmp) cc_final: 0.8114 (mmm) REVERT: H 96 GLU cc_start: 0.8072 (pt0) cc_final: 0.7687 (pm20) REVERT: H 100 GLU cc_start: 0.7986 (pp20) cc_final: 0.7731 (tp30) REVERT: H 134 MET cc_start: 0.6338 (mtt) cc_final: 0.5870 (ttt) REVERT: I 50 ASN cc_start: 0.8322 (m-40) cc_final: 0.7870 (m110) REVERT: I 134 MET cc_start: 0.6844 (mmt) cc_final: 0.6485 (mmm) REVERT: I 141 ASP cc_start: 0.7040 (OUTLIER) cc_final: 0.6796 (m-30) REVERT: J 55 ARG cc_start: 0.6903 (ttm-80) cc_final: 0.6645 (ttm-80) REVERT: J 151 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.7420 (p0) REVERT: J 189 ILE cc_start: 0.7795 (mm) cc_final: 0.7527 (tp) REVERT: K 7 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: K 97 GLN cc_start: 0.5665 (tp40) cc_final: 0.5318 (tp40) REVERT: L 134 MET cc_start: 0.6834 (tmm) cc_final: 0.6191 (tmm) REVERT: L 191 LYS cc_start: 0.4994 (OUTLIER) cc_final: 0.4519 (ptmm) outliers start: 99 outliers final: 74 residues processed: 360 average time/residue: 0.2997 time to fit residues: 161.3103 Evaluate side-chains 361 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 280 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 26 MET Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 191 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 225 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 137 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN K 102 GLN ** K 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18044 Z= 0.257 Angle : 0.595 11.724 24450 Z= 0.303 Chirality : 0.043 0.186 2966 Planarity : 0.003 0.054 3102 Dihedral : 6.825 71.177 2578 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.23 % Favored : 92.68 % Rotamer: Outliers : 4.96 % Allowed : 20.65 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.59 (0.16), residues: 2350 helix: -0.99 (0.16), residues: 1001 sheet: -1.46 (0.30), residues: 300 loop : -2.50 (0.17), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 212 HIS 0.003 0.001 HIS B 208 PHE 0.012 0.001 PHE G 13 TYR 0.014 0.001 TYR K 169 ARG 0.005 0.000 ARG J 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 296 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7918 (tp30) REVERT: B 19 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8574 (pt) REVERT: C 19 ASN cc_start: 0.8500 (p0) cc_final: 0.8165 (p0) REVERT: C 91 ASP cc_start: 0.8640 (t0) cc_final: 0.8381 (t0) REVERT: D 24 MET cc_start: 0.9146 (ttp) cc_final: 0.8790 (ttm) REVERT: D 95 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7672 (tp30) REVERT: D 116 GLU cc_start: 0.7434 (tt0) cc_final: 0.7096 (mt-10) REVERT: D 234 ARG cc_start: 0.6452 (ttt180) cc_final: 0.6074 (mtm-85) REVERT: E 205 ILE cc_start: 0.8928 (mt) cc_final: 0.8639 (tt) REVERT: E 246 LYS cc_start: 0.9254 (tttp) cc_final: 0.8364 (pttp) REVERT: F 44 LYS cc_start: 0.7756 (mmtm) cc_final: 0.7247 (mmtt) REVERT: F 74 ASN cc_start: 0.7797 (t0) cc_final: 0.6963 (m-40) REVERT: F 78 LYS cc_start: 0.8955 (tmtt) cc_final: 0.8754 (tptp) REVERT: H 134 MET cc_start: 0.6381 (mtt) cc_final: 0.5867 (ttt) REVERT: H 135 ASN cc_start: 0.6796 (p0) cc_final: 0.6495 (p0) REVERT: I 50 ASN cc_start: 0.8314 (m-40) cc_final: 0.7847 (m110) REVERT: I 134 MET cc_start: 0.6862 (mmt) cc_final: 0.6506 (mmm) REVERT: I 141 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6779 (m-30) REVERT: J 55 ARG cc_start: 0.6908 (ttm-80) cc_final: 0.6623 (ttm-80) REVERT: J 151 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.7412 (p0) REVERT: J 189 ILE cc_start: 0.7778 (mm) cc_final: 0.7506 (tp) REVERT: K 7 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7279 (mm-30) REVERT: K 97 GLN cc_start: 0.5791 (tp40) cc_final: 0.5446 (tp40) REVERT: L 134 MET cc_start: 0.6837 (tmm) cc_final: 0.6215 (tmm) REVERT: L 191 LYS cc_start: 0.5000 (OUTLIER) cc_final: 0.4496 (ptmm) outliers start: 93 outliers final: 79 residues processed: 363 average time/residue: 0.3033 time to fit residues: 165.0889 Evaluate side-chains 369 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 283 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 26 MET Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 191 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 0.2980 chunk 134 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 153 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 205 optimal weight: 30.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN C 66 GLN L 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18044 Z= 0.163 Angle : 0.568 12.077 24450 Z= 0.285 Chirality : 0.041 0.177 2966 Planarity : 0.003 0.050 3102 Dihedral : 6.581 72.376 2578 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.43 % Favored : 93.49 % Rotamer: Outliers : 4.96 % Allowed : 21.34 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.38 (0.16), residues: 2350 helix: -0.78 (0.16), residues: 1013 sheet: -1.40 (0.31), residues: 300 loop : -2.43 (0.17), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 212 HIS 0.001 0.000 HIS F 71 PHE 0.045 0.001 PHE C 37 TYR 0.030 0.001 TYR E 29 ARG 0.006 0.000 ARG J 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 305 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8151 (tp30) cc_final: 0.7827 (tp30) REVERT: B 19 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8529 (pt) REVERT: C 19 ASN cc_start: 0.8500 (p0) cc_final: 0.8174 (p0) REVERT: C 54 LEU cc_start: 0.8553 (tp) cc_final: 0.8329 (tt) REVERT: D 24 MET cc_start: 0.9119 (ttp) cc_final: 0.8786 (ttm) REVERT: D 95 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7734 (tp30) REVERT: D 116 GLU cc_start: 0.7450 (tt0) cc_final: 0.7100 (mt-10) REVERT: D 234 ARG cc_start: 0.6325 (ttt180) cc_final: 0.6096 (mtm-85) REVERT: E 205 ILE cc_start: 0.8892 (mt) cc_final: 0.8661 (tt) REVERT: E 246 LYS cc_start: 0.9249 (tttp) cc_final: 0.8362 (pttp) REVERT: F 42 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7274 (p0) REVERT: F 44 LYS cc_start: 0.7763 (mmtm) cc_final: 0.7533 (mmtt) REVERT: F 73 LYS cc_start: 0.7670 (tppt) cc_final: 0.7356 (tppt) REVERT: F 74 ASN cc_start: 0.7856 (t0) cc_final: 0.7038 (m-40) REVERT: F 78 LYS cc_start: 0.8982 (tmtt) cc_final: 0.8570 (ttmt) REVERT: F 80 LEU cc_start: 0.8278 (pt) cc_final: 0.7984 (mt) REVERT: G 27 LYS cc_start: 0.8066 (tppp) cc_final: 0.7797 (mmmm) REVERT: H 134 MET cc_start: 0.6230 (mtt) cc_final: 0.5805 (ttt) REVERT: H 135 ASN cc_start: 0.6715 (p0) cc_final: 0.6155 (p0) REVERT: I 50 ASN cc_start: 0.8269 (m-40) cc_final: 0.7801 (m110) REVERT: I 134 MET cc_start: 0.6941 (mmt) cc_final: 0.6593 (mmm) REVERT: I 141 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6821 (m-30) REVERT: J 151 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.7391 (p0) REVERT: J 189 ILE cc_start: 0.7753 (mm) cc_final: 0.7458 (tp) REVERT: K 97 GLN cc_start: 0.5852 (tp40) cc_final: 0.5614 (tp40) REVERT: L 134 MET cc_start: 0.6854 (tmm) cc_final: 0.6191 (tmm) outliers start: 93 outliers final: 75 residues processed: 374 average time/residue: 0.2914 time to fit residues: 163.3047 Evaluate side-chains 370 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 290 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 26 MET Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 170 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 91 optimal weight: 0.0370 chunk 165 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 198 optimal weight: 0.4980 chunk 209 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 overall best weight: 1.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN C 89 GLN E 79 GLN L 135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18044 Z= 0.163 Angle : 0.573 13.153 24450 Z= 0.288 Chirality : 0.041 0.175 2966 Planarity : 0.003 0.054 3102 Dihedral : 6.401 72.818 2574 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.64 % Favored : 93.32 % Rotamer: Outliers : 4.38 % Allowed : 22.41 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.20 (0.17), residues: 2350 helix: -0.54 (0.16), residues: 1013 sheet: -1.49 (0.31), residues: 295 loop : -2.37 (0.17), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 212 HIS 0.002 0.000 HIS F 71 PHE 0.018 0.001 PHE G 22 TYR 0.009 0.001 TYR J 145 ARG 0.006 0.000 ARG J 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 298 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8142 (tp30) cc_final: 0.7837 (tp30) REVERT: B 19 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8529 (pt) REVERT: C 19 ASN cc_start: 0.8486 (p0) cc_final: 0.8194 (p0) REVERT: C 54 LEU cc_start: 0.8518 (tp) cc_final: 0.8282 (tt) REVERT: D 95 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7733 (tp30) REVERT: D 116 GLU cc_start: 0.7449 (tt0) cc_final: 0.7101 (mt-10) REVERT: D 234 ARG cc_start: 0.6338 (ttt180) cc_final: 0.6112 (mtm-85) REVERT: E 205 ILE cc_start: 0.8911 (mt) cc_final: 0.8697 (tt) REVERT: E 246 LYS cc_start: 0.9262 (tttp) cc_final: 0.8382 (pttp) REVERT: F 42 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7178 (p0) REVERT: F 44 LYS cc_start: 0.7847 (mmtm) cc_final: 0.7532 (mmtt) REVERT: F 74 ASN cc_start: 0.7892 (t0) cc_final: 0.7091 (m-40) REVERT: F 78 LYS cc_start: 0.8969 (tmtt) cc_final: 0.8548 (ttmt) REVERT: F 80 LEU cc_start: 0.8271 (pt) cc_final: 0.8015 (mt) REVERT: G 64 THR cc_start: 0.8304 (m) cc_final: 0.8046 (p) REVERT: H 96 GLU cc_start: 0.7253 (pm20) cc_final: 0.6989 (pm20) REVERT: H 100 GLU cc_start: 0.7787 (pp20) cc_final: 0.7328 (tp30) REVERT: H 134 MET cc_start: 0.6208 (mtt) cc_final: 0.5836 (ttt) REVERT: H 135 ASN cc_start: 0.6751 (p0) cc_final: 0.6208 (p0) REVERT: I 50 ASN cc_start: 0.8253 (m-40) cc_final: 0.7789 (m110) REVERT: I 134 MET cc_start: 0.6918 (mmt) cc_final: 0.6600 (mmm) REVERT: I 141 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6722 (m-30) REVERT: J 151 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.7420 (p0) REVERT: J 189 ILE cc_start: 0.7739 (mm) cc_final: 0.7470 (tp) REVERT: K 97 GLN cc_start: 0.5846 (tp40) cc_final: 0.5601 (tp40) REVERT: L 134 MET cc_start: 0.6726 (tmm) cc_final: 0.5979 (tmm) outliers start: 82 outliers final: 70 residues processed: 358 average time/residue: 0.2886 time to fit residues: 155.6439 Evaluate side-chains 361 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 286 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 26 MET Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 chunk 233 optimal weight: 6.9990 chunk 214 optimal weight: 0.9990 chunk 185 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 HIS H 35 ASN L 135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18044 Z= 0.304 Angle : 0.631 13.627 24450 Z= 0.318 Chirality : 0.044 0.179 2966 Planarity : 0.004 0.051 3102 Dihedral : 6.612 74.591 2573 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.91 % Favored : 92.04 % Rotamer: Outliers : 4.27 % Allowed : 22.47 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.22 (0.17), residues: 2350 helix: -0.59 (0.17), residues: 995 sheet: -1.51 (0.30), residues: 302 loop : -2.31 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 212 HIS 0.004 0.001 HIS B 208 PHE 0.043 0.002 PHE C 37 TYR 0.015 0.001 TYR K 169 ARG 0.007 0.000 ARG L 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 290 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8283 (tp30) cc_final: 0.7993 (tp30) REVERT: B 19 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8573 (pt) REVERT: C 19 ASN cc_start: 0.8576 (p0) cc_final: 0.8273 (p0) REVERT: D 95 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8130 (mm-30) REVERT: D 116 GLU cc_start: 0.7415 (tt0) cc_final: 0.7135 (mt-10) REVERT: D 234 ARG cc_start: 0.6523 (ttt180) cc_final: 0.6100 (mtm-85) REVERT: E 205 ILE cc_start: 0.8928 (mt) cc_final: 0.8673 (tt) REVERT: E 246 LYS cc_start: 0.9280 (tttp) cc_final: 0.8400 (pttp) REVERT: F 42 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7518 (p0) REVERT: F 73 LYS cc_start: 0.7981 (tppt) cc_final: 0.7653 (tppt) REVERT: F 74 ASN cc_start: 0.8206 (t0) cc_final: 0.7730 (m110) REVERT: F 78 LYS cc_start: 0.8964 (tmtt) cc_final: 0.8763 (tptp) REVERT: G 64 THR cc_start: 0.8414 (m) cc_final: 0.8091 (p) REVERT: H 134 MET cc_start: 0.6310 (mtt) cc_final: 0.5820 (ttt) REVERT: H 135 ASN cc_start: 0.6886 (p0) cc_final: 0.6621 (p0) REVERT: I 50 ASN cc_start: 0.8293 (m-40) cc_final: 0.7844 (m110) REVERT: I 141 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6822 (m-30) REVERT: J 55 ARG cc_start: 0.6827 (ttm-80) cc_final: 0.6535 (ttm-80) REVERT: J 151 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.7466 (p0) REVERT: J 189 ILE cc_start: 0.7769 (mm) cc_final: 0.7503 (tp) REVERT: K 7 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7269 (mm-30) REVERT: L 134 MET cc_start: 0.6950 (tmm) cc_final: 0.6336 (tmm) outliers start: 80 outliers final: 68 residues processed: 350 average time/residue: 0.2941 time to fit residues: 154.8322 Evaluate side-chains 353 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 279 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 26 MET Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 185 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 190 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN E 79 GLN H 35 ASN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.134380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.100617 restraints weight = 31221.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.099667 restraints weight = 24375.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100369 restraints weight = 25025.986| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18044 Z= 0.195 Angle : 0.592 13.631 24450 Z= 0.295 Chirality : 0.042 0.171 2966 Planarity : 0.003 0.054 3102 Dihedral : 6.420 74.322 2573 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.72 % Favored : 93.23 % Rotamer: Outliers : 4.27 % Allowed : 22.52 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.07 (0.17), residues: 2350 helix: -0.39 (0.17), residues: 993 sheet: -1.54 (0.31), residues: 297 loop : -2.28 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 212 HIS 0.002 0.001 HIS F 71 PHE 0.018 0.001 PHE G 22 TYR 0.038 0.001 TYR E 29 ARG 0.007 0.000 ARG L 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3928.12 seconds wall clock time: 72 minutes 1.77 seconds (4321.77 seconds total)