Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 14:40:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d09_30527/04_2023/7d09_30527_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d09_30527/04_2023/7d09_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_30527/04_2023/7d09_30527.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d09_30527/04_2023/7d09_30527.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d09_30527/04_2023/7d09_30527_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d09_30527/04_2023/7d09_30527_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 9.64, per 1000 atoms: 0.54 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: 6.51 Conformation dependent library (CDL) restraints added in 2.7 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: 1.33 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: 4.34 Time building geometry restraints manager: 7.08 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: 9505 17.65 - 35.31: 947 35.31 - 52.96: 222 52.96 - 70.61: 108 70.61 - 88.26: 30 Dihedral angle restraints: 10812 sinusoidal: 4070 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 10809 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: 1.130 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: 3.520 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 42.980 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.120 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.290 ------------------------------------------------------------------------------- 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 : 16.969 88.263 6484 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 % 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 *********************** 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 : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 161 outliers final: 37 residues processed: 524 average time/residue: 0.3207 time to fit residues: 244.7171 Evaluate side-chains 336 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 299 time to evaluate : 2.108 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1931 time to fit residues: 15.2218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.9980 chunk 177 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 111 optimal weight: 0.0670 chunk 136 optimal weight: 20.0000 chunk 212 optimal weight: 3.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 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 F 45 GLN G 128 GLN H 45 GLN H 102 GLN I 50 ASN ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 ASN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 ASN K 180 GLN L 129 GLN L 135 ASN L 180 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 18044 Z= 0.155 Angle : 0.615 9.759 24450 Z= 0.319 Chirality : 0.042 0.181 2966 Planarity : 0.004 0.050 3102 Dihedral : 5.899 54.549 2504 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.85 % Favored : 92.85 % Rotamer Outliers : 2.40 % 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: -4.57 (0.14), residues: 2350 helix: -3.18 (0.11), residues: 978 sheet: -2.26 (0.28), residues: 296 loop : -3.03 (0.16), residues: 1076 *********************** 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 400 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 355 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 16 residues processed: 382 average time/residue: 0.3108 time to fit residues: 176.6106 Evaluate side-chains 304 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 288 time to evaluate : 2.041 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1645 time to fit residues: 7.6767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 176 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 212 optimal weight: 20.0000 chunk 229 optimal weight: 20.0000 chunk 189 optimal weight: 0.0370 chunk 211 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 170 optimal weight: 30.0000 overall best weight: 2.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN C 93 HIS D 139 GLN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS F 84 GLN H 35 ASN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 18044 Z= 0.217 Angle : 0.592 8.432 24450 Z= 0.306 Chirality : 0.043 0.183 2966 Planarity : 0.004 0.052 3102 Dihedral : 5.551 56.311 2504 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.40 % Favored : 92.47 % Rotamer Outliers : 2.72 % 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: -3.67 (0.15), residues: 2350 helix: -2.18 (0.14), residues: 987 sheet: -1.84 (0.29), residues: 295 loop : -2.81 (0.16), residues: 1068 *********************** 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 357 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 306 time to evaluate : 2.307 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 outliers start: 51 outliers final: 31 residues processed: 341 average time/residue: 0.3086 time to fit residues: 156.5022 Evaluate side-chains 303 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 272 time to evaluate : 2.055 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1605 time to fit residues: 12.0241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 213 optimal weight: 20.0000 chunk 226 optimal weight: 40.0000 chunk 111 optimal weight: 9.9990 chunk 202 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 HIS E 79 GLN F 84 GLN H 35 ASN H 102 GLN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 18044 Z= 0.183 Angle : 0.577 9.120 24450 Z= 0.294 Chirality : 0.042 0.158 2966 Planarity : 0.003 0.047 3102 Dihedral : 5.348 57.017 2504 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer Outliers : 1.76 % 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: -3.16 (0.16), residues: 2350 helix: -1.59 (0.15), residues: 985 sheet: -1.62 (0.30), residues: 295 loop : -2.69 (0.16), residues: 1070 *********************** 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 329 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 296 time to evaluate : 2.133 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 outliers start: 33 outliers final: 19 residues processed: 323 average time/residue: 0.3035 time to fit residues: 145.9870 Evaluate side-chains 291 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 272 time to evaluate : 1.887 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1536 time to fit residues: 8.0410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 30.0000 chunk 128 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 168 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 chunk 156 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 HIS ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN G 133 ASN H 133 ASN ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 18044 Z= 0.393 Angle : 0.674 10.061 24450 Z= 0.346 Chirality : 0.046 0.219 2966 Planarity : 0.004 0.051 3102 Dihedral : 5.642 57.846 2504 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.89 % Favored : 91.02 % Rotamer Outliers : 2.29 % 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: -3.10 (0.16), residues: 2350 helix: -1.51 (0.15), residues: 985 sheet: -1.58 (0.31), residues: 300 loop : -2.71 (0.16), residues: 1065 *********************** 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 329 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 286 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 25 residues processed: 315 average time/residue: 0.3242 time to fit residues: 152.6878 Evaluate side-chains 285 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 260 time to evaluate : 1.945 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1616 time to fit residues: 10.2157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 226 optimal weight: 50.0000 chunk 187 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 GLN ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3612 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= 0.220 Angle : 0.594 11.349 24450 Z= 0.303 Chirality : 0.043 0.188 2966 Planarity : 0.003 0.047 3102 Dihedral : 5.388 59.507 2504 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.72 % Favored : 93.19 % Rotamer Outliers : 1.28 % 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: -2.79 (0.16), residues: 2350 helix: -1.22 (0.16), residues: 1007 sheet: -1.53 (0.30), residues: 300 loop : -2.55 (0.17), residues: 1043 *********************** 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 322 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 298 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 313 average time/residue: 0.3243 time to fit residues: 150.0552 Evaluate side-chains 285 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 271 time to evaluate : 1.860 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1832 time to fit residues: 7.7602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.0470 chunk 25 optimal weight: 0.0970 chunk 128 optimal weight: 0.3980 chunk 165 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 225 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN I 129 GLN L 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3786 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= 0.184 Angle : 0.575 11.891 24450 Z= 0.291 Chirality : 0.042 0.182 2966 Planarity : 0.003 0.056 3102 Dihedral : 5.201 60.498 2504 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.81 % Favored : 93.11 % Rotamer Outliers : 1.44 % 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: -2.52 (0.16), residues: 2350 helix: -0.89 (0.16), residues: 999 sheet: -1.54 (0.30), residues: 304 loop : -2.47 (0.17), residues: 1047 *********************** 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 315 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 288 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 19 residues processed: 304 average time/residue: 0.3276 time to fit residues: 146.7364 Evaluate side-chains 292 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 273 time to evaluate : 2.120 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1710 time to fit residues: 8.5878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 0.0670 chunk 134 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 18044 Z= 0.265 Angle : 0.610 12.270 24450 Z= 0.310 Chirality : 0.043 0.186 2966 Planarity : 0.003 0.047 3102 Dihedral : 5.303 62.189 2504 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.53 % Favored : 92.38 % Rotamer Outliers : 1.28 % 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: -2.46 (0.16), residues: 2350 helix: -0.84 (0.16), residues: 996 sheet: -1.58 (0.30), residues: 302 loop : -2.41 (0.17), residues: 1052 *********************** 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 312 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 288 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 19 residues processed: 304 average time/residue: 0.3328 time to fit residues: 150.9631 Evaluate side-chains 290 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 271 time to evaluate : 2.481 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3455 time to fit residues: 16.9707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 198 optimal weight: 0.9990 chunk 209 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN F 71 HIS ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 18044 Z= 0.373 Angle : 0.678 13.136 24450 Z= 0.347 Chirality : 0.045 0.186 2966 Planarity : 0.004 0.055 3102 Dihedral : 5.558 60.470 2504 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.77 % Favored : 91.15 % Rotamer Outliers : 0.75 % 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: -2.64 (0.16), residues: 2350 helix: -1.00 (0.16), residues: 999 sheet: -1.71 (0.30), residues: 300 loop : -2.48 (0.17), residues: 1051 *********************** 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 287 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 273 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 284 average time/residue: 0.3312 time to fit residues: 139.8437 Evaluate side-chains 274 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 262 time to evaluate : 2.118 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1636 time to fit residues: 6.5639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 105 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 214 optimal weight: 20.0000 chunk 185 optimal weight: 0.0770 chunk 19 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 overall best weight: 3.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 180 GLN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 GLN ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 18044 Z= 0.262 Angle : 0.631 14.230 24450 Z= 0.321 Chirality : 0.043 0.181 2966 Planarity : 0.003 0.044 3102 Dihedral : 5.437 55.869 2504 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.53 % Favored : 92.43 % Rotamer Outliers : 0.43 % 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: -2.44 (0.17), residues: 2350 helix: -0.82 (0.16), residues: 996 sheet: -1.62 (0.30), residues: 298 loop : -2.37 (0.18), residues: 1056 ********************** 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 288 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 280 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 283 average time/residue: 0.3348 time to fit residues: 141.5048 Evaluate side-chains 270 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 265 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1780 time to fit residues: 4.7292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 171 optimal weight: 0.0170 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 185 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.135575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102416 restraints weight = 31127.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102071 restraints weight = 26725.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.103069 restraints weight = 23610.430| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 18044 Z= 0.147 Angle : 0.584 13.971 24450 Z= 0.293 Chirality : 0.041 0.166 2966 Planarity : 0.003 0.046 3102 Dihedral : 5.025 59.373 2504 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.09 % Favored : 93.87 % Rotamer Outliers : 0.27 % 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: -2.10 (0.17), residues: 2350 helix: -0.44 (0.16), residues: 1004 sheet: -1.62 (0.30), residues: 295 loop : -2.25 (0.18), residues: 1051 =============================================================================== Job complete usr+sys time: 3534.43 seconds wall clock time: 65 minutes 8.51 seconds (3908.51 seconds total)