Starting phenix.real_space_refine on Thu Mar 5 01:54:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d06_30525/03_2026/7d06_30525.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d06_30525/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7d06_30525/03_2026/7d06_30525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d06_30525/03_2026/7d06_30525.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d06_30525/03_2026/7d06_30525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d06_30525/03_2026/7d06_30525.map" } 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-dev-5986/lib/python3.9/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: 4.31, per 1000 atoms: 0.24 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: 1.22 Conformation dependent library (CDL) restraints added in 830.2 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: 0.53 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: 3.05 Time building geometry restraints manager: 1.72 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: 10561 30.10 - 60.19: 678 60.19 - 90.29: 64 90.29 - 120.39: 9 120.39 - 150.48: 12 Dihedral angle restraints: 11324 sinusoidal: 4582 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 11321 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: 0.570 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 16.450 Find NCS groups from input model: 0.310 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 19.877 150.482 6996 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 covalent geometry : bond 0.01243 (18554) covalent geometry : angle 1.54417 (24994) hydrogen bonds : bond 0.32205 ( 792) hydrogen bonds : angle 10.27611 ( 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 : 0.640 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: 0.1480 time to fit residues: 110.6394 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 : 0.646 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3744 r_free = 0.3744 target = 0.146671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.105178 restraints weight = 24599.826| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.89 r_work: 0.2929 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18554 Z= 0.148 Angle : 0.721 10.367 24994 Z= 0.378 Chirality : 0.044 0.292 2982 Planarity : 0.005 0.058 3134 Dihedral : 17.418 170.308 3095 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.72 % Favored : 91.06 % Rotamer: Outliers : 3.09 % Allowed : 14.03 % Favored : 82.87 % 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: -2.12 (0.12), residues: 1046 sheet: -1.52 (0.31), 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 0.005 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00310 (18554) covalent geometry : angle 0.72051 (24994) hydrogen bonds : bond 0.05814 ( 792) hydrogen bonds : angle 5.22538 ( 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: 58 poor density : 363 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8856 (t0) cc_final: 0.8492 (t0) REVERT: B 135 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8632 (tm-30) REVERT: B 262 SER cc_start: 0.5300 (OUTLIER) cc_final: 0.4606 (m) REVERT: C 66 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7255 (tm-30) REVERT: E 17 LYS cc_start: 0.8889 (mtpt) cc_final: 0.8557 (mtpt) REVERT: F 61 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7974 (tp) REVERT: F 70 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6800 (mt) REVERT: G 85 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8488 (p0) REVERT: H 50 ASN cc_start: 0.8984 (t0) cc_final: 0.8607 (t0) REVERT: H 60 MET cc_start: 0.8849 (tpp) cc_final: 0.8500 (tpp) REVERT: H 97 GLN cc_start: 0.8100 (mp10) cc_final: 0.7882 (mp10) REVERT: I 23 PHE cc_start: 0.7942 (m-10) cc_final: 0.7286 (t80) REVERT: I 78 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7423 (mmt90) REVERT: I 185 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7805 (pp) REVERT: I 186 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7837 (mm-30) REVERT: J 43 LYS cc_start: 0.8365 (ptpp) cc_final: 0.8020 (pttp) REVERT: J 134 MET cc_start: 0.6612 (pmm) cc_final: 0.6221 (pmm) REVERT: J 141 ASP cc_start: 0.8080 (p0) cc_final: 0.7663 (p0) REVERT: J 147 MET cc_start: 0.9062 (ptm) cc_final: 0.8657 (ptp) REVERT: K 85 ASP cc_start: 0.8660 (p0) cc_final: 0.8403 (p0) REVERT: K 142 GLU cc_start: 0.8155 (pt0) cc_final: 0.7712 (pt0) REVERT: K 174 ASP cc_start: 0.9010 (m-30) cc_final: 0.8770 (m-30) REVERT: K 192 PHE cc_start: 0.7084 (t80) cc_final: 0.6856 (t80) outliers start: 58 outliers final: 30 residues processed: 401 average time/residue: 0.1386 time to fit residues: 83.5239 Evaluate side-chains 350 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 313 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 140 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 196 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3744 r_free = 0.3744 target = 0.146803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.104567 restraints weight = 24901.963| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.88 r_work: 0.2927 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 18554 Z= 0.145 Angle : 0.639 11.495 24994 Z= 0.333 Chirality : 0.043 0.287 2982 Planarity : 0.004 0.053 3134 Dihedral : 16.341 167.321 3050 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.40 % Favored : 90.43 % Rotamer: Outliers : 3.52 % Allowed : 14.57 % Favored : 81.91 % 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: -2.32 (0.16), residues: 2350 helix: -0.49 (0.15), residues: 1050 sheet: -1.22 (0.31), residues: 278 loop : -2.80 (0.17), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 140 TYR 0.016 0.001 TYR G 145 PHE 0.018 0.001 PHE D 182 TRP 0.008 0.001 TRP A 212 HIS 0.009 0.001 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00327 (18554) covalent geometry : angle 0.63907 (24994) hydrogen bonds : bond 0.04981 ( 792) hydrogen bonds : angle 4.68436 ( 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 407 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 341 time to evaluate : 0.721 Fit side-chains REVERT: B 82 ARG cc_start: 0.8165 (mtp-110) cc_final: 0.7873 (mtm110) REVERT: B 120 LYS cc_start: 0.8827 (mppt) cc_final: 0.8485 (mmtt) REVERT: B 135 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8460 (tp30) REVERT: B 262 SER cc_start: 0.4889 (OUTLIER) cc_final: 0.4419 (m) REVERT: C 66 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: D 188 ASN cc_start: 0.9034 (m-40) cc_final: 0.8752 (m-40) REVERT: E 105 MET cc_start: 0.8896 (mmm) cc_final: 0.8340 (mtp) REVERT: E 263 HIS cc_start: 0.5691 (m-70) cc_final: 0.5468 (m170) REVERT: F 61 LEU cc_start: 0.8325 (mm) cc_final: 0.8086 (tp) REVERT: G 85 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8452 (p0) REVERT: G 99 LYS cc_start: 0.8605 (mmtm) cc_final: 0.8400 (mmtm) REVERT: G 141 ASP cc_start: 0.7950 (p0) cc_final: 0.7581 (p0) REVERT: H 35 ASN cc_start: 0.7582 (OUTLIER) cc_final: 0.6959 (t0) REVERT: H 50 ASN cc_start: 0.9013 (t0) cc_final: 0.8632 (t0) REVERT: H 60 MET cc_start: 0.8889 (tpp) cc_final: 0.8392 (ttt) REVERT: H 93 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.6310 (p90) REVERT: H 97 GLN cc_start: 0.8148 (mp10) cc_final: 0.7889 (mp10) REVERT: I 23 PHE cc_start: 0.7876 (m-10) cc_final: 0.7194 (t80) REVERT: I 78 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7117 (mmt180) REVERT: I 171 LYS cc_start: 0.8486 (mptt) cc_final: 0.8265 (mttm) REVERT: I 191 LYS cc_start: 0.8448 (ttmm) cc_final: 0.7924 (tttt) REVERT: J 43 LYS cc_start: 0.8370 (ptpp) cc_final: 0.8044 (pttp) REVERT: J 73 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7998 (tt) REVERT: J 134 MET cc_start: 0.6596 (pmm) cc_final: 0.6226 (pmm) REVERT: K 142 GLU cc_start: 0.8237 (pt0) cc_final: 0.7756 (pt0) REVERT: K 174 ASP cc_start: 0.8996 (m-30) cc_final: 0.8752 (m-30) REVERT: L 42 MET cc_start: 0.8751 (mmm) cc_final: 0.8501 (mtt) outliers start: 66 outliers final: 41 residues processed: 388 average time/residue: 0.1331 time to fit residues: 78.3807 Evaluate side-chains 368 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 320 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 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 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 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 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 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 76 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 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: 0.8980 chunk 44 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN E 264 GLN 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 = 0.3739 r_free = 0.3739 target = 0.146419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.104743 restraints weight = 24751.568| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.92 r_work: 0.2921 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2733 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= 0.143 Angle : 0.626 12.394 24994 Z= 0.325 Chirality : 0.043 0.327 2982 Planarity : 0.004 0.052 3134 Dihedral : 15.589 153.446 3036 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.19 % Favored : 90.68 % Rotamer: Outliers : 3.74 % Allowed : 15.31 % Favored : 80.95 % 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: -1.68 (0.17), residues: 2350 helix: 0.25 (0.16), residues: 1052 sheet: -1.05 (0.32), residues: 278 loop : -2.67 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 140 TYR 0.016 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 covalent geometry : bond 0.00329 (18554) covalent geometry : angle 0.62600 (24994) hydrogen bonds : bond 0.04441 ( 792) hydrogen bonds : angle 4.50392 ( 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 405 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 335 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.8932 (mttm) cc_final: 0.8673 (mttp) REVERT: B 63 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8446 (mt) REVERT: B 135 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8459 (tp30) REVERT: B 262 SER cc_start: 0.4904 (OUTLIER) cc_final: 0.4261 (m) REVERT: D 108 ARG cc_start: 0.8998 (tmt-80) cc_final: 0.8719 (ttp80) REVERT: D 226 GLU cc_start: 0.8719 (pp20) cc_final: 0.8151 (pp20) REVERT: E 105 MET cc_start: 0.8928 (mmm) cc_final: 0.8609 (mtp) REVERT: E 219 TYR cc_start: 0.8570 (t80) cc_final: 0.8284 (t80) REVERT: F 61 LEU cc_start: 0.8338 (mm) cc_final: 0.8122 (tp) REVERT: G 67 ARG cc_start: 0.8819 (mtm-85) cc_final: 0.8563 (mtp-110) REVERT: G 85 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8487 (p0) REVERT: H 35 ASN cc_start: 0.7545 (OUTLIER) cc_final: 0.6884 (t0) REVERT: H 50 ASN cc_start: 0.9032 (t0) cc_final: 0.8713 (t0) REVERT: H 60 MET cc_start: 0.8879 (tpp) cc_final: 0.8400 (ttt) REVERT: H 93 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6279 (p90) REVERT: H 97 GLN cc_start: 0.8192 (mp10) cc_final: 0.7860 (mp10) REVERT: I 16 ILE cc_start: 0.8416 (mm) cc_final: 0.8201 (mm) REVERT: I 23 PHE cc_start: 0.7845 (m-10) cc_final: 0.7209 (t80) REVERT: I 78 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7152 (mmt180) REVERT: I 134 MET cc_start: 0.6472 (ppp) cc_final: 0.6226 (ppp) REVERT: I 174 ASP cc_start: 0.8834 (m-30) cc_final: 0.8469 (m-30) REVERT: I 191 LYS cc_start: 0.8404 (ttmm) cc_final: 0.7908 (tttt) REVERT: J 43 LYS cc_start: 0.8411 (ptpp) cc_final: 0.8088 (pttp) REVERT: J 73 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7995 (tt) REVERT: J 134 MET cc_start: 0.6615 (pmm) cc_final: 0.6336 (pmm) REVERT: J 141 ASP cc_start: 0.7814 (p0) cc_final: 0.7477 (p0) REVERT: K 142 GLU cc_start: 0.8270 (pt0) cc_final: 0.7711 (pt0) REVERT: L 42 MET cc_start: 0.8725 (mmm) cc_final: 0.8520 (mtt) outliers start: 70 outliers final: 45 residues processed: 383 average time/residue: 0.1271 time to fit residues: 74.4661 Evaluate side-chains 367 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 315 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 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 61 LEU 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 188 LEU 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 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 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 70 SER Chi-restraints excluded: chain H residue 93 PHE 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 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 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 19 ILE 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: 0.7980 chunk 228 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 161 optimal weight: 0.0570 chunk 210 optimal weight: 6.9990 chunk 226 optimal weight: 20.0000 chunk 136 optimal weight: 0.8980 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN G 45 GLN ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.105616 restraints weight = 24479.341| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.87 r_work: 0.2948 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2929 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= 0.120 Angle : 0.594 12.078 24994 Z= 0.310 Chirality : 0.042 0.284 2982 Planarity : 0.003 0.051 3134 Dihedral : 15.074 146.877 3033 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.89 % Favored : 91.06 % Rotamer: Outliers : 3.47 % Allowed : 16.65 % Favored : 79.88 % 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: -1.28 (0.17), residues: 2350 helix: 0.69 (0.17), residues: 1054 sheet: -1.03 (0.33), residues: 264 loop : -2.51 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 140 TYR 0.014 0.001 TYR J 145 PHE 0.012 0.001 PHE G 13 TRP 0.005 0.001 TRP D 212 HIS 0.005 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00266 (18554) covalent geometry : angle 0.59378 (24994) hydrogen bonds : bond 0.03958 ( 792) hydrogen bonds : angle 4.34497 ( 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 399 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 334 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.8922 (mttm) cc_final: 0.8615 (mttp) REVERT: B 135 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8415 (tp30) REVERT: B 246 LYS cc_start: 0.8359 (tptm) cc_final: 0.7973 (ptpt) REVERT: D 108 ARG cc_start: 0.8957 (tmt-80) cc_final: 0.8668 (ttp80) REVERT: D 226 GLU cc_start: 0.8723 (pp20) cc_final: 0.8184 (pp20) REVERT: E 105 MET cc_start: 0.8892 (mmm) cc_final: 0.8625 (mtp) REVERT: E 219 TYR cc_start: 0.8557 (t80) cc_final: 0.8234 (t80) REVERT: G 67 ARG cc_start: 0.8816 (mtm-85) cc_final: 0.8574 (mtp-110) REVERT: G 85 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8507 (p0) REVERT: G 141 ASP cc_start: 0.7899 (p0) cc_final: 0.7635 (p0) REVERT: H 35 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.6762 (t0) REVERT: H 50 ASN cc_start: 0.9002 (t0) cc_final: 0.8672 (t0) REVERT: H 60 MET cc_start: 0.8870 (tpp) cc_final: 0.8409 (ttt) REVERT: H 97 GLN cc_start: 0.8163 (mp10) cc_final: 0.7854 (mp10) REVERT: I 23 PHE cc_start: 0.7783 (m-10) cc_final: 0.7199 (t80) REVERT: I 78 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7127 (mmt180) REVERT: I 134 MET cc_start: 0.6508 (ppp) cc_final: 0.6261 (ppp) REVERT: I 174 ASP cc_start: 0.8837 (m-30) cc_final: 0.8458 (m-30) REVERT: I 191 LYS cc_start: 0.8290 (ttmm) cc_final: 0.7862 (tttt) REVERT: J 43 LYS cc_start: 0.8390 (ptpp) cc_final: 0.8090 (pttp) REVERT: J 73 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7847 (tt) REVERT: J 134 MET cc_start: 0.6635 (pmm) cc_final: 0.6336 (pmm) REVERT: K 142 GLU cc_start: 0.8257 (pt0) cc_final: 0.7710 (pt0) REVERT: L 184 ASP cc_start: 0.7044 (t0) cc_final: 0.6813 (t0) outliers start: 65 outliers final: 43 residues processed: 377 average time/residue: 0.1333 time to fit residues: 76.3663 Evaluate side-chains 365 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 318 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 118 HIS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 51 THR 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 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 F residue 80 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 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 I residue 136 SER 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 184 ASP Chi-restraints excluded: chain L residue 19 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 204 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 231 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN E 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.145236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.102929 restraints weight = 24463.902| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.85 r_work: 0.2904 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18554 Z= 0.179 Angle : 0.648 12.688 24994 Z= 0.334 Chirality : 0.045 0.305 2982 Planarity : 0.004 0.051 3134 Dihedral : 14.831 137.532 3032 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.66 % Favored : 90.17 % Rotamer: Outliers : 4.06 % Allowed : 16.44 % Favored : 79.51 % 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: -1.17 (0.17), residues: 2350 helix: 0.80 (0.17), residues: 1052 sheet: -0.99 (0.33), residues: 264 loop : -2.48 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 140 TYR 0.015 0.002 TYR G 40 PHE 0.021 0.002 PHE F 17 TRP 0.007 0.001 TRP D 212 HIS 0.005 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00430 (18554) covalent geometry : angle 0.64832 (24994) hydrogen bonds : bond 0.04786 ( 792) hydrogen bonds : angle 4.45267 ( 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 399 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 323 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.8916 (mttm) cc_final: 0.8616 (mttp) REVERT: B 63 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8462 (mt) REVERT: B 120 LYS cc_start: 0.8719 (mppt) cc_final: 0.8382 (mmtt) REVERT: B 135 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8444 (tp30) REVERT: D 108 ARG cc_start: 0.9001 (tmt-80) cc_final: 0.8728 (ttp80) REVERT: D 226 GLU cc_start: 0.8667 (pp20) cc_final: 0.8141 (pp20) REVERT: E 105 MET cc_start: 0.8846 (mmm) cc_final: 0.8624 (mtp) REVERT: E 219 TYR cc_start: 0.8582 (t80) cc_final: 0.8349 (t80) REVERT: G 141 ASP cc_start: 0.7841 (p0) cc_final: 0.7571 (p0) REVERT: H 35 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.6919 (t0) REVERT: H 50 ASN cc_start: 0.9042 (t0) cc_final: 0.8701 (t0) REVERT: H 60 MET cc_start: 0.8917 (tpp) cc_final: 0.8516 (ttt) REVERT: H 97 GLN cc_start: 0.8178 (mp10) cc_final: 0.7843 (mp10) REVERT: I 23 PHE cc_start: 0.7771 (m-10) cc_final: 0.7219 (t80) REVERT: I 174 ASP cc_start: 0.8890 (m-30) cc_final: 0.8449 (m-30) REVERT: I 191 LYS cc_start: 0.8315 (ttmm) cc_final: 0.7914 (tttt) REVERT: J 42 MET cc_start: 0.9071 (mtp) cc_final: 0.8688 (mtp) REVERT: J 73 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7978 (tt) REVERT: J 89 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7813 (mtpp) REVERT: J 134 MET cc_start: 0.6611 (pmm) cc_final: 0.6307 (pmm) REVERT: K 142 GLU cc_start: 0.8239 (pt0) cc_final: 0.7679 (pt0) REVERT: L 156 GLU cc_start: 0.6713 (pm20) cc_final: 0.6442 (pm20) REVERT: L 184 ASP cc_start: 0.7071 (t0) cc_final: 0.6821 (t0) outliers start: 76 outliers final: 60 residues processed: 373 average time/residue: 0.1309 time to fit residues: 73.8592 Evaluate side-chains 368 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 305 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 63 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 124 ASN 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 C residue 64 THR 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 80 MET Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 118 HIS 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 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 19 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 31 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 90 optimal weight: 0.0000 chunk 77 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 222 optimal weight: 0.6980 chunk 107 optimal weight: 0.0040 chunk 41 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN J 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.106757 restraints weight = 24464.635| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.82 r_work: 0.2999 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3224 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 : 0.588 12.167 24994 Z= 0.307 Chirality : 0.042 0.282 2982 Planarity : 0.003 0.051 3134 Dihedral : 14.155 133.214 3030 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.51 % Favored : 91.40 % Rotamer: Outliers : 2.77 % Allowed : 17.93 % Favored : 79.30 % 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: -0.80 (0.18), residues: 2350 helix: 1.22 (0.17), residues: 1048 sheet: -0.98 (0.33), residues: 264 loop : -2.35 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 140 TYR 0.013 0.001 TYR G 145 PHE 0.013 0.001 PHE D 182 TRP 0.005 0.001 TRP A 6 HIS 0.005 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00223 (18554) covalent geometry : angle 0.58752 (24994) hydrogen bonds : bond 0.03350 ( 792) hydrogen bonds : angle 4.21511 ( 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 373 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 321 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8305 (mt) REVERT: B 135 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8404 (tp30) REVERT: B 246 LYS cc_start: 0.8301 (tppp) cc_final: 0.7954 (ptpt) REVERT: D 108 ARG cc_start: 0.8892 (tmt-80) cc_final: 0.8572 (ttp80) REVERT: D 226 GLU cc_start: 0.8599 (pp20) cc_final: 0.8296 (pm20) REVERT: E 105 MET cc_start: 0.8738 (mmm) cc_final: 0.8470 (mtp) REVERT: F 79 MET cc_start: 0.8739 (mmm) cc_final: 0.8203 (mmm) REVERT: G 85 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8531 (p0) REVERT: G 141 ASP cc_start: 0.7724 (p0) cc_final: 0.7439 (p0) REVERT: H 35 ASN cc_start: 0.7412 (OUTLIER) cc_final: 0.6772 (t0) REVERT: H 50 ASN cc_start: 0.8944 (t0) cc_final: 0.8604 (t0) REVERT: H 60 MET cc_start: 0.8878 (tpp) cc_final: 0.8464 (ttt) REVERT: H 97 GLN cc_start: 0.8180 (mp10) cc_final: 0.7949 (mp10) REVERT: H 183 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8403 (mtp) REVERT: I 23 PHE cc_start: 0.7693 (m-10) cc_final: 0.7211 (t80) REVERT: I 174 ASP cc_start: 0.8788 (m-30) cc_final: 0.8379 (m-30) REVERT: I 191 LYS cc_start: 0.8236 (ttmm) cc_final: 0.7807 (tttt) REVERT: J 73 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7811 (tt) REVERT: J 89 LYS cc_start: 0.7982 (mmmt) cc_final: 0.7738 (mtpp) REVERT: J 134 MET cc_start: 0.6512 (pmm) cc_final: 0.6242 (pmm) REVERT: K 142 GLU cc_start: 0.8163 (pt0) cc_final: 0.7666 (pt0) REVERT: K 187 ASP cc_start: 0.7213 (t70) cc_final: 0.6809 (t0) REVERT: L 50 ASN cc_start: 0.8017 (t0) cc_final: 0.7496 (p0) REVERT: L 184 ASP cc_start: 0.7083 (t0) cc_final: 0.6820 (t0) outliers start: 52 outliers final: 36 residues processed: 357 average time/residue: 0.1328 time to fit residues: 71.8936 Evaluate side-chains 350 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 309 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 64 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 142 THR Chi-restraints excluded: chain E residue 145 LEU 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 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 H residue 35 ASN Chi-restraints excluded: chain H residue 69 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 73 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 194 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN J 102 GLN L 97 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.147448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.105399 restraints weight = 24430.002| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.85 r_work: 0.2943 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3243 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= 0.133 Angle : 0.615 12.594 24994 Z= 0.319 Chirality : 0.043 0.274 2982 Planarity : 0.004 0.050 3134 Dihedral : 13.873 128.765 3025 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.81 % Favored : 91.02 % Rotamer: Outliers : 3.47 % Allowed : 17.24 % Favored : 79.30 % 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: -0.74 (0.18), residues: 2350 helix: 1.28 (0.17), residues: 1054 sheet: -0.95 (0.33), residues: 264 loop : -2.36 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 140 TYR 0.022 0.001 TYR G 145 PHE 0.014 0.001 PHE G 13 TRP 0.005 0.001 TRP D 212 HIS 0.005 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00307 (18554) covalent geometry : angle 0.61503 (24994) hydrogen bonds : bond 0.03881 ( 792) hydrogen bonds : angle 4.26038 ( 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 379 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 314 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: B 63 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8400 (mt) REVERT: B 82 ARG cc_start: 0.8334 (mtp-110) cc_final: 0.8110 (mtm110) REVERT: B 120 LYS cc_start: 0.8729 (mppt) cc_final: 0.8416 (mmtt) REVERT: B 135 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8438 (tp30) REVERT: B 246 LYS cc_start: 0.8357 (tppp) cc_final: 0.7963 (ptpt) REVERT: D 108 ARG cc_start: 0.8965 (tmt-80) cc_final: 0.8679 (ttp80) REVERT: D 226 GLU cc_start: 0.8662 (pp20) cc_final: 0.8353 (pm20) REVERT: F 79 MET cc_start: 0.8764 (mmm) cc_final: 0.8191 (mmm) REVERT: G 85 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8523 (p0) REVERT: G 141 ASP cc_start: 0.7807 (p0) cc_final: 0.7490 (p0) REVERT: H 35 ASN cc_start: 0.7436 (OUTLIER) cc_final: 0.6868 (t0) REVERT: H 50 ASN cc_start: 0.8984 (t0) cc_final: 0.8668 (t0) REVERT: H 60 MET cc_start: 0.8921 (tpp) cc_final: 0.8523 (ttt) REVERT: H 97 GLN cc_start: 0.8228 (mp10) cc_final: 0.7933 (mp10) REVERT: I 23 PHE cc_start: 0.7691 (m-10) cc_final: 0.7191 (t80) REVERT: I 156 GLU cc_start: 0.6840 (pm20) cc_final: 0.6595 (pm20) REVERT: I 174 ASP cc_start: 0.8832 (m-30) cc_final: 0.8401 (m-30) REVERT: J 73 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7834 (tt) REVERT: J 99 LYS cc_start: 0.8441 (mtmt) cc_final: 0.8086 (ptmt) REVERT: J 134 MET cc_start: 0.6613 (pmm) cc_final: 0.6365 (pmm) REVERT: K 142 GLU cc_start: 0.8210 (pt0) cc_final: 0.7666 (pt0) REVERT: L 24 LEU cc_start: 0.8603 (tt) cc_final: 0.8368 (tp) outliers start: 65 outliers final: 49 residues processed: 357 average time/residue: 0.1341 time to fit residues: 72.7993 Evaluate side-chains 356 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 303 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL 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 124 ASN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 145 LEU 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 64 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 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 75 LYS Chi-restraints excluded: chain E residue 80 MET 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 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 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 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 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: 9.9990 chunk 185 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 179 optimal weight: 0.2980 chunk 136 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 220 optimal weight: 8.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 HIS E 155 ASN I 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.103287 restraints weight = 24230.380| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.86 r_work: 0.2902 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18554 Z= 0.176 Angle : 0.664 13.095 24994 Z= 0.342 Chirality : 0.045 0.296 2982 Planarity : 0.004 0.052 3134 Dihedral : 13.767 124.983 3021 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.40 % Favored : 90.38 % Rotamer: Outliers : 3.36 % Allowed : 17.61 % Favored : 79.03 % 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: -0.81 (0.18), residues: 2350 helix: 1.22 (0.17), residues: 1050 sheet: -0.92 (0.33), residues: 264 loop : -2.39 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 140 TYR 0.022 0.002 TYR G 145 PHE 0.020 0.002 PHE F 17 TRP 0.007 0.001 TRP D 212 HIS 0.005 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00422 (18554) covalent geometry : angle 0.66417 (24994) hydrogen bonds : bond 0.04597 ( 792) hydrogen bonds : angle 4.37951 ( 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 368 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 305 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.8964 (mttp) cc_final: 0.8764 (mttp) REVERT: B 63 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8441 (mt) REVERT: B 82 ARG cc_start: 0.8329 (mtp-110) cc_final: 0.8064 (mtm110) REVERT: B 120 LYS cc_start: 0.8738 (mppt) cc_final: 0.8423 (mmtt) REVERT: B 135 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8457 (tp30) REVERT: B 246 LYS cc_start: 0.8368 (tppp) cc_final: 0.7968 (ptpp) REVERT: C 47 GLU cc_start: 0.7882 (pm20) cc_final: 0.7636 (pm20) REVERT: D 108 ARG cc_start: 0.9007 (tmt-80) cc_final: 0.8726 (ttp80) REVERT: D 226 GLU cc_start: 0.8691 (pp20) cc_final: 0.8395 (pm20) REVERT: G 55 ARG cc_start: 0.8823 (mtm-85) cc_final: 0.7903 (mmp80) REVERT: H 35 ASN cc_start: 0.7550 (OUTLIER) cc_final: 0.6988 (t0) REVERT: H 50 ASN cc_start: 0.9077 (t0) cc_final: 0.8729 (t0) REVERT: H 60 MET cc_start: 0.8928 (tpp) cc_final: 0.8567 (ttt) REVERT: H 97 GLN cc_start: 0.8250 (mp10) cc_final: 0.7936 (mp10) REVERT: I 23 PHE cc_start: 0.7744 (m-10) cc_final: 0.7230 (t80) REVERT: I 156 GLU cc_start: 0.6947 (pm20) cc_final: 0.6724 (pm20) REVERT: I 174 ASP cc_start: 0.8923 (m-30) cc_final: 0.8474 (m-30) REVERT: I 191 LYS cc_start: 0.8244 (ttmm) cc_final: 0.7919 (tttt) REVERT: J 73 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7948 (tt) REVERT: J 99 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8084 (ptmt) REVERT: J 134 MET cc_start: 0.6644 (pmm) cc_final: 0.6372 (pmm) REVERT: K 142 GLU cc_start: 0.8207 (pt0) cc_final: 0.7662 (pt0) outliers start: 63 outliers final: 54 residues processed: 347 average time/residue: 0.1344 time to fit residues: 71.1660 Evaluate side-chains 358 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 301 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 63 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 145 LEU 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 64 THR Chi-restraints excluded: chain C residue 70 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 75 LYS Chi-restraints excluded: chain E residue 80 MET 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 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 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 H residue 188 LEU Chi-restraints excluded: chain I residue 63 VAL 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 32 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 168 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 85 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 178 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 119 optimal weight: 0.0670 chunk 53 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.105762 restraints weight = 24314.508| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.80 r_work: 0.2964 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3387 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= 0.120 Angle : 0.618 12.428 24994 Z= 0.322 Chirality : 0.043 0.286 2982 Planarity : 0.004 0.051 3134 Dihedral : 13.348 124.141 3021 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.11 % Favored : 90.77 % Rotamer: Outliers : 2.83 % Allowed : 18.30 % Favored : 78.87 % 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: -0.61 (0.18), residues: 2350 helix: 1.42 (0.17), residues: 1054 sheet: -0.94 (0.33), residues: 264 loop : -2.31 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 140 TYR 0.020 0.001 TYR G 145 PHE 0.013 0.001 PHE D 182 TRP 0.006 0.001 TRP A 6 HIS 0.006 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00271 (18554) covalent geometry : angle 0.61755 (24994) hydrogen bonds : bond 0.03573 ( 792) hydrogen bonds : angle 4.23511 ( 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 358 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 305 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: B 63 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8382 (mt) REVERT: B 75 LYS cc_start: 0.8538 (mmmt) cc_final: 0.8279 (tttp) REVERT: B 82 ARG cc_start: 0.8287 (mtp-110) cc_final: 0.8021 (mtm110) REVERT: B 135 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8422 (tp30) REVERT: B 246 LYS cc_start: 0.8316 (tppp) cc_final: 0.7942 (ptpt) REVERT: D 108 ARG cc_start: 0.8931 (tmt-80) cc_final: 0.8651 (ttp80) REVERT: D 226 GLU cc_start: 0.8615 (pp20) cc_final: 0.8298 (pm20) REVERT: F 34 GLN cc_start: 0.6163 (tp-100) cc_final: 0.5640 (tp-100) REVERT: F 79 MET cc_start: 0.8726 (mmm) cc_final: 0.8306 (mmm) REVERT: G 42 MET cc_start: 0.8732 (mtt) cc_final: 0.8237 (mtt) REVERT: G 55 ARG cc_start: 0.8766 (mtm-85) cc_final: 0.7897 (mmp80) REVERT: H 35 ASN cc_start: 0.7313 (OUTLIER) cc_final: 0.6937 (t0) REVERT: H 50 ASN cc_start: 0.9037 (t0) cc_final: 0.8672 (t0) REVERT: H 60 MET cc_start: 0.8911 (tpp) cc_final: 0.8520 (ttt) REVERT: H 97 GLN cc_start: 0.8218 (mp10) cc_final: 0.7879 (mp10) REVERT: I 23 PHE cc_start: 0.7644 (m-10) cc_final: 0.7150 (t80) REVERT: I 134 MET cc_start: 0.6428 (ttm) cc_final: 0.6226 (ppp) REVERT: I 174 ASP cc_start: 0.8859 (m-30) cc_final: 0.8392 (m-30) REVERT: J 42 MET cc_start: 0.9039 (mtp) cc_final: 0.8583 (mtp) REVERT: J 73 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7793 (tt) REVERT: J 99 LYS cc_start: 0.8441 (mtmt) cc_final: 0.8109 (ptmt) REVERT: J 134 MET cc_start: 0.6602 (pmm) cc_final: 0.6340 (pmm) REVERT: K 142 GLU cc_start: 0.8163 (pt0) cc_final: 0.7668 (pt0) outliers start: 53 outliers final: 46 residues processed: 340 average time/residue: 0.1279 time to fit residues: 66.2952 Evaluate side-chains 354 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 305 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL 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 124 ASN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 145 LEU 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 64 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 55 ILE 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 75 LYS Chi-restraints excluded: chain E residue 80 MET 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 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 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 69 ASP 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 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 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: 7.9990 chunk 113 optimal weight: 5.9990 chunk 51 optimal weight: 0.0030 chunk 7 optimal weight: 0.7980 chunk 224 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 186 optimal weight: 0.9980 chunk 151 optimal weight: 20.0000 chunk 220 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.105906 restraints weight = 24353.934| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.81 r_work: 0.2959 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18554 Z= 0.124 Angle : 0.620 12.221 24994 Z= 0.322 Chirality : 0.043 0.283 2982 Planarity : 0.004 0.051 3134 Dihedral : 13.127 123.101 3021 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.98 % Favored : 90.81 % Rotamer: Outliers : 2.83 % Allowed : 18.20 % Favored : 78.98 % 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: -0.52 (0.18), residues: 2350 helix: 1.50 (0.17), residues: 1056 sheet: -0.90 (0.33), residues: 264 loop : -2.28 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 D 212 HIS 0.010 0.001 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00281 (18554) covalent geometry : angle 0.62000 (24994) hydrogen bonds : bond 0.03674 ( 792) hydrogen bonds : angle 4.21035 ( 2295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5271.65 seconds wall clock time: 91 minutes 13.67 seconds (5473.67 seconds total)