Starting phenix.real_space_refine on Mon Jul 22 08:17:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d09_30527/07_2024/7d09_30527.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d09_30527/07_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_30527/07_2024/7d09_30527.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d09_30527/07_2024/7d09_30527.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d09_30527/07_2024/7d09_30527.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d09_30527/07_2024/7d09_30527.cif" } 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-5388/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: 9.60, 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: 6.17 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... Secondary structure from input PDB file: 93 helices and 17 sheets defined 46.4% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 1 through 30 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) removed outlier: 3.667A pdb=" N PHE A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.815A pdb=" N ARG A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) 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 52 through 76 removed outlier: 3.556A pdb=" N ILE A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 95 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 95 through 104 removed outlier: 3.580A pdb=" N VAL A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) 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 104 through 109 Processing helix chain 'A' and resid 109 through 123 removed outlier: 3.868A pdb=" N LEU A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) 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) removed outlier: 3.505A pdb=" N SER A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 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) removed outlier: 3.678A pdb=" N GLY A 133 " --> pdb=" O MET A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 141 through 152 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) Processing helix chain 'A' and resid 152 through 172 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 178 through 190 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 197 through 220 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 233 through 255 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 51 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 84 through 89 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.632A pdb=" N HIS B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 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 151 through 164 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 181 through 200 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 209 through 217 removed outlier: 3.607A pdb=" N SER B 215 " --> pdb=" O PRO B 211 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 217 " --> pdb=" O THR B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.563A pdb=" N THR B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 32 removed outlier: 3.788A pdb=" N GLN C 25 " --> pdb=" O GLU C 21 " (cutoff:3.500A) 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) Processing helix chain 'C' and resid 51 through 64 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) removed outlier: 3.542A pdb=" N THR C 64 " --> pdb=" O TRP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 86 Processing helix chain 'D' and resid 2 through 30 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) removed outlier: 3.665A pdb=" N PHE D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 49 removed outlier: 3.814A pdb=" N ARG D 40 " --> pdb=" O GLY D 36 " (cutoff:3.500A) 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 52 through 76 removed outlier: 3.555A pdb=" N ILE D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 95 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 95 through 104 removed outlier: 3.580A pdb=" N VAL D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) 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 104 through 109 Processing helix chain 'D' and resid 109 through 123 removed outlier: 3.868A pdb=" N LEU D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) 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) removed outlier: 3.505A pdb=" N SER D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 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) removed outlier: 3.679A pdb=" N GLY D 133 " --> pdb=" O MET D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 141 through 152 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) Processing helix chain 'D' and resid 152 through 172 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 178 through 190 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 197 through 220 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 233 through 255 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 51 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 84 through 89 Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 112 through 119 removed outlier: 3.633A pdb=" N HIS E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 138 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 151 through 164 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 181 through 200 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 209 through 217 removed outlier: 3.606A pdb=" N SER E 215 " --> pdb=" O PRO E 211 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA E 217 " --> pdb=" O THR E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 240 Processing helix chain 'E' and resid 244 through 251 removed outlier: 3.563A pdb=" N THR E 250 " --> pdb=" O LYS E 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 32 removed outlier: 3.789A pdb=" N GLN F 25 " --> pdb=" O GLU F 21 " (cutoff:3.500A) 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) Processing helix chain 'F' and resid 51 through 63 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) removed outlier: 3.869A pdb=" N GLN F 63 " --> pdb=" O GLN F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 86 Processing helix chain 'G' and resid 4 through 26 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 96 through 101 Processing helix chain 'G' and resid 101 through 109 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 123 through 133 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) removed outlier: 3.586A pdb=" N ASN G 133 " --> pdb=" O GLN G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 193 Processing helix chain 'H' and resid 4 through 20 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 24 through 30 removed outlier: 3.577A pdb=" N SER H 29 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY H 30 " --> pdb=" O MET H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 94 through 110 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 112 through 116 Processing helix chain 'H' and resid 124 through 132 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) removed outlier: 3.526A pdb=" N SER H 132 " --> pdb=" O GLN H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 193 removed outlier: 4.198A pdb=" N ILE H 189 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) 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) Processing helix chain 'I' and resid 5 through 28 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) removed outlier: 3.522A pdb=" N VAL I 28 " --> pdb=" O LEU I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 101 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) Processing helix chain 'I' and resid 102 through 108 removed outlier: 3.835A pdb=" N ASP I 107 " --> pdb=" O LYS I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 119 removed outlier: 3.668A pdb=" N THR I 119 " --> pdb=" O THR I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 132 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 184 through 192 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 9 Processing helix chain 'J' and resid 10 through 28 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 95 through 100 removed outlier: 3.837A pdb=" N LEU J 98 " --> pdb=" O ALA J 95 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS J 99 " --> pdb=" O GLU J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 106 Processing helix chain 'J' and resid 111 through 116 Processing helix chain 'J' and resid 123 through 132 removed outlier: 4.495A pdb=" N LEU J 130 " --> pdb=" O MET J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 removed outlier: 3.604A pdb=" N ILE J 189 " --> pdb=" O LEU J 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 23 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 97 through 106 removed outlier: 3.680A pdb=" N VAL K 101 " --> pdb=" O GLN K 97 " (cutoff:3.500A) 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 126 through 134 removed outlier: 3.771A pdb=" N LEU K 130 " --> pdb=" O MET K 126 " (cutoff:3.500A) 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) removed outlier: 3.508A pdb=" N MET K 134 " --> pdb=" O LEU K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 193 removed outlier: 3.666A pdb=" N LEU K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) 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) removed outlier: 3.703A pdb=" N ILE K 193 " --> pdb=" O ILE K 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 8 Processing helix chain 'L' and resid 9 through 28 removed outlier: 3.501A pdb=" N PHE L 13 " --> pdb=" O ALA L 9 " (cutoff:3.500A) 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) removed outlier: 3.650A pdb=" N VAL L 28 " --> pdb=" O LEU L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 92 removed outlier: 3.519A pdb=" N THR L 91 " --> pdb=" O ASP L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 102 removed outlier: 3.646A pdb=" N GLU L 100 " --> pdb=" O GLU L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 110 removed outlier: 3.963A pdb=" N GLU L 108 " --> pdb=" O ASN L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 122 Processing helix chain 'L' and resid 123 through 135 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 184 through 192 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 37 removed outlier: 6.373A pdb=" N LEU B 34 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU B 15 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 36 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 17 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 69 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'B' and resid 93 through 95 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: 6.345A pdb=" N ALA B 43 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL B 223 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET B 45 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 222 " --> pdb=" O GLN B 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 3 through 4 removed outlier: 7.612A pdb=" N VAL C 11 " --> pdb=" O GLN C 45 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AA6, first strand: chain 'E' and resid 33 through 37 removed outlier: 6.372A pdb=" N LEU E 34 " --> pdb=" O GLU E 15 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU E 15 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE E 36 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS E 17 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU E 69 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 21 through 22 Processing sheet with id=AA8, first strand: chain 'E' and resid 93 through 95 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: 6.345A pdb=" N ALA E 43 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL E 223 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET E 45 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL E 222 " --> pdb=" O GLN E 229 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 12 through 13 removed outlier: 3.893A pdb=" N GLY F 13 " --> pdb=" O GLN F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 68 through 73 removed outlier: 5.985A pdb=" N VAL G 68 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP G 85 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER G 70 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR G 83 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N ILE G 176 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LYS G 43 " --> pdb=" O ILE G 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 64 through 66 removed outlier: 6.606A pdb=" N VAL G 58 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA G 149 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing sheet with id=AB3, 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: 6.527A pdb=" N THR H 83 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE H 65 " --> 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) removed outlier: 6.517A pdb=" N LYS H 57 " --> pdb=" O LEU H 159 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE H 161 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR H 59 " --> pdb=" O ILE H 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 41 through 46 removed outlier: 6.171A pdb=" N THR I 81 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE I 71 " --> pdb=" O THR I 81 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR I 83 " --> pdb=" O ASP I 69 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL I 58 " --> pdb=" O ILE I 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 42 through 44 removed outlier: 4.024A pdb=" N SER J 70 " --> pdb=" O THR J 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 58 through 59 removed outlier: 3.738A pdb=" N VAL J 162 " --> pdb=" O TYR J 145 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR J 145 " --> pdb=" O VAL J 162 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 40 through 44 removed outlier: 3.632A pdb=" N ALA K 44 " --> pdb=" O VAL K 82 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR K 81 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE K 71 " --> pdb=" O THR K 81 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR K 83 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL K 58 " --> pdb=" O ILE K 65 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR K 59 " --> pdb=" O ILE K 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR K 158 " --> pdb=" O ALA K 149 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR K 145 " --> pdb=" O VAL K 162 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE K 146 " --> pdb=" O GLN K 180 " (cutoff:3.500A) Processing sheet with id=AB8, 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) removed outlier: 6.859A pdb=" N VAL L 58 " --> pdb=" O ILE L 65 " (cutoff:3.500A) 652 hydrogen bonds defined for protein. 1878 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: 5.02 Time building geometry restraints manager: 6.85 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: 1675 2.72 - 3.27: 16762 3.27 - 3.81: 27568 3.81 - 4.36: 32858 4.36 - 4.90: 56712 Nonbonded interactions: 135575 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 135570 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: 0.420 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: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 46.770 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.460 ------------------------------------------------------------------------------- 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= 0.495 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 : 2.025 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: 0.3187 time to fit residues: 244.3793 Evaluate side-chains 354 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 308 time to evaluate : 2.094 ------------------------------------------------------------------------------- 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: 0.0870 chunk 177 optimal weight: 0.5980 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.5364 ------------------------------------------------------------------------------- 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 D 139 GLN E 31 ASN E 263 HIS F 45 GLN 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: 0.7908 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18044 Z= 0.190 Angle : 0.637 8.433 24450 Z= 0.333 Chirality : 0.043 0.172 2966 Planarity : 0.004 0.047 3102 Dihedral : 9.533 75.544 2663 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.85 % Favored : 92.85 % Rotamer: Outliers : 4.59 % Allowed : 15.85 % Favored : 79.56 % 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: -4.34 (0.14), residues: 2350 helix: -2.79 (0.12), residues: 983 sheet: -2.27 (0.27), residues: 309 loop : -3.07 (0.16), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 212 HIS 0.002 0.001 HIS B 208 PHE 0.037 0.001 PHE C 37 TYR 0.017 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 443 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 357 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 THR cc_start: 0.7420 (OUTLIER) cc_final: 0.7205 (m) REVERT: A 27 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: A 87 MET cc_start: 0.8023 (tmm) cc_final: 0.7674 (tmm) REVERT: B 75 LYS cc_start: 0.7184 (tttm) cc_final: 0.6972 (tttm) REVERT: C 18 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7444 (pm20) REVERT: C 19 ASN cc_start: 0.8306 (p0) cc_final: 0.7922 (p0) REVERT: D 24 MET cc_start: 0.9125 (ttp) cc_final: 0.8783 (ttm) REVERT: D 77 ASN cc_start: 0.8240 (m110) cc_final: 0.8008 (m-40) REVERT: D 116 GLU cc_start: 0.7410 (tt0) cc_final: 0.6979 (mt-10) REVERT: D 230 THR cc_start: 0.9289 (t) cc_final: 0.9029 (m) REVERT: D 234 ARG cc_start: 0.6090 (ttt180) cc_final: 0.5770 (mtm-85) REVERT: E 135 GLU cc_start: 0.7659 (tp30) cc_final: 0.7320 (tm-30) REVERT: E 246 LYS cc_start: 0.9237 (tttp) cc_final: 0.8298 (pttp) REVERT: F 73 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7714 (tppt) REVERT: H 85 ASP cc_start: 0.8294 (p0) cc_final: 0.8011 (p0) REVERT: H 143 ASP cc_start: 0.7960 (p0) cc_final: 0.7638 (p0) REVERT: I 48 ASN cc_start: 0.7949 (t0) cc_final: 0.7320 (t0) REVERT: I 50 ASN cc_start: 0.8226 (m-40) cc_final: 0.7775 (m110) REVERT: I 134 MET cc_start: 0.6918 (mmt) cc_final: 0.6559 (mmm) REVERT: I 141 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6907 (m-30) REVERT: J 151 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.7410 (p0) REVERT: K 7 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: K 97 GLN cc_start: 0.6479 (tt0) cc_final: 0.5642 (mm110) REVERT: K 102 GLN cc_start: 0.6721 (mt0) cc_final: 0.6353 (pp30) REVERT: K 186 GLU cc_start: 0.7594 (mp0) cc_final: 0.7375 (pp20) REVERT: L 191 LYS cc_start: 0.5389 (OUTLIER) cc_final: 0.4875 (ptmm) outliers start: 86 outliers final: 42 residues processed: 409 average time/residue: 0.2984 time to fit residues: 181.3046 Evaluate side-chains 348 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 298 time to evaluate : 2.118 ------------------------------------------------------------------------------- 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 55 ILE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 145 LEU 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 95 GLU Chi-restraints excluded: chain D residue 181 SER 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 210 VAL Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 6 ASN 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 88 LEU Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 16 ILE 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 98 LEU Chi-restraints excluded: chain K residue 153 LEU 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: 0.0970 chunk 65 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 212 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 170 optimal weight: 20.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN C 48 HIS C 66 GLN C 74 ASN C 89 GLN E 79 GLN E 97 GLN F 48 HIS ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 18044 Z= 0.374 Angle : 0.684 9.104 24450 Z= 0.356 Chirality : 0.045 0.157 2966 Planarity : 0.004 0.049 3102 Dihedral : 8.158 68.479 2597 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.51 % Favored : 91.36 % Rotamer: Outliers : 4.75 % Allowed : 19.32 % Favored : 75.93 % 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: -3.53 (0.15), residues: 2350 helix: -1.82 (0.15), residues: 991 sheet: -1.90 (0.29), residues: 304 loop : -2.96 (0.16), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 212 HIS 0.005 0.001 HIS F 48 PHE 0.016 0.002 PHE G 13 TYR 0.023 0.002 TYR E 259 ARG 0.005 0.001 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 385 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 296 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8104 (tpp) cc_final: 0.7690 (ttt) REVERT: A 95 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7891 (tp30) REVERT: A 130 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7267 (tm-30) REVERT: C 19 ASN cc_start: 0.8285 (p0) cc_final: 0.7908 (p0) REVERT: C 91 ASP cc_start: 0.8616 (t0) cc_final: 0.8116 (t0) REVERT: D 24 MET cc_start: 0.9165 (ttp) cc_final: 0.8822 (ttm) REVERT: D 116 GLU cc_start: 0.7440 (tt0) cc_final: 0.7149 (mt-10) REVERT: D 130 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7780 (tm-30) REVERT: D 230 THR cc_start: 0.9324 (t) cc_final: 0.9027 (m) REVERT: E 246 LYS cc_start: 0.9311 (tttp) cc_final: 0.8391 (pttp) REVERT: F 18 GLU cc_start: 0.8085 (pm20) cc_final: 0.7855 (pm20) REVERT: F 62 ARG cc_start: 0.8378 (mmm160) cc_final: 0.8103 (mmm160) REVERT: H 61 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.8368 (t) REVERT: H 134 MET cc_start: 0.6196 (mtt) cc_final: 0.5782 (ttt) REVERT: H 143 ASP cc_start: 0.7940 (p0) cc_final: 0.7633 (p0) REVERT: I 50 ASN cc_start: 0.8304 (m-40) cc_final: 0.7826 (m110) REVERT: I 60 MET cc_start: 0.8278 (tpp) cc_final: 0.8000 (tpt) REVERT: J 151 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.7451 (p0) REVERT: K 7 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: K 97 GLN cc_start: 0.6548 (tt0) cc_final: 0.5655 (mm110) REVERT: K 186 GLU cc_start: 0.7467 (mp0) cc_final: 0.7177 (pp20) REVERT: L 191 LYS cc_start: 0.5180 (OUTLIER) cc_final: 0.4641 (ptmm) outliers start: 89 outliers final: 66 residues processed: 360 average time/residue: 0.2938 time to fit residues: 157.6717 Evaluate side-chains 347 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 276 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 VAL 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 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 55 ILE Chi-restraints excluded: chain D residue 63 ILE 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 E residue 18 ASN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 76 ASP 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 F residue 8 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 142 GLU 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 91 THR Chi-restraints excluded: chain J residue 151 ASN 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 35 ASN Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 189 ILE 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 191 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 chunk 226 optimal weight: 50.0000 chunk 111 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 E 79 GLN F 74 ASN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 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** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18044 Z= 0.309 Angle : 0.641 11.395 24450 Z= 0.330 Chirality : 0.044 0.152 2966 Planarity : 0.004 0.044 3102 Dihedral : 7.719 70.758 2587 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.74 % Favored : 92.13 % Rotamer: Outliers : 5.34 % Allowed : 20.44 % Favored : 74.23 % 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: -3.04 (0.16), residues: 2350 helix: -1.30 (0.16), residues: 994 sheet: -1.67 (0.30), residues: 304 loop : -2.83 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 212 HIS 0.003 0.001 HIS B 208 PHE 0.035 0.001 PHE C 37 TYR 0.023 0.002 TYR E 29 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 393 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 293 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8148 (tpp) cc_final: 0.7686 (ttt) REVERT: A 95 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7845 (tp30) REVERT: B 19 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8599 (pt) REVERT: C 19 ASN cc_start: 0.8366 (p0) cc_final: 0.8049 (p0) REVERT: C 91 ASP cc_start: 0.8565 (t0) cc_final: 0.8280 (t0) REVERT: D 24 MET cc_start: 0.9166 (ttp) cc_final: 0.8823 (ttm) REVERT: D 116 GLU cc_start: 0.7481 (tt0) cc_final: 0.7270 (mt-10) REVERT: D 130 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7729 (tm-30) REVERT: E 246 LYS cc_start: 0.9284 (tttp) cc_final: 0.8369 (pttp) REVERT: F 18 GLU cc_start: 0.7879 (pm20) cc_final: 0.7504 (pm20) REVERT: F 62 ARG cc_start: 0.8404 (mmm160) cc_final: 0.8110 (mmm160) REVERT: H 96 GLU cc_start: 0.7176 (pm20) cc_final: 0.6905 (pm20) REVERT: H 134 MET cc_start: 0.6429 (mtt) cc_final: 0.5615 (ttp) REVERT: I 50 ASN cc_start: 0.8310 (m-40) cc_final: 0.7855 (m110) REVERT: I 60 MET cc_start: 0.8267 (tpp) cc_final: 0.7926 (tpt) REVERT: I 141 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.7011 (m-30) REVERT: J 151 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.7478 (p0) REVERT: K 7 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7437 (mm-30) REVERT: K 97 GLN cc_start: 0.6523 (tt0) cc_final: 0.6087 (tp40) REVERT: K 186 GLU cc_start: 0.7559 (mp0) cc_final: 0.7241 (pp20) REVERT: L 191 LYS cc_start: 0.5247 (OUTLIER) cc_final: 0.4584 (ptmm) outliers start: 100 outliers final: 74 residues processed: 367 average time/residue: 0.2916 time to fit residues: 160.5908 Evaluate side-chains 350 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 270 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 95 GLU 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 151 SER 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 235 GLU 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 63 ILE Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 MET 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 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 208 HIS Chi-restraints excluded: chain E residue 210 VAL 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 41 VAL Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain G residue 64 THR 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 98 LEU Chi-restraints excluded: chain H residue 102 GLN Chi-restraints excluded: chain H residue 142 GLU 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 91 THR Chi-restraints excluded: chain J residue 151 ASN 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 35 ASN Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 170 LEU 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: 20.0000 chunk 128 optimal weight: 0.2980 chunk 3 optimal weight: 0.0170 chunk 168 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 193 optimal weight: 20.0000 chunk 156 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 203 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 overall best weight: 1.3820 ------------------------------------------------------------------------------- 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 F 84 GLN ** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18044 Z= 0.160 Angle : 0.567 10.563 24450 Z= 0.291 Chirality : 0.042 0.185 2966 Planarity : 0.003 0.047 3102 Dihedral : 7.078 72.154 2586 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 4.11 % Allowed : 21.88 % Favored : 74.01 % 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: -2.53 (0.16), residues: 2350 helix: -0.76 (0.17), residues: 986 sheet: -1.50 (0.30), residues: 306 loop : -2.64 (0.17), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 212 HIS 0.002 0.000 HIS E 208 PHE 0.009 0.001 PHE D 159 TYR 0.016 0.001 TYR E 259 ARG 0.006 0.000 ARG L 55 *********************** 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 390 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 313 time to evaluate : 2.055 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: 0.8531 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: A 45 MET cc_start: 0.8149 (tpp) cc_final: 0.7561 (ttt) REVERT: A 108 ARG cc_start: 0.8560 (tpt90) cc_final: 0.8290 (tpt-90) REVERT: B 19 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8570 (pt) REVERT: B 235 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7126 (pm20) REVERT: C 19 ASN cc_start: 0.8304 (p0) cc_final: 0.7914 (p0) REVERT: C 54 LEU cc_start: 0.8639 (tp) cc_final: 0.8331 (tt) REVERT: C 91 ASP cc_start: 0.8596 (t0) cc_final: 0.8340 (t0) REVERT: D 24 MET cc_start: 0.9128 (ttp) cc_final: 0.8801 (ttm) REVERT: D 116 GLU cc_start: 0.7570 (tt0) cc_final: 0.7220 (mt-10) REVERT: D 130 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7682 (tm-30) REVERT: D 234 ARG cc_start: 0.6276 (ttt180) cc_final: 0.5892 (mtm-85) REVERT: E 29 TYR cc_start: 0.7365 (m-80) cc_final: 0.7143 (m-80) REVERT: E 149 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6351 (pt0) REVERT: E 205 ILE cc_start: 0.8842 (mt) cc_final: 0.8541 (tt) REVERT: E 246 LYS cc_start: 0.9283 (tttp) cc_final: 0.8373 (pttp) REVERT: F 62 ARG cc_start: 0.8386 (mmm160) cc_final: 0.8079 (mmm160) REVERT: F 78 LYS cc_start: 0.7890 (ttpt) cc_final: 0.7612 (mtpt) REVERT: F 79 MET cc_start: 0.7975 (mmp) cc_final: 0.7752 (mmt) REVERT: G 167 LEU cc_start: 0.7957 (tp) cc_final: 0.7027 (pt) REVERT: H 134 MET cc_start: 0.6254 (mtt) cc_final: 0.5818 (ttt) REVERT: H 143 ASP cc_start: 0.7751 (p0) cc_final: 0.7352 (p0) REVERT: I 50 ASN cc_start: 0.8258 (m-40) cc_final: 0.7806 (m110) REVERT: I 141 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6808 (m-30) REVERT: J 151 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.7442 (p0) REVERT: K 99 LYS cc_start: 0.7996 (mttt) cc_final: 0.7710 (mttt) REVERT: K 186 GLU cc_start: 0.7764 (mp0) cc_final: 0.7285 (pp20) REVERT: L 134 MET cc_start: 0.6574 (tmm) cc_final: 0.5996 (tmm) REVERT: L 191 LYS cc_start: 0.5210 (OUTLIER) cc_final: 0.4540 (ptmm) outliers start: 77 outliers final: 56 residues processed: 367 average time/residue: 0.2983 time to fit residues: 162.7599 Evaluate side-chains 347 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 284 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 VAL 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 177 PHE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 263 HIS 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 D residue 13 GLU Chi-restraints excluded: chain D residue 95 GLU 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 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 149 GLU Chi-restraints excluded: chain E residue 177 PHE 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 50 ASN Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain G residue 93 PHE 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 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 91 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 8 LEU 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 189 ILE 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 170 LEU 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: 2.9990 chunk 203 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18044 Z= 0.229 Angle : 0.590 11.094 24450 Z= 0.301 Chirality : 0.042 0.182 2966 Planarity : 0.003 0.050 3102 Dihedral : 6.968 73.637 2584 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.32 % Favored : 92.60 % Rotamer: Outliers : 4.27 % Allowed : 22.89 % Favored : 72.84 % 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: -2.30 (0.17), residues: 2350 helix: -0.53 (0.17), residues: 984 sheet: -1.41 (0.30), residues: 306 loop : -2.53 (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 B 208 PHE 0.039 0.001 PHE C 37 TYR 0.014 0.001 TYR E 259 ARG 0.006 0.000 ARG E 82 *********************** 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 372 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 292 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8161 (tpp) cc_final: 0.7572 (ttt) REVERT: B 19 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8593 (pt) REVERT: B 235 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: C 19 ASN cc_start: 0.8479 (p0) cc_final: 0.8138 (p0) REVERT: C 54 LEU cc_start: 0.8607 (tp) cc_final: 0.8384 (tt) REVERT: C 91 ASP cc_start: 0.8524 (t0) cc_final: 0.8293 (t0) REVERT: D 24 MET cc_start: 0.9127 (ttp) cc_final: 0.8804 (ttm) REVERT: D 116 GLU cc_start: 0.7528 (tt0) cc_final: 0.7244 (mt-10) REVERT: D 130 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7735 (tm-30) REVERT: D 234 ARG cc_start: 0.6518 (ttt180) cc_final: 0.5996 (mtm-85) REVERT: E 55 LEU cc_start: 0.9292 (tp) cc_final: 0.9065 (tt) REVERT: E 205 ILE cc_start: 0.8876 (mt) cc_final: 0.8590 (tt) REVERT: E 246 LYS cc_start: 0.9294 (tttp) cc_final: 0.8365 (pttp) REVERT: F 18 GLU cc_start: 0.8027 (pm20) cc_final: 0.7779 (pm20) REVERT: F 62 ARG cc_start: 0.8431 (mmm160) cc_final: 0.8163 (mmt90) REVERT: F 78 LYS cc_start: 0.7893 (ttpt) cc_final: 0.7616 (mtpt) REVERT: F 79 MET cc_start: 0.7797 (mmp) cc_final: 0.7484 (mmt) REVERT: G 167 LEU cc_start: 0.8059 (tp) cc_final: 0.7102 (pt) REVERT: H 134 MET cc_start: 0.6273 (mtt) cc_final: 0.5824 (ttt) REVERT: H 135 ASN cc_start: 0.6787 (p0) cc_final: 0.6503 (p0) REVERT: H 143 ASP cc_start: 0.7756 (p0) cc_final: 0.7378 (p0) REVERT: I 50 ASN cc_start: 0.8266 (m-40) cc_final: 0.7809 (m110) REVERT: I 141 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6812 (m-30) REVERT: J 151 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.7439 (p0) REVERT: J 189 ILE cc_start: 0.7573 (mm) cc_final: 0.7304 (tp) REVERT: K 7 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7275 (mm-30) REVERT: K 97 GLN cc_start: 0.6187 (tp40) cc_final: 0.5750 (tp40) REVERT: K 102 GLN cc_start: 0.6666 (mp10) cc_final: 0.6207 (pm20) REVERT: K 186 GLU cc_start: 0.7608 (mp0) cc_final: 0.7271 (pp20) REVERT: L 134 MET cc_start: 0.6586 (tmm) cc_final: 0.6020 (tmm) outliers start: 80 outliers final: 70 residues processed: 349 average time/residue: 0.3003 time to fit residues: 158.4315 Evaluate side-chains 357 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 282 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 93 LEU 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 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 177 PHE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 GLU 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 95 GLU 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 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 154 MET Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 177 PHE 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 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 28 VAL 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 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 91 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 151 ASN 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 35 ASN Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 150 THR 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 170 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 190 optimal weight: 0.2980 chunk 126 optimal weight: 7.9990 chunk 225 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN F 84 GLN ** H 133 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18044 Z= 0.192 Angle : 0.576 11.350 24450 Z= 0.291 Chirality : 0.042 0.170 2966 Planarity : 0.003 0.053 3102 Dihedral : 6.657 75.649 2576 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.94 % Favored : 92.98 % Rotamer: Outliers : 4.54 % Allowed : 22.63 % Favored : 72.84 % 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: -2.05 (0.17), residues: 2350 helix: -0.30 (0.17), residues: 994 sheet: -1.31 (0.30), residues: 306 loop : -2.44 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 212 HIS 0.002 0.000 HIS E 208 PHE 0.013 0.001 PHE G 22 TYR 0.009 0.001 TYR J 145 ARG 0.006 0.000 ARG E 82 *********************** 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 378 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 293 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8117 (tpp) cc_final: 0.7560 (ttt) REVERT: B 19 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8579 (pt) REVERT: C 19 ASN cc_start: 0.8452 (p0) cc_final: 0.8100 (p0) REVERT: C 54 LEU cc_start: 0.8589 (tp) cc_final: 0.8366 (tt) REVERT: D 24 MET cc_start: 0.9125 (ttp) cc_final: 0.8823 (ttm) REVERT: D 116 GLU cc_start: 0.7566 (tt0) cc_final: 0.7240 (mt-10) REVERT: D 130 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7695 (tm-30) REVERT: D 234 ARG cc_start: 0.6512 (ttt180) cc_final: 0.6040 (mtm-85) REVERT: E 29 TYR cc_start: 0.8026 (m-80) cc_final: 0.7797 (m-80) REVERT: E 55 LEU cc_start: 0.9284 (tp) cc_final: 0.9070 (tt) REVERT: E 205 ILE cc_start: 0.8879 (mt) cc_final: 0.8603 (tt) REVERT: E 246 LYS cc_start: 0.9295 (tttp) cc_final: 0.8360 (pttp) REVERT: F 62 ARG cc_start: 0.8470 (mmm160) cc_final: 0.8176 (mmt90) REVERT: F 78 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7573 (mtpt) REVERT: F 84 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8176 (mp10) REVERT: G 167 LEU cc_start: 0.8048 (tp) cc_final: 0.7097 (pt) REVERT: H 96 GLU cc_start: 0.7152 (pm20) cc_final: 0.6911 (pm20) REVERT: H 134 MET cc_start: 0.6290 (mtt) cc_final: 0.5868 (ttt) REVERT: H 135 ASN cc_start: 0.6773 (p0) cc_final: 0.6504 (p0) REVERT: I 50 ASN cc_start: 0.8250 (m-40) cc_final: 0.7785 (m110) REVERT: I 134 MET cc_start: 0.6853 (mmt) cc_final: 0.6460 (mmm) REVERT: I 141 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6886 (m-30) REVERT: J 151 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.7413 (p0) REVERT: J 189 ILE cc_start: 0.7572 (mm) cc_final: 0.7294 (tp) REVERT: K 97 GLN cc_start: 0.5923 (tp40) cc_final: 0.5595 (tp40) REVERT: K 102 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6299 (pm20) REVERT: K 186 GLU cc_start: 0.7567 (mp0) cc_final: 0.7328 (pp20) REVERT: L 134 MET cc_start: 0.6585 (tmm) cc_final: 0.6049 (tmm) outliers start: 85 outliers final: 72 residues processed: 356 average time/residue: 0.2828 time to fit residues: 151.8868 Evaluate side-chains 359 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 282 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 93 LEU 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 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 177 PHE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 233 THR 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 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 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 154 MET Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 177 PHE 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 50 ASN Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 28 VAL 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 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 91 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 102 GLN Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 189 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 F 71 HIS F 84 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** 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: 0.8017 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18044 Z= 0.426 Angle : 0.697 11.991 24450 Z= 0.355 Chirality : 0.046 0.181 2966 Planarity : 0.004 0.053 3102 Dihedral : 7.143 77.641 2576 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.06 % Favored : 90.85 % Rotamer: Outliers : 4.96 % Allowed : 22.47 % Favored : 72.57 % 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: -2.30 (0.17), residues: 2350 helix: -0.59 (0.16), residues: 994 sheet: -1.41 (0.31), residues: 304 loop : -2.49 (0.17), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 212 HIS 0.005 0.001 HIS B 208 PHE 0.039 0.002 PHE C 37 TYR 0.018 0.002 TYR G 40 ARG 0.006 0.001 ARG E 82 *********************** 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 368 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 275 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6684 (mmt) cc_final: 0.6454 (mmp) REVERT: A 45 MET cc_start: 0.8194 (tpp) cc_final: 0.7664 (ttt) REVERT: A 95 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7964 (tp30) REVERT: C 19 ASN cc_start: 0.8559 (p0) cc_final: 0.8284 (p0) REVERT: D 24 MET cc_start: 0.9171 (ttp) cc_final: 0.8857 (ttm) REVERT: D 116 GLU cc_start: 0.7493 (tt0) cc_final: 0.7062 (mt-10) REVERT: D 130 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7834 (tm-30) REVERT: E 246 LYS cc_start: 0.9320 (tttp) cc_final: 0.8399 (pttp) REVERT: F 18 GLU cc_start: 0.7997 (pm20) cc_final: 0.7544 (pm20) REVERT: F 62 ARG cc_start: 0.8609 (mmm160) cc_final: 0.8325 (mmt90) REVERT: H 87 ASP cc_start: 0.7230 (m-30) cc_final: 0.6970 (t70) REVERT: H 134 MET cc_start: 0.6540 (mtt) cc_final: 0.5788 (ttt) REVERT: H 143 ASP cc_start: 0.7698 (p0) cc_final: 0.7370 (p0) REVERT: I 50 ASN cc_start: 0.8305 (m-40) cc_final: 0.7862 (m110) REVERT: I 60 MET cc_start: 0.8265 (tpp) cc_final: 0.7948 (tpt) REVERT: I 134 MET cc_start: 0.6920 (mmt) cc_final: 0.6532 (mmm) REVERT: J 151 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.7531 (p0) REVERT: K 7 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7331 (mm-30) REVERT: K 97 GLN cc_start: 0.6011 (tp40) cc_final: 0.5751 (tp40) REVERT: K 186 GLU cc_start: 0.7608 (mp0) cc_final: 0.7127 (pp20) REVERT: L 134 MET cc_start: 0.6663 (tmm) cc_final: 0.6066 (tmm) outliers start: 93 outliers final: 80 residues processed: 344 average time/residue: 0.2993 time to fit residues: 154.9666 Evaluate side-chains 349 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 266 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 83 MET 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 233 THR 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 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 208 HIS Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 233 THR 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 2 ASN Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 63 ILE 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 230 THR 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 154 MET Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 206 VAL 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 G residue 64 THR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 98 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 26 MET Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 151 ASN 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 28 VAL Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 189 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 91 optimal weight: 0.4980 chunk 165 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 198 optimal weight: 0.9980 chunk 209 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3915 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= 0.192 Angle : 0.603 13.619 24450 Z= 0.304 Chirality : 0.042 0.163 2966 Planarity : 0.003 0.050 3102 Dihedral : 6.693 77.762 2576 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.68 % Favored : 93.23 % Rotamer: Outliers : 4.43 % Allowed : 23.53 % Favored : 72.04 % 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: -1.87 (0.17), residues: 2350 helix: -0.14 (0.17), residues: 985 sheet: -1.31 (0.31), residues: 306 loop : -2.31 (0.18), residues: 1059 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 0.011 0.001 PHE G 22 TYR 0.009 0.001 TYR I 145 ARG 0.008 0.000 ARG E 82 *********************** 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 384 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 301 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6646 (mmt) cc_final: 0.6391 (mmp) REVERT: A 45 MET cc_start: 0.8116 (tpp) cc_final: 0.7593 (ttt) REVERT: B 19 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8545 (pt) REVERT: C 19 ASN cc_start: 0.8475 (p0) cc_final: 0.8116 (p0) REVERT: D 24 MET cc_start: 0.9123 (ttp) cc_final: 0.8842 (ttm) REVERT: D 81 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8778 (mm-30) REVERT: D 116 GLU cc_start: 0.7410 (tt0) cc_final: 0.7153 (mt-10) REVERT: D 130 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7720 (tm-30) REVERT: D 234 ARG cc_start: 0.6417 (ttt180) cc_final: 0.5950 (mtm-85) REVERT: E 205 ILE cc_start: 0.8904 (mt) cc_final: 0.8653 (tt) REVERT: E 246 LYS cc_start: 0.9313 (tttp) cc_final: 0.8402 (pttp) REVERT: F 18 GLU cc_start: 0.8057 (pm20) cc_final: 0.7830 (pm20) REVERT: F 62 ARG cc_start: 0.8588 (mmm160) cc_final: 0.8286 (mmt90) REVERT: F 78 LYS cc_start: 0.7864 (ttmt) cc_final: 0.7607 (mtpt) REVERT: G 167 LEU cc_start: 0.8047 (tp) cc_final: 0.7091 (pt) REVERT: G 183 MET cc_start: 0.7811 (mmm) cc_final: 0.7409 (tpt) REVERT: H 45 GLN cc_start: 0.7581 (mm110) cc_final: 0.7257 (mm110) REVERT: H 87 ASP cc_start: 0.7013 (m-30) cc_final: 0.6698 (t70) REVERT: H 134 MET cc_start: 0.6406 (mtt) cc_final: 0.5912 (ttt) REVERT: H 135 ASN cc_start: 0.6821 (p0) cc_final: 0.6560 (p0) REVERT: H 143 ASP cc_start: 0.7731 (p0) cc_final: 0.7359 (p0) REVERT: I 50 ASN cc_start: 0.8241 (m-40) cc_final: 0.7779 (m110) REVERT: I 134 MET cc_start: 0.7000 (mmt) cc_final: 0.6738 (mmp) REVERT: I 141 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6911 (m-30) REVERT: J 151 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.7678 (p0) REVERT: K 97 GLN cc_start: 0.5689 (tp40) cc_final: 0.5478 (tp40) REVERT: K 102 GLN cc_start: 0.6473 (mp10) cc_final: 0.6134 (pm20) REVERT: K 186 GLU cc_start: 0.7476 (mp0) cc_final: 0.7087 (pp20) REVERT: L 134 MET cc_start: 0.6590 (tmm) cc_final: 0.6043 (tmm) outliers start: 83 outliers final: 74 residues processed: 364 average time/residue: 0.3086 time to fit residues: 169.2773 Evaluate side-chains 362 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 285 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 83 MET 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 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 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 208 HIS Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 233 THR 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 13 GLU Chi-restraints excluded: chain D residue 55 ILE 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 E residue 29 TYR 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 171 ILE Chi-restraints excluded: chain E residue 177 PHE 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 G residue 64 THR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 98 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 26 MET Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 189 ILE 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 170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 214 optimal weight: 0.0970 chunk 185 optimal weight: 5.9990 chunk 19 optimal weight: 0.0970 chunk 143 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 overall best weight: 2.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3983 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= 0.222 Angle : 0.619 13.148 24450 Z= 0.312 Chirality : 0.043 0.161 2966 Planarity : 0.003 0.051 3102 Dihedral : 6.602 75.940 2576 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.70 % Favored : 92.26 % Rotamer: Outliers : 4.32 % Allowed : 24.33 % Favored : 71.34 % 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: -1.82 (0.17), residues: 2350 helix: -0.11 (0.17), residues: 1001 sheet: -1.18 (0.31), residues: 299 loop : -2.32 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 212 HIS 0.002 0.001 HIS F 71 PHE 0.042 0.001 PHE C 37 TYR 0.010 0.001 TYR B 108 ARG 0.008 0.000 ARG E 82 ********************** 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 373 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 292 time to evaluate : 2.063 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 1 MET cc_start: 0.6618 (mmt) cc_final: 0.6351 (mmp) REVERT: A 45 MET cc_start: 0.8149 (tpp) cc_final: 0.7626 (ttt) REVERT: B 19 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8552 (pt) REVERT: C 19 ASN cc_start: 0.8460 (p0) cc_final: 0.8110 (p0) REVERT: C 79 MET cc_start: 0.8945 (mmm) cc_final: 0.8667 (tpp) REVERT: D 24 MET cc_start: 0.9123 (ttp) cc_final: 0.8839 (ttm) REVERT: D 116 GLU cc_start: 0.7416 (tt0) cc_final: 0.7134 (mt-10) REVERT: D 130 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7741 (tm-30) REVERT: D 234 ARG cc_start: 0.6448 (ttt180) cc_final: 0.6022 (mtm-85) REVERT: E 205 ILE cc_start: 0.8912 (mt) cc_final: 0.8656 (tt) REVERT: E 246 LYS cc_start: 0.9316 (tttp) cc_final: 0.8404 (pttp) REVERT: F 62 ARG cc_start: 0.8511 (mmm160) cc_final: 0.8225 (mmt90) REVERT: G 167 LEU cc_start: 0.8064 (tp) cc_final: 0.7113 (pt) REVERT: G 183 MET cc_start: 0.7889 (mmm) cc_final: 0.7478 (tpt) REVERT: H 45 GLN cc_start: 0.7573 (mm110) cc_final: 0.7229 (mm110) REVERT: H 96 GLU cc_start: 0.7079 (pm20) cc_final: 0.6832 (pm20) REVERT: H 100 GLU cc_start: 0.7728 (pp20) cc_final: 0.7236 (tp30) REVERT: H 134 MET cc_start: 0.6326 (mtt) cc_final: 0.5531 (ttp) REVERT: H 135 ASN cc_start: 0.6855 (p0) cc_final: 0.6604 (p0) REVERT: I 50 ASN cc_start: 0.8273 (m-40) cc_final: 0.7809 (m110) REVERT: I 134 MET cc_start: 0.6991 (mmt) cc_final: 0.6742 (mmp) REVERT: I 141 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6955 (m-30) REVERT: J 151 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.7451 (p0) REVERT: K 97 GLN cc_start: 0.5739 (tp40) cc_final: 0.5513 (tp40) REVERT: K 186 GLU cc_start: 0.7352 (mp0) cc_final: 0.7038 (pp20) REVERT: L 134 MET cc_start: 0.6660 (tmm) cc_final: 0.6103 (tmm) outliers start: 81 outliers final: 74 residues processed: 357 average time/residue: 0.2876 time to fit residues: 154.7858 Evaluate side-chains 356 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 279 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 83 MET 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 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 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 208 HIS Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 233 THR 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 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 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 E residue 55 LEU 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 171 ILE Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 206 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 G residue 64 THR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 98 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 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 179 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 28 VAL 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 189 ILE 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 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: 3.9990 chunk 171 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.133777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.101036 restraints weight = 31343.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.100357 restraints weight = 29430.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.101311 restraints weight = 26621.577| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 18044 Z= 0.252 Angle : 0.781 59.200 24450 Z= 0.433 Chirality : 0.043 0.389 2966 Planarity : 0.004 0.116 3102 Dihedral : 6.603 75.945 2575 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.53 % Favored : 92.43 % Rotamer: Outliers : 4.32 % Allowed : 24.23 % Favored : 71.45 % 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: -1.81 (0.17), residues: 2350 helix: -0.10 (0.17), residues: 1001 sheet: -1.17 (0.31), residues: 299 loop : -2.32 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 212 HIS 0.002 0.001 HIS B 208 PHE 0.021 0.001 PHE C 37 TYR 0.012 0.001 TYR K 145 ARG 0.007 0.000 ARG E 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3773.13 seconds wall clock time: 67 minutes 59.64 seconds (4079.64 seconds total)