Starting phenix.real_space_refine on Sat Sep 12 20:27:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d06_30525/09_2026/7d06_30525.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d06_30525/09_2026/7d06_30525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7d06_30525/09_2026/7d06_30525.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d06_30525/09_2026/7d06_30525.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d06_30525/09_2026/7d06_30525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d06_30525/09_2026/7d06_30525.map" model { file = "/net/cci-nas-00/data/ceres_data/7d06_30525/09_2026/7d06_30525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d06_30525/09_2026/7d06_30525.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.008 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 12 5.49 5 S 88 5.16 5 C 11778 2.51 5 N 2978 2.21 5 O 3472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18328 Number of models: 1 Model: "" Number of chains: 15 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: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} 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: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} 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: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} 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: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} 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: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} 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: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 294 Unusual residues: {'PGV': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 243 Unusual residues: {'PGV': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.79, per 1000 atoms: 0.21 Number of scatterers: 18328 At special positions: 0 Unit cell: (134.788, 121.744, 153.267, 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 12 15.00 O 3472 8.00 N 2978 7.00 C 11778 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 - 3.00 Amino acid : True - 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: 1.11 Conformation dependent library (CDL) restraints added in 601.1 milliseconds 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: 84 helices and 20 sheets defined 47.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 2 through 30 removed outlier: 3.514A pdb=" N PHE A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.712A pdb=" N ARG A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 76 removed outlier: 3.571A pdb=" N TYR A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 83 through 95 removed outlier: 3.628A pdb=" N ARG A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.589A pdb=" N VAL A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 123 removed outlier: 3.657A pdb=" N GLY A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 140 through 172 removed outlier: 3.949A pdb=" N ARG A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Proline residue: A 153 - end of helix removed outlier: 3.806A pdb=" N VAL A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 190 removed outlier: 3.530A pdb=" N ASN A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 196 through 220 removed outlier: 3.534A pdb=" N LYS A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 214 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 255 removed outlier: 3.886A pdb=" N ALA A 229 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 236 " --> pdb=" O MET A 232 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 60 removed outlier: 3.624A pdb=" N ARG B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.747A pdb=" N ALA B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 112 removed outlier: 3.535A pdb=" N VAL B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.733A pdb=" N GLU B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 163 removed outlier: 3.623A pdb=" N LEU B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.656A pdb=" N ARG B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.802A pdb=" N ALA B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'C' and resid 21 through 34 removed outlier: 3.687A pdb=" N GLY C 27 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 63 removed outlier: 3.673A pdb=" N GLN C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 86 removed outlier: 3.872A pdb=" N ILE C 82 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 30 removed outlier: 3.513A pdb=" N PHE D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 49 removed outlier: 3.712A pdb=" N ARG D 40 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS D 46 " --> pdb=" O VAL D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 76 removed outlier: 3.571A pdb=" N TYR D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 83 through 95 removed outlier: 3.629A pdb=" N ARG D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 106 removed outlier: 3.589A pdb=" N VAL D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 123 removed outlier: 3.658A pdb=" N GLY D 118 " --> pdb=" O THR D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 140 through 172 removed outlier: 3.948A pdb=" N ARG D 144 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP D 146 " --> pdb=" O SER D 142 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY D 148 " --> pdb=" O ARG D 144 " (cutoff:3.500A) Proline residue: D 153 - end of helix removed outlier: 3.806A pdb=" N VAL D 157 " --> pdb=" O PRO D 153 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 190 removed outlier: 3.531A pdb=" N ASN D 189 " --> pdb=" O GLY D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 196 Processing helix chain 'D' and resid 196 through 220 removed outlier: 3.534A pdb=" N LYS D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 214 " --> pdb=" O CYS D 210 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 255 removed outlier: 3.886A pdb=" N ALA D 229 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 231 " --> pdb=" O GLY D 227 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 236 " --> pdb=" O MET D 232 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 60 removed outlier: 3.624A pdb=" N ARG E 57 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 89 removed outlier: 3.747A pdb=" N ALA E 87 " --> pdb=" O GLN E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 112 removed outlier: 3.852A pdb=" N GLU E 109 " --> pdb=" O MET E 105 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 118 Processing helix chain 'E' and resid 122 through 138 removed outlier: 3.733A pdb=" N GLU E 128 " --> pdb=" O ASN E 124 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.624A pdb=" N LEU E 160 " --> pdb=" O ARG E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.656A pdb=" N ARG E 193 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 214 Processing helix chain 'E' and resid 235 through 240 removed outlier: 3.801A pdb=" N ALA E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 251 Processing helix chain 'F' and resid 21 through 34 removed outlier: 3.687A pdb=" N GLY F 27 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE F 31 " --> pdb=" O GLY F 27 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS F 33 " --> pdb=" O ALA F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 63 removed outlier: 3.673A pdb=" N GLN F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN F 63 " --> pdb=" O GLN F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 86 removed outlier: 3.871A pdb=" N ILE F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN F 84 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 27 removed outlier: 3.788A pdb=" N VAL G 10 " --> pdb=" O SER G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 110 removed outlier: 3.728A pdb=" N VAL G 101 " --> pdb=" O GLN G 97 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG G 110 " --> pdb=" O LEU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 116 removed outlier: 4.260A pdb=" N THR G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 134 removed outlier: 3.903A pdb=" N ILE G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER G 132 " --> pdb=" O GLN G 128 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN G 133 " --> pdb=" O GLN G 129 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 191 removed outlier: 3.680A pdb=" N LYS G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 30 removed outlier: 3.893A pdb=" N ILE H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 92 Processing helix chain 'H' and resid 94 through 110 removed outlier: 3.608A pdb=" N LYS H 103 " --> pdb=" O LYS H 99 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA H 105 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU H 106 " --> pdb=" O GLN H 102 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 removed outlier: 4.027A pdb=" N THR H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 135 removed outlier: 3.899A pdb=" N ILE H 131 " --> pdb=" O GLU H 127 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER H 132 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN H 133 " --> pdb=" O GLN H 129 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN H 135 " --> pdb=" O ILE H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 193 removed outlier: 3.504A pdb=" N LEU H 188 " --> pdb=" O ASP H 184 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE H 189 " --> pdb=" O LEU H 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 26 removed outlier: 3.569A pdb=" N ALA I 9 " --> pdb=" O THR I 5 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE I 15 " --> pdb=" O GLY I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 92 removed outlier: 3.542A pdb=" N THR I 91 " --> pdb=" O ASP I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 110 removed outlier: 3.650A pdb=" N LYS I 99 " --> pdb=" O ALA I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 118 removed outlier: 4.176A pdb=" N THR I 116 " --> pdb=" O SER I 112 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 135 removed outlier: 3.789A pdb=" N ILE I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER I 132 " --> pdb=" O GLN I 128 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN I 135 " --> pdb=" O ILE I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 193 Processing helix chain 'J' and resid 5 through 27 Processing helix chain 'J' and resid 94 through 110 removed outlier: 3.612A pdb=" N LYS J 99 " --> pdb=" O ALA J 95 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN J 104 " --> pdb=" O GLU J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 132 removed outlier: 4.124A pdb=" N LEU J 130 " --> pdb=" O MET J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 193 removed outlier: 3.592A pdb=" N SER J 190 " --> pdb=" O GLU J 186 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE J 192 " --> pdb=" O LEU J 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 30 removed outlier: 3.605A pdb=" N VAL K 10 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 110 removed outlier: 3.754A pdb=" N ASN K 104 " --> pdb=" O GLU K 100 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP K 107 " --> pdb=" O LYS K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 116 removed outlier: 4.453A pdb=" N THR K 116 " --> pdb=" O SER K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 132 removed outlier: 3.601A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU K 130 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE K 131 " --> pdb=" O GLU K 127 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER K 132 " --> pdb=" O GLN K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 193 removed outlier: 3.833A pdb=" N ILE K 189 " --> pdb=" O LEU K 185 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS K 191 " --> pdb=" O ASP K 187 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE K 193 " --> pdb=" O ILE K 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 28 removed outlier: 3.515A pdb=" N ILE L 15 " --> pdb=" O GLY L 11 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE L 22 " --> pdb=" O GLY L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 109 removed outlier: 3.604A pdb=" N GLU L 100 " --> pdb=" O GLU L 96 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS L 103 " --> pdb=" O LYS L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 134 removed outlier: 4.056A pdb=" N GLN L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU L 130 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE L 131 " --> pdb=" O GLU L 127 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER L 132 " --> pdb=" O GLN L 128 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET L 134 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 192 Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 37 removed outlier: 6.696A pdb=" N ILE B 36 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 17 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 3.781A 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 92 through 95 removed outlier: 3.547A pdb=" N ASP B 174 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 207 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA B 43 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL B 223 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET B 45 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 220 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU B 231 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL B 222 " --> pdb=" O GLN B 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 13 removed outlier: 7.144A pdb=" N VAL C 11 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN C 45 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 13 " --> pdb=" O GLN C 45 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 35 through 37 removed outlier: 6.696A pdb=" N ILE E 36 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS E 17 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU E 69 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 21 through 22 Processing sheet with id=AA7, first strand: chain 'E' and resid 92 through 95 removed outlier: 3.547A pdb=" N ASP E 174 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 207 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA E 43 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL E 223 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET E 45 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE E 220 " --> pdb=" O GLU E 231 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU E 231 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL E 222 " --> pdb=" O GLN E 229 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 10 through 13 removed outlier: 7.143A pdb=" N VAL F 11 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN F 45 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY F 13 " --> pdb=" O GLN F 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 175 through 176 removed outlier: 7.172A pdb=" N LYS G 43 " --> pdb=" O ILE G 176 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER G 70 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASP G 85 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL G 68 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL G 58 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS G 57 " --> pdb=" O LEU G 159 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE G 161 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR G 59 " --> pdb=" O ILE G 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 148 " --> pdb=" O GLN G 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 137 through 141 removed outlier: 5.491A pdb=" N ILE G 140 " --> pdb=" O LEU G 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 175 through 176 removed outlier: 8.801A pdb=" N ILE H 176 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS H 43 " --> pdb=" O ILE H 176 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR H 81 " --> pdb=" O ILE H 71 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE H 71 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR H 83 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL H 58 " --> pdb=" O ILE H 65 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LYS H 57 " --> pdb=" O LEU H 159 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE H 161 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR H 59 " --> pdb=" O ILE H 161 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE H 146 " --> pdb=" O GLN H 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 137 through 141 removed outlier: 5.519A pdb=" N ILE H 140 " --> pdb=" O LEU H 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 175 through 176 removed outlier: 7.208A pdb=" N LYS I 43 " --> pdb=" O ILE I 176 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP I 85 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL I 68 " --> pdb=" O ASP I 85 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL I 58 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS I 57 " --> pdb=" O LEU I 159 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE I 161 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR I 59 " --> pdb=" O ILE I 161 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL I 148 " --> pdb=" O GLN I 180 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 137 through 141 removed outlier: 5.509A pdb=" N ILE I 140 " --> pdb=" O LEU I 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 42 through 46 removed outlier: 6.665A pdb=" N ASP J 85 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL J 68 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL J 58 " --> pdb=" O ILE J 65 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS J 57 " --> pdb=" O LEU J 159 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE J 161 " --> pdb=" O LYS J 57 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR J 59 " --> pdb=" O ILE J 161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 137 through 141 removed outlier: 6.082A pdb=" N ILE J 140 " --> pdb=" O LEU J 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 41 through 46 removed outlier: 6.453A pdb=" N THR K 81 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE K 71 " --> pdb=" O THR K 81 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR K 83 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL K 58 " --> pdb=" O ILE K 65 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS K 57 " --> pdb=" O LEU K 159 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE K 161 " --> pdb=" O LYS K 57 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR K 59 " --> pdb=" O ILE K 161 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL K 148 " --> pdb=" O GLN K 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 137 through 141 removed outlier: 5.714A pdb=" N ILE K 140 " --> pdb=" O LEU K 170 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 175 through 176 removed outlier: 8.865A pdb=" N ILE L 176 " --> pdb=" O THR L 41 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS L 43 " --> pdb=" O ILE L 176 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP L 85 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL L 68 " --> pdb=" O ASP L 85 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL L 58 " --> pdb=" O ILE L 65 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LYS L 57 " --> pdb=" O LEU L 159 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE L 161 " --> pdb=" O LYS L 57 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR L 59 " --> pdb=" O ILE L 161 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL L 148 " --> pdb=" O GLN L 180 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 137 through 141 removed outlier: 5.379A pdb=" N ILE L 140 " --> pdb=" O LEU L 170 " (cutoff:3.500A) 792 hydrogen bonds defined for protein. 2295 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: 2.81 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3035 1.30 - 1.43: 4276 1.43 - 1.56: 10999 1.56 - 1.68: 76 1.68 - 1.81: 168 Bond restraints: 18554 Sorted by residual: bond pdb=" C11 PGV A 304 " pdb=" C12 PGV A 304 " ideal model delta sigma weight residual 1.332 1.553 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C11 PGV A 303 " pdb=" C12 PGV A 303 " ideal model delta sigma weight residual 1.332 1.552 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C11 PGV D 304 " pdb=" C12 PGV D 304 " ideal model delta sigma weight residual 1.332 1.552 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C11 PGV D 303 " pdb=" C12 PGV D 303 " ideal model delta sigma weight residual 1.332 1.552 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C11 PGV D 302 " pdb=" C12 PGV D 302 " ideal model delta sigma weight residual 1.332 1.552 -0.220 2.00e-02 2.50e+03 1.21e+02 ... (remaining 18549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.70: 24844 6.70 - 13.41: 106 13.41 - 20.11: 32 20.11 - 26.81: 0 26.81 - 33.52: 12 Bond angle restraints: 24994 Sorted by residual: angle pdb=" C19 PGV D 305 " pdb=" C20 PGV D 305 " pdb=" C21 PGV D 305 " ideal model delta sigma weight residual 113.71 80.19 33.52 3.00e+00 1.11e-01 1.25e+02 angle pdb=" C19 PGV A 301 " pdb=" C20 PGV A 301 " pdb=" C21 PGV A 301 " ideal model delta sigma weight residual 113.71 81.12 32.59 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C19 PGV D 301 " pdb=" C20 PGV D 301 " pdb=" C21 PGV D 301 " ideal model delta sigma weight residual 113.71 81.14 32.57 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C19 PGV A 305 " pdb=" C20 PGV A 305 " pdb=" C21 PGV A 305 " ideal model delta sigma weight residual 113.71 81.47 32.24 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C19 PGV A 306 " pdb=" C20 PGV A 306 " pdb=" C21 PGV A 306 " ideal model delta sigma weight residual 113.71 82.13 31.58 3.00e+00 1.11e-01 1.11e+02 ... (remaining 24989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.10: 10497 30.10 - 60.19: 638 60.19 - 90.29: 54 90.29 - 120.39: 9 120.39 - 150.48: 6 Dihedral angle restraints: 11204 sinusoidal: 4462 harmonic: 6742 Sorted by residual: dihedral pdb=" CA GLU L 156 " pdb=" C GLU L 156 " pdb=" N LYS L 157 " pdb=" CA LYS L 157 " ideal model delta harmonic sigma weight residual 180.00 151.19 28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA GLU I 156 " pdb=" C GLU I 156 " pdb=" N LYS I 157 " pdb=" CA LYS I 157 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA THR B 119 " pdb=" C THR B 119 " pdb=" N LYS B 120 " pdb=" CA LYS B 120 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 11201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2563 0.087 - 0.174: 368 0.174 - 0.261: 46 0.261 - 0.348: 3 0.348 - 0.435: 2 Chirality restraints: 2982 Sorted by residual: chirality pdb=" CB THR B 119 " pdb=" CA THR B 119 " pdb=" OG1 THR B 119 " pdb=" CG2 THR B 119 " both_signs ideal model delta sigma weight residual False 2.55 2.12 0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CB THR E 119 " pdb=" CA THR E 119 " pdb=" OG1 THR E 119 " pdb=" CG2 THR E 119 " both_signs ideal model delta sigma weight residual False 2.55 2.12 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ASN H 35 " pdb=" N ASN H 35 " pdb=" C ASN H 35 " pdb=" CB ASN H 35 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 2979 not shown) Planarity restraints: 3134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PGV D 303 " 0.166 2.00e-02 2.50e+03 3.24e-01 1.05e+03 pdb=" C11 PGV D 303 " -0.428 2.00e-02 2.50e+03 pdb=" C12 PGV D 303 " 0.428 2.00e-02 2.50e+03 pdb=" C13 PGV D 303 " -0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PGV A 303 " -0.166 2.00e-02 2.50e+03 3.24e-01 1.05e+03 pdb=" C11 PGV A 303 " 0.428 2.00e-02 2.50e+03 pdb=" C12 PGV A 303 " -0.427 2.00e-02 2.50e+03 pdb=" C13 PGV A 303 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PGV A 304 " 0.160 2.00e-02 2.50e+03 2.78e-01 7.73e+02 pdb=" C11 PGV A 304 " -0.360 2.00e-02 2.50e+03 pdb=" C12 PGV A 304 " 0.359 2.00e-02 2.50e+03 pdb=" C13 PGV A 304 " -0.159 2.00e-02 2.50e+03 ... (remaining 3131 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 212 2.60 - 3.17: 14250 3.17 - 3.75: 25968 3.75 - 4.32: 37448 4.32 - 4.90: 62645 Nonbonded interactions: 140523 Sorted by model distance: nonbonded pdb=" O MET E 105 " pdb=" OG SER E 106 " model vdw 2.021 3.040 nonbonded pdb=" O MET B 105 " pdb=" OG SER B 106 " model vdw 2.082 3.040 nonbonded pdb=" O06 PGV D 305 " pdb=" O12 PGV D 305 " model vdw 2.112 3.040 nonbonded pdb=" OD1 ASN G 94 " pdb=" N ALA G 95 " model vdw 2.129 3.120 nonbonded pdb=" O LEU L 73 " pdb=" O ASP L 74 " model vdw 2.143 3.040 ... (remaining 140518 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 305) 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' and resid 3 through 193) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.060 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.012 0.221 18554 Z= 0.578 Angle : 1.544 33.516 24994 Z= 0.713 Chirality : 0.063 0.435 2982 Planarity : 0.016 0.324 3134 Dihedral : 19.078 150.482 6876 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 1.02 % Allowed : 10.38 % Favored : 88.60 % Rotamer: Outliers : 4.91 % Allowed : 9.82 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.86 (0.12), residues: 2350 helix: -4.75 (0.05), residues: 992 sheet: -2.06 (0.29), residues: 278 loop : -3.44 (0.15), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 190 TYR 0.039 0.003 TYR J 40 PHE 0.030 0.003 PHE C 17 TRP 0.013 0.002 TRP A 212 HIS 0.005 0.002 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.01243 / 0.58 (18554) covalent geometry : angle 1.54417 / 0.71 (24994) hydrogen bonds : bond 0.32205 / 21.18 ( 792) hydrogen bonds : angle 10.27611 / 7.09 ( 2295) *********************** 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 537 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 445 time to evaluate : 0.692 Fit side-chains REVERT: A 120 MET cc_start: 0.9144 (mtt) cc_final: 0.8916 (mtt) REVERT: A 188 ASN cc_start: 0.8657 (t0) cc_final: 0.8289 (t0) REVERT: B 17 LYS cc_start: 0.8533 (mtpt) cc_final: 0.8324 (mtmm) REVERT: B 120 LYS cc_start: 0.8653 (mppt) cc_final: 0.8397 (mmtt) REVERT: B 185 LYS cc_start: 0.9016 (ttmt) cc_final: 0.8732 (mtpt) REVERT: B 190 ARG cc_start: 0.7932 (mpp80) cc_final: 0.7698 (mtm180) REVERT: B 262 SER cc_start: 0.5448 (OUTLIER) cc_final: 0.4928 (m) REVERT: C 33 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6905 (pttp) REVERT: C 34 GLN cc_start: 0.7401 (tp-100) cc_final: 0.7158 (tp40) REVERT: C 67 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7293 (tppt) REVERT: C 93 HIS cc_start: 0.6548 (m90) cc_final: 0.6303 (m-70) REVERT: E 17 LYS cc_start: 0.8570 (mtpt) cc_final: 0.8262 (mtpt) REVERT: E 25 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6615 (mt-10) REVERT: E 33 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8647 (p) REVERT: F 30 ILE cc_start: 0.7108 (mt) cc_final: 0.6830 (mp) REVERT: F 45 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6601 (mp10) REVERT: F 73 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8015 (ttmm) REVERT: G 141 ASP cc_start: 0.7866 (p0) cc_final: 0.7566 (p0) REVERT: G 160 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8397 (tttp) REVERT: H 45 GLN cc_start: 0.8058 (mt0) cc_final: 0.7853 (mt0) REVERT: H 50 ASN cc_start: 0.8600 (t0) cc_final: 0.8280 (t0) REVERT: H 97 GLN cc_start: 0.8047 (mp10) cc_final: 0.7610 (mp10) REVERT: H 187 ASP cc_start: 0.7242 (t0) cc_final: 0.7035 (t0) REVERT: I 43 LYS cc_start: 0.8778 (ptpp) cc_final: 0.8525 (ptmm) REVERT: I 191 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8086 (tttt) REVERT: J 43 LYS cc_start: 0.8370 (ptpp) cc_final: 0.8067 (pttp) REVERT: J 133 ASN cc_start: 0.6886 (m-40) cc_final: 0.6615 (m-40) REVERT: J 134 MET cc_start: 0.6031 (pmm) cc_final: 0.5608 (pmm) REVERT: J 147 MET cc_start: 0.8458 (ptm) cc_final: 0.8256 (ptp) REVERT: K 135 ASN cc_start: 0.5731 (OUTLIER) cc_final: 0.5438 (p0) outliers start: 92 outliers final: 27 residues processed: 513 average time/residue: 0.1430 time to fit residues: 108.2116 Evaluate side-chains 363 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 327 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 191 LYS Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 192 PHE Chi-restraints excluded: chain L residue 193 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 HIS A 139 GLN A 191 GLN B 144 GLN C 66 GLN C 93 HIS D 46 HIS D 139 GLN D 191 GLN F 89 GLN G 45 GLN G 97 GLN H 35 ASN H 45 GLN H 50 ASN I 45 GLN I 104 ASN L 102 GLN L 128 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.146522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.104930 restraints weight = 24590.912| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.89 r_work: 0.2933 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18554 Z= 0.150 Angle : 0.724 10.451 24994 Z= 0.381 Chirality : 0.044 0.291 2982 Planarity : 0.005 0.058 3134 Dihedral : 15.939 152.917 2975 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.77 % Favored : 91.02 % Rotamer: Outliers : 3.04 % Allowed : 13.93 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.14), residues: 2350 helix: -2.11 (0.12), residues: 1046 sheet: -1.54 (0.30), residues: 270 loop : -3.10 (0.16), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 55 TYR 0.014 0.001 TYR B 173 PHE 0.019 0.001 PHE A 182 TRP 0.013 0.001 TRP D 212 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (18554) covalent geometry : angle 0.72387 / 0.38 (24994) hydrogen bonds : bond 0.05877 / 3.85 ( 792) hydrogen bonds : angle 5.23499 / 3.63 ( 2295) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 364 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8849 (t0) cc_final: 0.8485 (t0) REVERT: B 109 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8406 (mm-30) REVERT: B 135 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8615 (tm-30) REVERT: B 262 SER cc_start: 0.5304 (OUTLIER) cc_final: 0.4609 (m) REVERT: C 66 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7263 (tm-30) REVERT: E 17 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8560 (mtpt) REVERT: E 33 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8745 (p) REVERT: F 61 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7957 (tp) REVERT: F 70 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6756 (mt) REVERT: G 85 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8468 (p0) REVERT: G 97 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6649 (mp10) REVERT: H 50 ASN cc_start: 0.9001 (t0) cc_final: 0.8618 (t0) REVERT: H 60 MET cc_start: 0.8845 (tpp) cc_final: 0.8487 (tpp) REVERT: H 97 GLN cc_start: 0.8091 (mp10) cc_final: 0.7874 (mp10) REVERT: I 23 PHE cc_start: 0.7912 (m-10) cc_final: 0.7250 (t80) REVERT: I 78 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7425 (mmt90) REVERT: I 185 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7832 (pp) REVERT: I 186 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7817 (mm-30) REVERT: J 43 LYS cc_start: 0.8350 (ptpp) cc_final: 0.7988 (pttp) REVERT: J 134 MET cc_start: 0.6591 (pmm) cc_final: 0.6200 (pmm) REVERT: J 141 ASP cc_start: 0.8088 (p0) cc_final: 0.7652 (p0) REVERT: J 147 MET cc_start: 0.9063 (ptm) cc_final: 0.8643 (ptp) REVERT: K 85 ASP cc_start: 0.8638 (p0) cc_final: 0.8376 (p0) REVERT: K 142 GLU cc_start: 0.8133 (pt0) cc_final: 0.7676 (pt0) REVERT: K 174 ASP cc_start: 0.8996 (m-30) cc_final: 0.8749 (m-30) REVERT: K 192 PHE cc_start: 0.7082 (t80) cc_final: 0.6850 (t80) outliers start: 57 outliers final: 31 residues processed: 401 average time/residue: 0.1420 time to fit residues: 86.0845 Evaluate side-chains 354 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 314 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 192 PHE Chi-restraints excluded: chain L residue 193 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 chunk 196 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 155 ASN E 208 HIS F 89 GLN G 45 GLN H 102 GLN L 102 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105984 restraints weight = 24813.968| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.01 r_work: 0.2933 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18554 Z= 0.136 Angle : 0.628 11.343 24994 Z= 0.330 Chirality : 0.043 0.268 2982 Planarity : 0.004 0.053 3134 Dihedral : 15.041 149.445 2931 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.19 % Favored : 90.64 % Rotamer: Outliers : 3.31 % Allowed : 14.83 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.16), residues: 2350 helix: -0.55 (0.15), residues: 1046 sheet: -1.25 (0.31), residues: 278 loop : -2.80 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 140 TYR 0.015 0.001 TYR G 145 PHE 0.018 0.001 PHE D 182 TRP 0.008 0.001 TRP A 212 HIS 0.008 0.001 HIS E 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (18554) covalent geometry : angle 0.62811 / 0.33 (24994) hydrogen bonds : bond 0.04808 / 3.15 ( 792) hydrogen bonds : angle 4.68268 / 3.26 ( 2295) *********************** 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 405 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 343 time to evaluate : 1.027 Fit side-chains REVERT: A 188 ASN cc_start: 0.8849 (t0) cc_final: 0.8618 (t0) REVERT: B 82 ARG cc_start: 0.8169 (mtp-110) cc_final: 0.7895 (mtm110) REVERT: B 104 ASP cc_start: 0.7936 (p0) cc_final: 0.7560 (p0) REVERT: B 120 LYS cc_start: 0.8809 (mppt) cc_final: 0.8481 (mmtt) REVERT: B 135 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8642 (tm-30) REVERT: B 262 SER cc_start: 0.5132 (OUTLIER) cc_final: 0.4490 (m) REVERT: C 66 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: E 105 MET cc_start: 0.8883 (mmm) cc_final: 0.8312 (mtp) REVERT: E 263 HIS cc_start: 0.5719 (m-70) cc_final: 0.5505 (m170) REVERT: F 61 LEU cc_start: 0.8314 (mm) cc_final: 0.8083 (tp) REVERT: G 85 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8452 (p0) REVERT: G 97 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.6662 (tp40) REVERT: G 141 ASP cc_start: 0.7966 (p0) cc_final: 0.7591 (p0) REVERT: H 35 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.6945 (t0) REVERT: H 50 ASN cc_start: 0.9005 (t0) cc_final: 0.8616 (t0) REVERT: H 60 MET cc_start: 0.8879 (tpp) cc_final: 0.8380 (ttt) REVERT: H 93 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6267 (p90) REVERT: H 97 GLN cc_start: 0.8150 (mp10) cc_final: 0.7914 (mp10) REVERT: I 23 PHE cc_start: 0.7897 (m-10) cc_final: 0.7225 (t80) REVERT: I 78 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7092 (mmt-90) REVERT: I 191 LYS cc_start: 0.8437 (ttmm) cc_final: 0.7910 (tttt) REVERT: J 43 LYS cc_start: 0.8383 (ptpp) cc_final: 0.8067 (pttp) REVERT: J 73 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7940 (tt) REVERT: J 134 MET cc_start: 0.6610 (pmm) cc_final: 0.6245 (pmm) REVERT: J 147 MET cc_start: 0.9077 (ptm) cc_final: 0.8697 (ptp) REVERT: J 183 MET cc_start: 0.8383 (mmt) cc_final: 0.8177 (mmm) REVERT: K 142 GLU cc_start: 0.8201 (pt0) cc_final: 0.7741 (pt0) REVERT: K 174 ASP cc_start: 0.9026 (m-30) cc_final: 0.8791 (m-30) REVERT: L 42 MET cc_start: 0.8756 (mmm) cc_final: 0.8495 (mtt) outliers start: 62 outliers final: 35 residues processed: 385 average time/residue: 0.1440 time to fit residues: 84.4570 Evaluate side-chains 355 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 312 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 93 PHE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 117 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 163 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 264 GLN E 155 ASN E 264 GLN G 97 GLN ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.147178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106089 restraints weight = 24736.470| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.90 r_work: 0.2910 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18554 Z= 0.137 Angle : 0.620 11.637 24994 Z= 0.323 Chirality : 0.043 0.334 2982 Planarity : 0.004 0.052 3134 Dihedral : 14.405 144.366 2916 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.15 % Favored : 90.72 % Rotamer: Outliers : 3.52 % Allowed : 15.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.17), residues: 2350 helix: 0.22 (0.16), residues: 1048 sheet: -1.04 (0.32), residues: 278 loop : -2.66 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 140 TYR 0.014 0.001 TYR B 173 PHE 0.016 0.001 PHE G 13 TRP 0.007 0.001 TRP A 212 HIS 0.006 0.001 HIS E 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (18554) covalent geometry : angle 0.62021 / 0.32 (24994) hydrogen bonds : bond 0.04365 / 2.87 ( 792) hydrogen bonds : angle 4.48934 / 3.12 ( 2295) *********************** 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 397 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 331 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.8932 (mttm) cc_final: 0.8696 (mttp) REVERT: B 63 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8462 (mt) REVERT: B 82 ARG cc_start: 0.8144 (mtp-110) cc_final: 0.7930 (mtm110) REVERT: B 120 LYS cc_start: 0.8766 (mppt) cc_final: 0.8434 (mmtt) REVERT: B 135 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8440 (tp30) REVERT: B 262 SER cc_start: 0.4956 (OUTLIER) cc_final: 0.4331 (m) REVERT: C 66 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7314 (tm-30) REVERT: D 108 ARG cc_start: 0.8985 (tmt-80) cc_final: 0.8709 (ttp80) REVERT: D 226 GLU cc_start: 0.8698 (pp20) cc_final: 0.8126 (pp20) REVERT: E 69 GLU cc_start: 0.7194 (pm20) cc_final: 0.6974 (pt0) REVERT: E 105 MET cc_start: 0.8891 (mmm) cc_final: 0.8536 (mtp) REVERT: F 61 LEU cc_start: 0.8331 (mm) cc_final: 0.8115 (tp) REVERT: G 85 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8457 (p0) REVERT: G 97 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6598 (tp40) REVERT: H 35 ASN cc_start: 0.7548 (OUTLIER) cc_final: 0.6894 (t0) REVERT: H 50 ASN cc_start: 0.9015 (t0) cc_final: 0.8693 (t0) REVERT: H 60 MET cc_start: 0.8864 (tpp) cc_final: 0.8382 (ttt) REVERT: H 97 GLN cc_start: 0.8191 (mp10) cc_final: 0.7870 (mp10) REVERT: I 23 PHE cc_start: 0.7817 (m-10) cc_final: 0.7192 (t80) REVERT: I 78 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7132 (mmt180) REVERT: I 191 LYS cc_start: 0.8409 (ttmm) cc_final: 0.7913 (tttt) REVERT: J 43 LYS cc_start: 0.8389 (ptpp) cc_final: 0.8052 (pttp) REVERT: J 73 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7986 (tt) REVERT: J 134 MET cc_start: 0.6584 (pmm) cc_final: 0.6265 (pmm) REVERT: J 147 MET cc_start: 0.9077 (ptm) cc_final: 0.8755 (ptp) REVERT: K 142 GLU cc_start: 0.8248 (pt0) cc_final: 0.7745 (pt0) outliers start: 66 outliers final: 42 residues processed: 376 average time/residue: 0.1395 time to fit residues: 80.0758 Evaluate side-chains 372 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 322 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 183 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 136 optimal weight: 0.3980 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 194 HIS E 155 ASN G 45 GLN ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.100114 restraints weight = 24525.540| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.78 r_work: 0.2889 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 18554 Z= 0.243 Angle : 0.700 12.105 24994 Z= 0.361 Chirality : 0.047 0.297 2982 Planarity : 0.004 0.054 3134 Dihedral : 14.361 142.719 2916 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.04 % Favored : 89.79 % Rotamer: Outliers : 4.11 % Allowed : 16.33 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.17), residues: 2350 helix: 0.32 (0.16), residues: 1040 sheet: -1.05 (0.33), residues: 264 loop : -2.58 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 140 TYR 0.020 0.002 TYR G 40 PHE 0.029 0.002 PHE F 17 TRP 0.009 0.002 TRP A 212 HIS 0.004 0.001 HIS E 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.24 (18554) covalent geometry : angle 0.70035 / 0.36 (24994) hydrogen bonds : bond 0.05600 / 3.66 ( 792) hydrogen bonds : angle 4.65808 / 3.22 ( 2295) *********************** 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 402 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 325 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.8923 (mttm) cc_final: 0.8603 (mttp) REVERT: B 82 ARG cc_start: 0.8200 (mtp-110) cc_final: 0.7970 (mtm110) REVERT: B 120 LYS cc_start: 0.8803 (mppt) cc_final: 0.8456 (mmtt) REVERT: B 135 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8448 (tp30) REVERT: D 108 ARG cc_start: 0.9001 (tmt-80) cc_final: 0.8735 (ttp80) REVERT: D 226 GLU cc_start: 0.8712 (pp20) cc_final: 0.8154 (pp20) REVERT: E 105 MET cc_start: 0.8802 (mmm) cc_final: 0.8543 (mtp) REVERT: G 67 ARG cc_start: 0.8740 (mtm-85) cc_final: 0.8500 (mtp-110) REVERT: G 141 ASP cc_start: 0.7892 (p0) cc_final: 0.7661 (p0) REVERT: H 26 MET cc_start: 0.8734 (mmp) cc_final: 0.8453 (mmp) REVERT: H 35 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.6958 (t0) REVERT: H 50 ASN cc_start: 0.9060 (t0) cc_final: 0.8719 (t0) REVERT: H 60 MET cc_start: 0.8914 (tpp) cc_final: 0.8523 (ttt) REVERT: H 97 GLN cc_start: 0.8188 (mp10) cc_final: 0.7838 (mp10) REVERT: I 23 PHE cc_start: 0.7802 (m-10) cc_final: 0.7200 (t80) REVERT: I 191 LYS cc_start: 0.8388 (ttmm) cc_final: 0.7927 (tttt) REVERT: J 43 LYS cc_start: 0.8395 (ptpp) cc_final: 0.8022 (pttp) REVERT: J 73 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8124 (tt) REVERT: J 134 MET cc_start: 0.6613 (pmm) cc_final: 0.6320 (pmm) REVERT: J 147 MET cc_start: 0.9069 (ptm) cc_final: 0.8661 (ptp) REVERT: K 142 GLU cc_start: 0.8231 (pt0) cc_final: 0.7677 (pt0) outliers start: 77 outliers final: 57 residues processed: 375 average time/residue: 0.1423 time to fit residues: 81.0630 Evaluate side-chains 373 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 314 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 204 optimal weight: 0.5980 chunk 149 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 131 optimal weight: 50.0000 chunk 181 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 67 GLN E 155 ASN G 45 GLN I 102 GLN I 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.147633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.104534 restraints weight = 24440.044| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.81 r_work: 0.2962 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18554 Z= 0.116 Angle : 0.596 11.743 24994 Z= 0.311 Chirality : 0.042 0.295 2982 Planarity : 0.004 0.053 3134 Dihedral : 13.590 143.001 2910 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.85 % Favored : 91.06 % Rotamer: Outliers : 3.58 % Allowed : 17.29 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.18), residues: 2350 helix: 0.93 (0.17), residues: 1048 sheet: -1.02 (0.33), residues: 264 loop : -2.42 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 140 TYR 0.014 0.001 TYR G 145 PHE 0.012 0.001 PHE D 182 TRP 0.005 0.001 TRP D 6 HIS 0.005 0.001 HIS E 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (18554) covalent geometry : angle 0.59563 / 0.31 (24994) hydrogen bonds : bond 0.03754 / 2.48 ( 792) hydrogen bonds : angle 4.31722 / 3.00 ( 2295) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 324 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.8837 (mttm) cc_final: 0.8627 (mttp) REVERT: B 63 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8351 (mt) REVERT: B 82 ARG cc_start: 0.8197 (mtp-110) cc_final: 0.7961 (mtm110) REVERT: B 135 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8418 (tp30) REVERT: B 246 LYS cc_start: 0.8339 (tptm) cc_final: 0.7972 (ptpt) REVERT: D 108 ARG cc_start: 0.8911 (tmt-80) cc_final: 0.8600 (ttp80) REVERT: D 226 GLU cc_start: 0.8662 (pp20) cc_final: 0.8164 (pp20) REVERT: E 105 MET cc_start: 0.8767 (mmm) cc_final: 0.8486 (mtp) REVERT: G 67 ARG cc_start: 0.8761 (mtm-85) cc_final: 0.8513 (mtp-110) REVERT: G 85 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8513 (p0) REVERT: G 141 ASP cc_start: 0.7725 (p0) cc_final: 0.7466 (p0) REVERT: H 35 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.6850 (t0) REVERT: H 50 ASN cc_start: 0.8974 (t0) cc_final: 0.8626 (t0) REVERT: H 60 MET cc_start: 0.8841 (tpp) cc_final: 0.8412 (ttt) REVERT: H 97 GLN cc_start: 0.8173 (mp10) cc_final: 0.7930 (mp10) REVERT: H 128 GLN cc_start: 0.5041 (OUTLIER) cc_final: 0.4830 (mp10) REVERT: I 23 PHE cc_start: 0.7726 (m-10) cc_final: 0.7193 (t80) REVERT: I 78 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7046 (mmt-90) REVERT: I 134 MET cc_start: 0.6371 (ppp) cc_final: 0.6161 (ppp) REVERT: I 191 LYS cc_start: 0.8297 (ttmm) cc_final: 0.7910 (tttt) REVERT: J 42 MET cc_start: 0.9036 (mtp) cc_final: 0.8625 (mtp) REVERT: J 73 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7866 (tt) REVERT: J 134 MET cc_start: 0.6582 (pmm) cc_final: 0.6313 (pmm) REVERT: J 147 MET cc_start: 0.9064 (ptm) cc_final: 0.8674 (ptp) REVERT: K 142 GLU cc_start: 0.8178 (pt0) cc_final: 0.7669 (pt0) REVERT: L 100 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7996 (tm-30) REVERT: L 156 GLU cc_start: 0.6744 (pm20) cc_final: 0.6531 (pm20) REVERT: L 183 MET cc_start: 0.7868 (ttt) cc_final: 0.7664 (ttt) outliers start: 67 outliers final: 40 residues processed: 370 average time/residue: 0.1313 time to fit residues: 74.0233 Evaluate side-chains 345 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 299 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 31 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 90 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 155 ASN G 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.147024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.103519 restraints weight = 24523.480| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.86 r_work: 0.2935 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18554 Z= 0.129 Angle : 0.603 11.869 24994 Z= 0.314 Chirality : 0.043 0.289 2982 Planarity : 0.004 0.051 3134 Dihedral : 13.245 143.113 2905 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.06 % Favored : 90.77 % Rotamer: Outliers : 3.26 % Allowed : 17.98 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.18), residues: 2350 helix: 1.11 (0.17), residues: 1052 sheet: -0.97 (0.33), residues: 264 loop : -2.39 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 140 TYR 0.014 0.001 TYR G 145 PHE 0.013 0.001 PHE G 13 TRP 0.005 0.001 TRP D 212 HIS 0.006 0.001 HIS E 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (18554) covalent geometry : angle 0.60297 / 0.31 (24994) hydrogen bonds : bond 0.03933 / 2.59 ( 792) hydrogen bonds : angle 4.28397 / 2.98 ( 2295) *********************** 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 382 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 321 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.8844 (mttm) cc_final: 0.8640 (mttp) REVERT: B 82 ARG cc_start: 0.8194 (mtp-110) cc_final: 0.7948 (mtm110) REVERT: B 135 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8427 (tp30) REVERT: B 246 LYS cc_start: 0.8333 (tptm) cc_final: 0.7971 (ptpp) REVERT: D 108 ARG cc_start: 0.8948 (tmt-80) cc_final: 0.8671 (ttp80) REVERT: D 226 GLU cc_start: 0.8627 (pp20) cc_final: 0.8325 (pm20) REVERT: E 105 MET cc_start: 0.8748 (mmm) cc_final: 0.8524 (mtp) REVERT: F 70 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6608 (mt) REVERT: F 79 MET cc_start: 0.8783 (mmm) cc_final: 0.8235 (mmm) REVERT: G 67 ARG cc_start: 0.8783 (mtm-85) cc_final: 0.8543 (mtp-110) REVERT: G 85 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8502 (p0) REVERT: G 141 ASP cc_start: 0.7742 (p0) cc_final: 0.7461 (p0) REVERT: H 35 ASN cc_start: 0.7445 (OUTLIER) cc_final: 0.6877 (t0) REVERT: H 50 ASN cc_start: 0.8970 (t0) cc_final: 0.8620 (t0) REVERT: H 60 MET cc_start: 0.8844 (tpp) cc_final: 0.8438 (ttt) REVERT: H 97 GLN cc_start: 0.8205 (mp10) cc_final: 0.7960 (mp10) REVERT: H 128 GLN cc_start: 0.4994 (OUTLIER) cc_final: 0.4781 (mp10) REVERT: I 23 PHE cc_start: 0.7706 (m-10) cc_final: 0.7184 (t80) REVERT: I 78 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7199 (mmt-90) REVERT: I 134 MET cc_start: 0.6374 (ppp) cc_final: 0.6119 (ppp) REVERT: I 191 LYS cc_start: 0.8300 (ttmm) cc_final: 0.7920 (tttt) REVERT: J 73 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7890 (tt) REVERT: J 134 MET cc_start: 0.6592 (pmm) cc_final: 0.6308 (pmm) REVERT: J 147 MET cc_start: 0.9060 (ptm) cc_final: 0.8656 (ptp) REVERT: K 142 GLU cc_start: 0.8188 (pt0) cc_final: 0.7623 (pt0) REVERT: L 100 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7980 (tm-30) outliers start: 61 outliers final: 46 residues processed: 362 average time/residue: 0.1309 time to fit residues: 72.9267 Evaluate side-chains 355 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 303 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 73 optimal weight: 0.9990 chunk 168 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 194 optimal weight: 0.0270 chunk 183 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 chunk 133 optimal weight: 0.1980 chunk 52 optimal weight: 0.0870 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 155 ASN G 45 GLN J 102 GLN L 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.150706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.107883 restraints weight = 24458.233| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.84 r_work: 0.3013 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18554 Z= 0.106 Angle : 0.591 11.630 24994 Z= 0.309 Chirality : 0.042 0.290 2982 Planarity : 0.003 0.052 3134 Dihedral : 12.625 145.774 2905 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.60 % Favored : 91.32 % Rotamer: Outliers : 2.93 % Allowed : 18.25 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.18), residues: 2350 helix: 1.48 (0.17), residues: 1048 sheet: -0.88 (0.33), residues: 260 loop : -2.32 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 140 TYR 0.013 0.001 TYR L 169 PHE 0.015 0.001 PHE D 182 TRP 0.006 0.001 TRP A 6 HIS 0.005 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (18554) covalent geometry : angle 0.59067 / 0.31 (24994) hydrogen bonds : bond 0.03006 / 1.99 ( 792) hydrogen bonds : angle 4.12811 / 2.88 ( 2295) *********************** 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 395 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 340 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 226 GLU cc_start: 0.8599 (pp20) cc_final: 0.8365 (pm20) REVERT: B 75 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8283 (tttp) REVERT: B 82 ARG cc_start: 0.8145 (mtp-110) cc_final: 0.7892 (mtm110) REVERT: B 246 LYS cc_start: 0.8311 (tptm) cc_final: 0.7973 (ptpt) REVERT: D 108 ARG cc_start: 0.8897 (tmt-80) cc_final: 0.8584 (ttp80) REVERT: D 226 GLU cc_start: 0.8619 (pp20) cc_final: 0.8329 (pm20) REVERT: F 34 GLN cc_start: 0.6239 (tp-100) cc_final: 0.5700 (tp-100) REVERT: G 55 ARG cc_start: 0.8766 (mtm-85) cc_final: 0.7884 (mmp80) REVERT: G 85 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8564 (p0) REVERT: G 141 ASP cc_start: 0.7845 (p0) cc_final: 0.7526 (p0) REVERT: H 35 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6699 (t0) REVERT: H 50 ASN cc_start: 0.8900 (t0) cc_final: 0.8621 (t0) REVERT: H 60 MET cc_start: 0.8835 (tpp) cc_final: 0.8416 (ttt) REVERT: H 97 GLN cc_start: 0.8169 (mp10) cc_final: 0.7433 (mp10) REVERT: I 23 PHE cc_start: 0.7649 (m-10) cc_final: 0.7170 (t80) REVERT: J 42 MET cc_start: 0.9050 (mtp) cc_final: 0.8542 (mtp) REVERT: J 43 LYS cc_start: 0.8314 (ptpp) cc_final: 0.8006 (pttp) REVERT: J 73 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7671 (tt) REVERT: J 134 MET cc_start: 0.6585 (pmm) cc_final: 0.6317 (pmm) REVERT: K 142 GLU cc_start: 0.8171 (pt0) cc_final: 0.7885 (pt0) REVERT: K 187 ASP cc_start: 0.7144 (t70) cc_final: 0.6753 (t0) REVERT: L 26 MET cc_start: 0.8139 (mmm) cc_final: 0.7790 (mmt) REVERT: L 50 ASN cc_start: 0.8057 (t0) cc_final: 0.7534 (p0) outliers start: 55 outliers final: 40 residues processed: 377 average time/residue: 0.1338 time to fit residues: 77.2438 Evaluate side-chains 352 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 309 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 152 optimal weight: 0.0970 chunk 185 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 220 optimal weight: 0.0770 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 ASN ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN L 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.150270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.107910 restraints weight = 24220.081| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.83 r_work: 0.3011 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18554 Z= 0.110 Angle : 0.602 11.743 24994 Z= 0.312 Chirality : 0.042 0.267 2982 Planarity : 0.003 0.053 3134 Dihedral : 12.320 145.697 2901 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.85 % Favored : 91.06 % Rotamer: Outliers : 2.45 % Allowed : 19.10 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.18), residues: 2350 helix: 1.53 (0.17), residues: 1054 sheet: -0.80 (0.33), residues: 260 loop : -2.29 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 140 TYR 0.021 0.001 TYR G 145 PHE 0.018 0.001 PHE L 13 TRP 0.005 0.001 TRP A 183 HIS 0.005 0.001 HIS E 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (18554) covalent geometry : angle 0.60177 / 0.31 (24994) hydrogen bonds : bond 0.03149 / 2.09 ( 792) hydrogen bonds : angle 4.10648 / 2.85 ( 2295) *********************** 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 359 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 313 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 226 GLU cc_start: 0.8585 (pp20) cc_final: 0.8364 (pm20) REVERT: B 63 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8289 (mt) REVERT: B 75 LYS cc_start: 0.8513 (mmmt) cc_final: 0.8289 (tttp) REVERT: B 82 ARG cc_start: 0.8138 (mtp-110) cc_final: 0.7883 (mtm110) REVERT: B 246 LYS cc_start: 0.8315 (tptm) cc_final: 0.7992 (ptpt) REVERT: D 108 ARG cc_start: 0.8900 (tmt-80) cc_final: 0.8615 (ttp80) REVERT: D 226 GLU cc_start: 0.8648 (pp20) cc_final: 0.8321 (pm20) REVERT: F 34 GLN cc_start: 0.6342 (tp-100) cc_final: 0.5838 (tp-100) REVERT: G 55 ARG cc_start: 0.8777 (mtm-85) cc_final: 0.7897 (mmp80) REVERT: G 85 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8571 (p0) REVERT: H 35 ASN cc_start: 0.7261 (OUTLIER) cc_final: 0.6902 (t0) REVERT: H 50 ASN cc_start: 0.8981 (t0) cc_final: 0.8641 (t0) REVERT: H 60 MET cc_start: 0.8850 (tpp) cc_final: 0.8429 (ttt) REVERT: H 69 ASP cc_start: 0.8821 (m-30) cc_final: 0.8561 (m-30) REVERT: H 192 PHE cc_start: 0.6252 (m-80) cc_final: 0.5752 (m-10) REVERT: I 23 PHE cc_start: 0.7581 (m-10) cc_final: 0.7183 (t80) REVERT: I 134 MET cc_start: 0.6303 (ttm) cc_final: 0.6048 (ppp) REVERT: J 73 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7757 (tt) REVERT: J 99 LYS cc_start: 0.8422 (mtmt) cc_final: 0.8073 (ptmt) REVERT: J 134 MET cc_start: 0.6579 (pmm) cc_final: 0.6311 (pmm) REVERT: K 60 MET cc_start: 0.8415 (tpp) cc_final: 0.8160 (tpp) REVERT: K 187 ASP cc_start: 0.7177 (t70) cc_final: 0.6840 (t0) REVERT: L 26 MET cc_start: 0.8196 (mmm) cc_final: 0.7847 (mmt) REVERT: L 50 ASN cc_start: 0.7991 (t0) cc_final: 0.7442 (p0) outliers start: 46 outliers final: 37 residues processed: 345 average time/residue: 0.1318 time to fit residues: 70.0644 Evaluate side-chains 346 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 305 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 85 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 ASN I 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.144633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.101801 restraints weight = 24359.178| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.83 r_work: 0.2900 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18554 Z= 0.214 Angle : 0.709 13.382 24994 Z= 0.365 Chirality : 0.046 0.300 2982 Planarity : 0.004 0.053 3134 Dihedral : 12.773 142.429 2901 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.79 % Favored : 90.00 % Rotamer: Outliers : 2.83 % Allowed : 18.84 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 2350 helix: 1.20 (0.17), residues: 1054 sheet: -0.93 (0.33), residues: 264 loop : -2.36 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 67 TYR 0.022 0.002 TYR G 145 PHE 0.025 0.002 PHE F 17 TRP 0.009 0.002 TRP D 212 HIS 0.005 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.21 (18554) covalent geometry : angle 0.70861 / 0.36 (24994) hydrogen bonds : bond 0.05031 / 3.31 ( 792) hydrogen bonds : angle 4.41408 / 3.05 ( 2295) ********************** 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 355 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 302 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: B 63 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8487 (mt) REVERT: B 82 ARG cc_start: 0.8292 (mtp-110) cc_final: 0.8016 (mtm110) REVERT: B 120 LYS cc_start: 0.8732 (mppt) cc_final: 0.8412 (mmtt) REVERT: B 135 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8426 (tp30) REVERT: B 246 LYS cc_start: 0.8365 (tptm) cc_final: 0.8009 (ptpp) REVERT: C 47 GLU cc_start: 0.7860 (pm20) cc_final: 0.7611 (pm20) REVERT: D 108 ARG cc_start: 0.9018 (tmt-80) cc_final: 0.8743 (ttp80) REVERT: D 226 GLU cc_start: 0.8706 (pp20) cc_final: 0.8440 (pm20) REVERT: F 34 GLN cc_start: 0.6182 (tp-100) cc_final: 0.5798 (tp-100) REVERT: G 55 ARG cc_start: 0.8812 (mtm-85) cc_final: 0.7923 (mmp80) REVERT: G 141 ASP cc_start: 0.7839 (p0) cc_final: 0.7576 (p0) REVERT: H 35 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.7013 (t0) REVERT: H 50 ASN cc_start: 0.9077 (t0) cc_final: 0.8717 (t0) REVERT: H 60 MET cc_start: 0.8911 (tpp) cc_final: 0.8571 (ttt) REVERT: H 69 ASP cc_start: 0.8853 (m-30) cc_final: 0.8639 (m-30) REVERT: I 23 PHE cc_start: 0.7652 (m-10) cc_final: 0.7211 (t80) REVERT: I 134 MET cc_start: 0.6731 (ttm) cc_final: 0.6317 (ppp) REVERT: I 191 LYS cc_start: 0.8230 (ttmm) cc_final: 0.7582 (mmtm) REVERT: J 73 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8030 (tt) REVERT: J 99 LYS cc_start: 0.8452 (mtmt) cc_final: 0.8109 (ptmt) REVERT: J 134 MET cc_start: 0.6669 (pmm) cc_final: 0.6380 (pmm) outliers start: 53 outliers final: 41 residues processed: 335 average time/residue: 0.1300 time to fit residues: 66.5961 Evaluate side-chains 344 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 300 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 48 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 ASN G 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.146520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.104655 restraints weight = 24400.562| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.90 r_work: 0.2924 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18554 Z= 0.147 Angle : 0.651 11.865 24994 Z= 0.338 Chirality : 0.044 0.294 2982 Planarity : 0.004 0.053 3134 Dihedral : 12.523 144.157 2901 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.89 % Favored : 90.89 % Rotamer: Outliers : 2.77 % Allowed : 19.21 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.18), residues: 2350 helix: 1.32 (0.17), residues: 1054 sheet: -0.93 (0.33), residues: 264 loop : -2.32 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 67 TYR 0.022 0.001 TYR G 145 PHE 0.017 0.001 PHE L 13 TRP 0.007 0.001 TRP D 212 HIS 0.006 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (18554) covalent geometry : angle 0.65118 / 0.34 (24994) hydrogen bonds : bond 0.04127 / 2.72 ( 792) hydrogen bonds : angle 4.28715 / 2.97 ( 2295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5449.63 seconds wall clock time: 93 minutes 41.22 seconds (5621.22 seconds total)