Starting phenix.real_space_refine on Fri Sep 11 16:54:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8amd_15524/09_2026/8amd_15524.cif Found real_map, /net/cci-nas-00/data/ceres_data/8amd_15524/09_2026/8amd_15524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8amd_15524/09_2026/8amd_15524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8amd_15524/09_2026/8amd_15524.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8amd_15524/09_2026/8amd_15524.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8amd_15524/09_2026/8amd_15524.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8amd_15524/09_2026/8amd_15524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8amd_15524/09_2026/8amd_15524.map" } resolution = 3.9 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= 1.000 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 23 5.49 5 S 32 5.16 5 C 6460 2.51 5 N 1772 2.21 5 O 2090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10377 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2504 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 237 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Chain: "B" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2504 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2504 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2504 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.24, per 1000 atoms: 0.22 Number of scatterers: 10377 At special positions: 0 Unit cell: (100.928, 130.112, 144.704, 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 32 16.00 P 23 15.00 O 2090 8.00 N 1772 7.00 C 6460 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 264.7 milliseconds 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 15 sheets defined 34.7% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 43 through 49 removed outlier: 5.462A pdb=" N ALA A 46 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N GLU A 47 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN A 48 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.923A pdb=" N GLY A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.596A pdb=" N VAL A 88 " --> pdb=" O GLY A 84 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.870A pdb=" N GLU A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.773A pdb=" N GLU A 167 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 192 removed outlier: 4.677A pdb=" N GLN A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 4.543A pdb=" N LYS A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 286 through 297 removed outlier: 3.627A pdb=" N LEU A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 327 removed outlier: 3.675A pdb=" N ALA A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 removed outlier: 4.168A pdb=" N LYS A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 43 through 49 removed outlier: 5.399A pdb=" N ALA B 46 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLU B 47 " --> pdb=" O GLU B 44 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN B 48 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 49 " --> pdb=" O ALA B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 49' Processing helix chain 'B' and resid 57 through 65 removed outlier: 3.640A pdb=" N GLY B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 99 removed outlier: 4.015A pdb=" N ALA B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B 99 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.500A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 147 removed outlier: 4.090A pdb=" N GLU B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.737A pdb=" N GLU B 167 " --> pdb=" O PRO B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 192 removed outlier: 4.342A pdb=" N GLN B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 removed outlier: 3.699A pdb=" N PHE B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 297 removed outlier: 3.681A pdb=" N LEU B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 341 removed outlier: 3.715A pdb=" N LYS B 338 " --> pdb=" O ASP B 334 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 45 through 49 removed outlier: 3.765A pdb=" N GLN F 48 " --> pdb=" O ARG F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 64 Processing helix chain 'F' and resid 84 through 99 removed outlier: 3.855A pdb=" N ALA F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU F 99 " --> pdb=" O GLN F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 121 removed outlier: 4.170A pdb=" N ALA F 119 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU F 120 " --> pdb=" O TYR F 116 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 147 removed outlier: 3.530A pdb=" N GLU F 140 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA F 142 " --> pdb=" O GLY F 138 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU F 145 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 168 removed outlier: 3.768A pdb=" N GLU F 167 " --> pdb=" O PRO F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 192 removed outlier: 4.618A pdb=" N GLN F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG F 189 " --> pdb=" O SER F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 232 removed outlier: 3.545A pdb=" N PHE F 230 " --> pdb=" O ARG F 226 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR F 231 " --> pdb=" O ALA F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 251 removed outlier: 3.790A pdb=" N GLN F 250 " --> pdb=" O THR F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 297 removed outlier: 3.768A pdb=" N LEU F 292 " --> pdb=" O THR F 288 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS F 293 " --> pdb=" O GLY F 289 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 327 removed outlier: 3.502A pdb=" N ALA F 327 " --> pdb=" O LYS F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 removed outlier: 3.933A pdb=" N LYS F 338 " --> pdb=" O ASP F 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 25 Processing helix chain 'G' and resid 25 through 30 Processing helix chain 'G' and resid 41 through 45 removed outlier: 3.780A pdb=" N GLU G 44 " --> pdb=" O ARG G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 64 Processing helix chain 'G' and resid 84 through 99 removed outlier: 3.958A pdb=" N ALA G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU G 99 " --> pdb=" O GLN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 removed outlier: 3.525A pdb=" N ALA G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA G 119 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU G 120 " --> pdb=" O TYR G 116 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 149 removed outlier: 3.548A pdb=" N GLU G 140 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA G 142 " --> pdb=" O GLY G 138 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU G 145 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER G 148 " --> pdb=" O LYS G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 168 removed outlier: 3.769A pdb=" N GLU G 167 " --> pdb=" O PRO G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 192 removed outlier: 4.316A pdb=" N GLN G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG G 189 " --> pdb=" O SER G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 232 removed outlier: 3.949A pdb=" N PHE G 230 " --> pdb=" O ARG G 226 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR G 231 " --> pdb=" O ALA G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 251 removed outlier: 3.779A pdb=" N GLN G 250 " --> pdb=" O THR G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 298 removed outlier: 3.551A pdb=" N LEU G 292 " --> pdb=" O THR G 288 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS G 293 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE G 294 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP G 297 " --> pdb=" O LYS G 293 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU G 298 " --> pdb=" O ILE G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 338 removed outlier: 4.055A pdb=" N LYS G 338 " --> pdb=" O ASP G 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.610A pdb=" N VAL A 155 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A 205 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A 75 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ASN A 206 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 77 " --> pdb=" O ASN A 206 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 234 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG A 235 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 264 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN A 241 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU A 258 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN A 243 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLY A 256 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LYS A 245 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASN A 254 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY A 284 " --> pdb=" O MET A 280 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 210 Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 156 removed outlier: 3.511A pdb=" N ILE B 203 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE B 75 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 234 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 238 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN B 241 " --> pdb=" O GLU B 258 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLU B 258 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLN B 243 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLY B 256 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LYS B 245 " --> pdb=" O ASN B 254 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASN B 254 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N THR B 247 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU B 252 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 277 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 261 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 210 Processing sheet with id=AA9, first strand: chain 'F' and resid 39 through 41 Processing sheet with id=AB1, first strand: chain 'F' and resid 52 through 53 Processing sheet with id=AB2, first strand: chain 'F' and resid 153 through 156 removed outlier: 6.958A pdb=" N ILE F 75 " --> pdb=" O PHE F 204 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL F 234 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG F 235 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN F 241 " --> pdb=" O GLU F 258 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU F 258 " --> pdb=" O ASN F 241 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLN F 243 " --> pdb=" O GLY F 256 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY F 256 " --> pdb=" O GLN F 243 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LYS F 245 " --> pdb=" O ASN F 254 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN F 254 " --> pdb=" O LYS F 245 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL F 277 " --> pdb=" O THR F 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 209 through 210 Processing sheet with id=AB4, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AB5, first strand: chain 'G' and resid 103 through 106 removed outlier: 3.680A pdb=" N VAL G 155 " --> pdb=" O ALA G 104 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE G 75 " --> pdb=" O PHE G 204 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL G 234 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG G 235 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL G 264 " --> pdb=" O ARG G 235 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN G 241 " --> pdb=" O GLU G 258 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU G 258 " --> pdb=" O ASN G 241 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN G 243 " --> pdb=" O GLY G 256 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY G 256 " --> pdb=" O GLN G 243 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS G 245 " --> pdb=" O ASN G 254 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASN G 254 " --> pdb=" O LYS G 245 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR G 259 " --> pdb=" O VAL G 277 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL G 277 " --> pdb=" O THR G 259 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY G 284 " --> pdb=" O MET G 280 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 209 through 210 259 hydrogen bonds defined for protein. 711 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: 1.54 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 3471 1.35 - 1.50: 2642 1.50 - 1.65: 4359 1.65 - 1.80: 43 1.80 - 1.94: 17 Bond restraints: 10532 Sorted by residual: bond pdb=" C1' DT D1013 " pdb=" N1 DT D1013 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.37e+01 bond pdb=" C3' DT D1003 " pdb=" O3' DT D1003 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.16e+01 bond pdb=" C1' DT D1002 " pdb=" N1 DT D1002 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.14e+01 bond pdb=" C3' DT D1012 " pdb=" O3' DT D1012 " ideal model delta sigma weight residual 1.435 1.397 0.038 1.30e-02 5.92e+03 8.73e+00 bond pdb=" C3' DT D1003 " pdb=" C2' DT D1003 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.91e+00 ... (remaining 10527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 13676 2.25 - 4.51: 496 4.51 - 6.76: 43 6.76 - 9.01: 13 9.01 - 11.26: 4 Bond angle restraints: 14232 Sorted by residual: angle pdb=" N ILE B 332 " pdb=" CA ILE B 332 " pdb=" C ILE B 332 " ideal model delta sigma weight residual 113.10 106.21 6.89 9.70e-01 1.06e+00 5.04e+01 angle pdb=" N ILE F 332 " pdb=" CA ILE F 332 " pdb=" C ILE F 332 " ideal model delta sigma weight residual 112.90 106.45 6.45 9.60e-01 1.09e+00 4.51e+01 angle pdb=" N ILE G 332 " pdb=" CA ILE G 332 " pdb=" C ILE G 332 " ideal model delta sigma weight residual 113.22 106.23 6.99 1.23e+00 6.61e-01 3.23e+01 angle pdb=" N VAL F 255 " pdb=" CA VAL F 255 " pdb=" C VAL F 255 " ideal model delta sigma weight residual 113.20 108.45 4.75 9.60e-01 1.09e+00 2.45e+01 angle pdb=" O4' DT D1011 " pdb=" C4' DT D1011 " pdb=" C3' DT D1011 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.24e+01 ... (remaining 14227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5475 17.86 - 35.73: 663 35.73 - 53.59: 186 53.59 - 71.46: 44 71.46 - 89.32: 16 Dihedral angle restraints: 6384 sinusoidal: 2648 harmonic: 3736 Sorted by residual: dihedral pdb=" CA LYS F 314 " pdb=" C LYS F 314 " pdb=" N ILE F 315 " pdb=" CA ILE F 315 " ideal model delta harmonic sigma weight residual -180.00 -150.33 -29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA LYS G 314 " pdb=" C LYS G 314 " pdb=" N ILE G 315 " pdb=" CA ILE G 315 " ideal model delta harmonic sigma weight residual 180.00 -150.48 -29.52 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA ASP A 312 " pdb=" C ASP A 312 " pdb=" N GLU A 313 " pdb=" CA GLU A 313 " ideal model delta harmonic sigma weight residual 180.00 150.81 29.19 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 6381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1118 0.053 - 0.106: 359 0.106 - 0.159: 109 0.159 - 0.211: 17 0.211 - 0.264: 8 Chirality restraints: 1611 Sorted by residual: chirality pdb=" CB ILE B 285 " pdb=" CA ILE B 285 " pdb=" CG1 ILE B 285 " pdb=" CG2 ILE B 285 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE G 285 " pdb=" CA ILE G 285 " pdb=" CG1 ILE G 285 " pdb=" CG2 ILE G 285 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA GLU G 313 " pdb=" N GLU G 313 " pdb=" C GLU G 313 " pdb=" CB GLU G 313 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1608 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP G 312 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.14e+00 pdb=" C ASP G 312 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP G 312 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU G 313 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 312 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.75e+00 pdb=" C ASP A 312 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP A 312 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU A 313 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 312 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.74e+00 pdb=" C ASP B 312 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP B 312 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU B 313 " -0.015 2.00e-02 2.50e+03 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3187 2.82 - 3.34: 9119 3.34 - 3.86: 15998 3.86 - 4.38: 17118 4.38 - 4.90: 28855 Nonbonded interactions: 74277 Sorted by model distance: nonbonded pdb=" O PHE F 34 " pdb=" OG SER F 38 " model vdw 2.298 3.040 nonbonded pdb=" O1A AGS G 500 " pdb=" O2G AGS G 500 " model vdw 2.298 3.040 nonbonded pdb=" OD1 ASP B 147 " pdb=" OG SER B 194 " model vdw 2.317 3.040 nonbonded pdb=" O PHE B 34 " pdb=" OG SER B 38 " model vdw 2.325 3.040 nonbonded pdb=" N SER B 83 " pdb=" O1B AGS B 500 " model vdw 2.329 2.496 ... (remaining 74272 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' selection = chain 'B' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.890 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 0.006 0.052 10548 Z= 0.320 Angle : 0.973 11.264 14232 Z= 0.588 Chirality : 0.059 0.264 1611 Planarity : 0.006 0.058 1796 Dihedral : 17.683 89.319 4008 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 0.87 % Allowed : 14.33 % Favored : 84.81 % 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: -5.17 (0.16), residues: 1324 helix: -4.23 (0.14), residues: 340 sheet: -3.36 (0.30), residues: 196 loop : -3.18 (0.16), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 209 TYR 0.031 0.004 TYR G 116 PHE 0.020 0.002 PHE B 34 TRP 0.016 0.002 TRP A 307 HIS 0.008 0.002 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.32 (10532) covalent geometry : angle 0.97263 / 0.59 (14232) hydrogen bonds : bond 0.23050 / 14.49 ( 259) hydrogen bonds : angle 7.71449 / 5.13 ( 711) Misc. bond : bond 0.00371 / 0.19 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 212 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLN cc_start: 0.8819 (tp40) cc_final: 0.7900 (tp40) REVERT: A 107 ASP cc_start: 0.8351 (t0) cc_final: 0.7888 (t0) REVERT: A 167 GLU cc_start: 0.8904 (pp20) cc_final: 0.8252 (tm-30) REVERT: A 197 LYS cc_start: 0.9104 (mtmt) cc_final: 0.8596 (tttt) REVERT: A 254 ASN cc_start: 0.8348 (m-40) cc_final: 0.7919 (p0) REVERT: B 18 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7175 (mm-30) REVERT: B 125 ASP cc_start: 0.8595 (p0) cc_final: 0.8315 (p0) REVERT: B 157 ASP cc_start: 0.7836 (p0) cc_final: 0.7569 (p0) REVERT: B 183 MET cc_start: 0.8670 (ttp) cc_final: 0.8430 (ttt) REVERT: F 157 ASP cc_start: 0.8085 (t0) cc_final: 0.7479 (t70) REVERT: F 183 MET cc_start: 0.8601 (ttp) cc_final: 0.8154 (tmm) REVERT: F 323 LYS cc_start: 0.9012 (ptpt) cc_final: 0.8390 (ptpt) REVERT: F 325 TYR cc_start: 0.7929 (t80) cc_final: 0.7598 (t80) REVERT: G 41 ARG cc_start: 0.8103 (mpt-90) cc_final: 0.6638 (tmt170) REVERT: G 197 LYS cc_start: 0.9201 (mtmt) cc_final: 0.8962 (ttmm) REVERT: G 205 ILE cc_start: 0.9194 (pt) cc_final: 0.8580 (pt) REVERT: G 211 LYS cc_start: 0.8965 (ttmt) cc_final: 0.8715 (ttmm) REVERT: G 252 GLU cc_start: 0.7350 (mp0) cc_final: 0.5747 (pp20) outliers start: 9 outliers final: 4 residues processed: 220 average time/residue: 0.0958 time to fit residues: 30.1766 Evaluate side-chains 159 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 154 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.0770 overall best weight: 1.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN A 186 GLN A 196 ASN A 317 GLN A 321 ASN B 91 HIS B 137 GLN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 207 GLN B 321 ASN F 137 GLN F 321 ASN G 131 GLN G 137 GLN G 196 ASN G 207 GLN ** G 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.134773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097330 restraints weight = 20522.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.101030 restraints weight = 10422.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103588 restraints weight = 6830.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.105201 restraints weight = 5201.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.106070 restraints weight = 4418.386| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10548 Z= 0.137 Angle : 0.654 9.305 14232 Z= 0.355 Chirality : 0.046 0.195 1611 Planarity : 0.004 0.043 1796 Dihedral : 14.095 91.471 1564 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 3.17 % Allowed : 19.71 % Favored : 77.12 % 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: -4.38 (0.18), residues: 1324 helix: -3.09 (0.21), residues: 344 sheet: -2.74 (0.32), residues: 196 loop : -2.97 (0.17), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 235 TYR 0.033 0.003 TYR B 78 PHE 0.015 0.001 PHE G 105 TRP 0.011 0.002 TRP A 307 HIS 0.005 0.001 HIS B 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (10532) covalent geometry : angle 0.65415 / 0.36 (14232) hydrogen bonds : bond 0.03799 / 2.38 ( 259) hydrogen bonds : angle 5.86282 / 3.95 ( 711) Misc. bond : bond 0.00144 / 0.07 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6800 (pm20) REVERT: A 95 GLN cc_start: 0.8745 (tp40) cc_final: 0.8303 (tp40) REVERT: A 107 ASP cc_start: 0.8232 (t0) cc_final: 0.7850 (t0) REVERT: A 167 GLU cc_start: 0.8961 (pp20) cc_final: 0.8390 (tm-30) REVERT: A 197 LYS cc_start: 0.9145 (mtmt) cc_final: 0.8672 (tttt) REVERT: A 254 ASN cc_start: 0.8478 (m-40) cc_final: 0.8238 (m-40) REVERT: B 18 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7024 (mm-30) REVERT: B 53 MET cc_start: 0.8261 (tmm) cc_final: 0.7904 (tmm) REVERT: B 76 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.6242 (pm20) REVERT: B 78 TYR cc_start: 0.8321 (p90) cc_final: 0.7920 (p90) REVERT: B 125 ASP cc_start: 0.8616 (p0) cc_final: 0.8316 (p0) REVERT: B 183 MET cc_start: 0.8672 (ttp) cc_final: 0.7898 (tmm) REVERT: B 186 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: B 266 ASN cc_start: 0.8792 (t0) cc_final: 0.8406 (t0) REVERT: F 40 MET cc_start: 0.6736 (ptm) cc_final: 0.6387 (ptp) REVERT: F 53 MET cc_start: 0.8923 (tmm) cc_final: 0.7898 (tmm) REVERT: F 69 TYR cc_start: 0.7842 (m-80) cc_final: 0.7424 (m-80) REVERT: F 76 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.6915 (pm20) REVERT: F 109 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7866 (mt-10) REVERT: F 183 MET cc_start: 0.8595 (ttp) cc_final: 0.8181 (tmm) REVERT: F 266 ASN cc_start: 0.8606 (t0) cc_final: 0.8297 (t0) REVERT: F 280 MET cc_start: 0.8670 (mtt) cc_final: 0.8355 (mpp) REVERT: F 325 TYR cc_start: 0.8006 (t80) cc_final: 0.7659 (t80) REVERT: G 40 MET cc_start: 0.8623 (ptp) cc_final: 0.8177 (pmm) REVERT: G 41 ARG cc_start: 0.8039 (mpt-90) cc_final: 0.6366 (tpt170) REVERT: G 76 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.6215 (pm20) REVERT: G 183 MET cc_start: 0.8819 (ttp) cc_final: 0.8434 (tmm) REVERT: G 207 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8504 (mm-40) REVERT: G 252 GLU cc_start: 0.7329 (mp0) cc_final: 0.6313 (pm20) outliers start: 33 outliers final: 22 residues processed: 202 average time/residue: 0.0848 time to fit residues: 25.3339 Evaluate side-chains 186 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 222 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 63 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 132 optimal weight: 0.0040 chunk 8 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 57 optimal weight: 0.0570 chunk 81 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 overall best weight: 4.6116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS A 196 ASN A 321 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 GLN G 243 GLN G 339 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.131799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.095871 restraints weight = 20227.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099530 restraints weight = 10204.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.101963 restraints weight = 6612.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103575 restraints weight = 5020.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104558 restraints weight = 4222.708| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10548 Z= 0.215 Angle : 0.680 8.845 14232 Z= 0.364 Chirality : 0.046 0.186 1611 Planarity : 0.004 0.043 1796 Dihedral : 14.292 100.028 1562 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 5.87 % Allowed : 19.42 % Favored : 74.71 % 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: -3.94 (0.19), residues: 1324 helix: -2.43 (0.24), residues: 344 sheet: -2.40 (0.33), residues: 192 loop : -2.86 (0.18), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 235 TYR 0.029 0.003 TYR B 78 PHE 0.016 0.002 PHE G 105 TRP 0.010 0.002 TRP G 307 HIS 0.006 0.001 HIS G 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.22 (10532) covalent geometry : angle 0.67990 / 0.36 (14232) hydrogen bonds : bond 0.03907 / 2.47 ( 259) hydrogen bonds : angle 5.67455 / 3.81 ( 711) Misc. bond : bond 0.00220 / 0.11 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 163 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: A 95 GLN cc_start: 0.8614 (tp40) cc_final: 0.8278 (tp40) REVERT: A 107 ASP cc_start: 0.8317 (t0) cc_final: 0.8028 (t0) REVERT: A 167 GLU cc_start: 0.8929 (pp20) cc_final: 0.8483 (tm-30) REVERT: A 197 LYS cc_start: 0.9192 (mtmt) cc_final: 0.8652 (tttt) REVERT: A 208 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8746 (mm) REVERT: A 254 ASN cc_start: 0.8342 (m-40) cc_final: 0.8068 (m-40) REVERT: A 325 TYR cc_start: 0.8433 (t80) cc_final: 0.7948 (t80) REVERT: B 18 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7157 (mm-30) REVERT: B 53 MET cc_start: 0.8277 (tmm) cc_final: 0.7081 (tmm) REVERT: B 76 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.6243 (pm20) REVERT: B 125 ASP cc_start: 0.8584 (p0) cc_final: 0.8279 (p0) REVERT: B 183 MET cc_start: 0.8673 (ttp) cc_final: 0.8337 (tmm) REVERT: B 186 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: B 266 ASN cc_start: 0.8780 (t0) cc_final: 0.8486 (t0) REVERT: F 40 MET cc_start: 0.6783 (ptm) cc_final: 0.6393 (ptp) REVERT: F 53 MET cc_start: 0.8938 (tmm) cc_final: 0.8001 (tmm) REVERT: F 109 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7949 (mt-10) REVERT: F 266 ASN cc_start: 0.8564 (t0) cc_final: 0.8319 (t0) REVERT: F 277 VAL cc_start: 0.8885 (t) cc_final: 0.8631 (p) REVERT: F 280 MET cc_start: 0.8591 (mtt) cc_final: 0.8310 (mtt) REVERT: F 290 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8865 (tm-30) REVERT: F 325 TYR cc_start: 0.7993 (t80) cc_final: 0.7628 (t80) REVERT: G 40 MET cc_start: 0.8546 (ptp) cc_final: 0.7856 (pmm) REVERT: G 41 ARG cc_start: 0.8106 (mpt-90) cc_final: 0.6470 (tpt170) REVERT: G 76 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.6532 (pm20) REVERT: G 183 MET cc_start: 0.8836 (ttp) cc_final: 0.8431 (tmm) REVERT: G 207 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8415 (mm-40) REVERT: G 215 MET cc_start: 0.7944 (pmm) cc_final: 0.7611 (pmm) REVERT: G 310 TYR cc_start: 0.6803 (t80) cc_final: 0.6367 (t80) REVERT: G 325 TYR cc_start: 0.7829 (t80) cc_final: 0.7489 (t80) outliers start: 61 outliers final: 41 residues processed: 207 average time/residue: 0.0857 time to fit residues: 26.2635 Evaluate side-chains 204 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 277 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 87 optimal weight: 0.1980 chunk 46 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 321 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN F 241 ASN G 137 GLN G 207 GLN G 243 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.135652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.100212 restraints weight = 19888.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103620 restraints weight = 10841.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105842 restraints weight = 7320.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.107323 restraints weight = 5735.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.108245 restraints weight = 4906.809| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10548 Z= 0.107 Angle : 0.596 8.676 14232 Z= 0.320 Chirality : 0.045 0.179 1611 Planarity : 0.004 0.041 1796 Dihedral : 13.954 95.334 1562 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.52 % Allowed : 21.83 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.63 (0.20), residues: 1324 helix: -1.91 (0.25), residues: 372 sheet: -2.06 (0.34), residues: 192 loop : -2.87 (0.18), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 235 TYR 0.027 0.002 TYR B 78 PHE 0.016 0.001 PHE G 105 TRP 0.009 0.001 TRP G 307 HIS 0.003 0.001 HIS G 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (10532) covalent geometry : angle 0.59597 / 0.32 (14232) hydrogen bonds : bond 0.02860 / 1.78 ( 259) hydrogen bonds : angle 5.24979 / 3.50 ( 711) Misc. bond : bond 0.00149 / 0.08 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6623 (pm20) REVERT: A 107 ASP cc_start: 0.8209 (t0) cc_final: 0.7795 (t0) REVERT: A 167 GLU cc_start: 0.9038 (pp20) cc_final: 0.8488 (tm-30) REVERT: A 197 LYS cc_start: 0.9164 (mtmt) cc_final: 0.8595 (tttt) REVERT: A 254 ASN cc_start: 0.8290 (m-40) cc_final: 0.8000 (m-40) REVERT: A 325 TYR cc_start: 0.8396 (t80) cc_final: 0.7949 (t80) REVERT: B 18 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7163 (mm-30) REVERT: B 53 MET cc_start: 0.8123 (tmm) cc_final: 0.6877 (tmm) REVERT: B 76 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.5784 (pm20) REVERT: B 125 ASP cc_start: 0.8613 (p0) cc_final: 0.8335 (p0) REVERT: B 183 MET cc_start: 0.8648 (ttp) cc_final: 0.8390 (ttt) REVERT: B 186 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7439 (tm-30) REVERT: B 258 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6755 (tm-30) REVERT: B 266 ASN cc_start: 0.8909 (t0) cc_final: 0.8481 (t0) REVERT: F 40 MET cc_start: 0.6649 (ptm) cc_final: 0.6263 (ptp) REVERT: F 53 MET cc_start: 0.8904 (tmm) cc_final: 0.7905 (tmm) REVERT: F 109 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7945 (mt-10) REVERT: F 183 MET cc_start: 0.8838 (tmm) cc_final: 0.8262 (tmm) REVERT: F 206 ASN cc_start: 0.9170 (t0) cc_final: 0.8948 (t0) REVERT: F 266 ASN cc_start: 0.8695 (t0) cc_final: 0.8396 (t0) REVERT: F 277 VAL cc_start: 0.8681 (t) cc_final: 0.8328 (p) REVERT: F 280 MET cc_start: 0.8635 (mtt) cc_final: 0.8308 (mtt) REVERT: F 290 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8805 (tm-30) REVERT: F 325 TYR cc_start: 0.7939 (t80) cc_final: 0.7626 (t80) REVERT: G 40 MET cc_start: 0.8408 (ptp) cc_final: 0.7823 (pmm) REVERT: G 41 ARG cc_start: 0.8063 (mpt-90) cc_final: 0.6486 (tmt170) REVERT: G 76 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.6878 (pm20) REVERT: G 183 MET cc_start: 0.8776 (ttp) cc_final: 0.8463 (tmm) REVERT: G 207 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8353 (mm-40) REVERT: G 215 MET cc_start: 0.7953 (pmm) cc_final: 0.7675 (pmm) REVERT: G 252 GLU cc_start: 0.7094 (mp0) cc_final: 0.6211 (pm20) REVERT: G 310 TYR cc_start: 0.6752 (t80) cc_final: 0.6381 (t80) REVERT: G 319 SER cc_start: 0.8155 (t) cc_final: 0.7773 (m) REVERT: G 325 TYR cc_start: 0.7831 (t80) cc_final: 0.7472 (t80) outliers start: 47 outliers final: 33 residues processed: 211 average time/residue: 0.0906 time to fit residues: 28.3471 Evaluate side-chains 199 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 285 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 39 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN F 241 ASN F 254 ASN G 137 GLN G 207 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.135343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099884 restraints weight = 19893.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.103369 restraints weight = 10589.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.105681 restraints weight = 7055.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107198 restraints weight = 5449.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108171 restraints weight = 4641.178| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10548 Z= 0.115 Angle : 0.583 8.680 14232 Z= 0.313 Chirality : 0.044 0.178 1611 Planarity : 0.004 0.039 1796 Dihedral : 13.862 94.320 1562 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 5.77 % Allowed : 21.83 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.26 (0.20), residues: 1324 helix: -1.44 (0.26), residues: 348 sheet: -1.80 (0.35), residues: 192 loop : -2.71 (0.18), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 235 TYR 0.031 0.002 TYR B 78 PHE 0.014 0.001 PHE G 105 TRP 0.008 0.001 TRP A 307 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (10532) covalent geometry : angle 0.58310 / 0.31 (14232) hydrogen bonds : bond 0.02790 / 1.74 ( 259) hydrogen bonds : angle 5.11129 / 3.40 ( 711) Misc. bond : bond 0.00151 / 0.08 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 165 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6500 (pm20) REVERT: A 95 GLN cc_start: 0.8749 (tp40) cc_final: 0.8371 (tp40) REVERT: A 107 ASP cc_start: 0.8196 (t0) cc_final: 0.7844 (t0) REVERT: A 167 GLU cc_start: 0.9033 (pp20) cc_final: 0.8535 (tm-30) REVERT: A 197 LYS cc_start: 0.9158 (mtmt) cc_final: 0.8630 (tttt) REVERT: A 211 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8072 (ptpp) REVERT: A 254 ASN cc_start: 0.8260 (m-40) cc_final: 0.7974 (m-40) REVERT: A 325 TYR cc_start: 0.8365 (t80) cc_final: 0.7945 (t80) REVERT: B 18 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7167 (mm-30) REVERT: B 76 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.5808 (pm20) REVERT: B 125 ASP cc_start: 0.8611 (p0) cc_final: 0.8356 (p0) REVERT: B 183 MET cc_start: 0.8660 (ttp) cc_final: 0.8394 (ttt) REVERT: B 186 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: B 266 ASN cc_start: 0.8885 (t0) cc_final: 0.8412 (t0) REVERT: F 40 MET cc_start: 0.6617 (ptm) cc_final: 0.6231 (ptp) REVERT: F 53 MET cc_start: 0.8887 (tmm) cc_final: 0.7935 (tmm) REVERT: F 157 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.6227 (t0) REVERT: F 183 MET cc_start: 0.8814 (tmm) cc_final: 0.8256 (tmm) REVERT: F 206 ASN cc_start: 0.9113 (t0) cc_final: 0.8860 (t0) REVERT: F 266 ASN cc_start: 0.8788 (t0) cc_final: 0.8485 (t0) REVERT: F 277 VAL cc_start: 0.8635 (t) cc_final: 0.8248 (p) REVERT: F 280 MET cc_start: 0.8579 (mtt) cc_final: 0.8108 (mtp) REVERT: F 290 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8699 (tm-30) REVERT: F 325 TYR cc_start: 0.8029 (t80) cc_final: 0.7652 (t80) REVERT: G 40 MET cc_start: 0.8387 (ptp) cc_final: 0.7926 (pmm) REVERT: G 41 ARG cc_start: 0.8029 (mpt-90) cc_final: 0.6403 (tpt170) REVERT: G 53 MET cc_start: 0.8635 (ttp) cc_final: 0.8289 (ttt) REVERT: G 76 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.6221 (pm20) REVERT: G 183 MET cc_start: 0.8820 (ttp) cc_final: 0.8450 (tmm) REVERT: G 215 MET cc_start: 0.7924 (pmm) cc_final: 0.7544 (pmm) REVERT: G 252 GLU cc_start: 0.7062 (mp0) cc_final: 0.6198 (pm20) REVERT: G 310 TYR cc_start: 0.6609 (t80) cc_final: 0.6255 (t80) REVERT: G 319 SER cc_start: 0.8014 (t) cc_final: 0.7652 (m) REVERT: G 325 TYR cc_start: 0.7752 (t80) cc_final: 0.7397 (t80) outliers start: 60 outliers final: 41 residues processed: 209 average time/residue: 0.0845 time to fit residues: 26.9305 Evaluate side-chains 205 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 285 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 24 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 63 optimal weight: 30.0000 chunk 36 optimal weight: 7.9990 chunk 57 optimal weight: 0.2980 chunk 40 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 339 GLN F 241 ASN G 137 GLN G 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.136573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.101862 restraints weight = 19708.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.105367 restraints weight = 10456.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107663 restraints weight = 6943.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.109142 restraints weight = 5365.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109879 restraints weight = 4561.196| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10548 Z= 0.100 Angle : 0.569 8.572 14232 Z= 0.304 Chirality : 0.044 0.175 1611 Planarity : 0.003 0.038 1796 Dihedral : 13.702 92.542 1562 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 5.38 % Allowed : 22.40 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.07 (0.20), residues: 1324 helix: -1.19 (0.27), residues: 348 sheet: -1.77 (0.35), residues: 200 loop : -2.62 (0.18), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 235 TYR 0.027 0.002 TYR B 78 PHE 0.014 0.001 PHE G 105 TRP 0.007 0.001 TRP A 307 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (10532) covalent geometry : angle 0.56891 / 0.30 (14232) hydrogen bonds : bond 0.02592 / 1.60 ( 259) hydrogen bonds : angle 4.94869 / 3.28 ( 711) Misc. bond : bond 0.00129 / 0.07 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 173 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6257 (pm20) REVERT: A 95 GLN cc_start: 0.8729 (tp40) cc_final: 0.8100 (tp-100) REVERT: A 107 ASP cc_start: 0.8154 (t0) cc_final: 0.7814 (t0) REVERT: A 167 GLU cc_start: 0.8995 (pp20) cc_final: 0.8546 (tm-30) REVERT: A 197 LYS cc_start: 0.9110 (mtmt) cc_final: 0.8407 (tttt) REVERT: A 211 LYS cc_start: 0.8374 (mtmm) cc_final: 0.8035 (ptpp) REVERT: A 254 ASN cc_start: 0.8235 (m-40) cc_final: 0.7943 (m-40) REVERT: A 325 TYR cc_start: 0.8407 (t80) cc_final: 0.8059 (t80) REVERT: B 76 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.5611 (pm20) REVERT: B 125 ASP cc_start: 0.8600 (p0) cc_final: 0.8339 (p0) REVERT: B 183 MET cc_start: 0.8645 (ttp) cc_final: 0.8389 (ttt) REVERT: B 186 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: B 207 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8740 (mt0) REVERT: B 266 ASN cc_start: 0.8953 (t0) cc_final: 0.8571 (t0) REVERT: F 40 MET cc_start: 0.6621 (ptm) cc_final: 0.6246 (ptp) REVERT: F 53 MET cc_start: 0.8903 (tmm) cc_final: 0.7920 (tmm) REVERT: F 183 MET cc_start: 0.8871 (tmm) cc_final: 0.8326 (tmm) REVERT: F 206 ASN cc_start: 0.9051 (t0) cc_final: 0.8773 (t0) REVERT: F 266 ASN cc_start: 0.8738 (t0) cc_final: 0.8420 (t0) REVERT: F 277 VAL cc_start: 0.8556 (t) cc_final: 0.8162 (p) REVERT: F 280 MET cc_start: 0.8497 (mtt) cc_final: 0.8144 (mtm) REVERT: F 290 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8657 (tm-30) REVERT: F 325 TYR cc_start: 0.8049 (t80) cc_final: 0.7665 (t80) REVERT: G 40 MET cc_start: 0.8376 (ptp) cc_final: 0.7861 (pmm) REVERT: G 41 ARG cc_start: 0.7953 (mpt-90) cc_final: 0.6253 (tpt170) REVERT: G 53 MET cc_start: 0.8550 (ttp) cc_final: 0.8288 (ttt) REVERT: G 76 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6118 (pm20) REVERT: G 207 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7269 (mm-40) REVERT: G 215 MET cc_start: 0.7939 (pmm) cc_final: 0.7455 (pmm) REVERT: G 252 GLU cc_start: 0.6968 (mp0) cc_final: 0.6142 (pm20) REVERT: G 310 TYR cc_start: 0.6463 (t80) cc_final: 0.6206 (t80) REVERT: G 319 SER cc_start: 0.7979 (t) cc_final: 0.7659 (m) REVERT: G 325 TYR cc_start: 0.7716 (t80) cc_final: 0.7357 (t80) outliers start: 56 outliers final: 37 residues processed: 213 average time/residue: 0.0881 time to fit residues: 28.2932 Evaluate side-chains 200 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 285 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 120 optimal weight: 0.7980 chunk 132 optimal weight: 0.0980 chunk 99 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 81 optimal weight: 0.0370 overall best weight: 1.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN F 241 ASN G 137 GLN G 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.135738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.100464 restraints weight = 19837.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.103855 restraints weight = 10639.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106127 restraints weight = 7149.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.107589 restraints weight = 5567.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108468 restraints weight = 4768.920| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10548 Z= 0.122 Angle : 0.582 8.609 14232 Z= 0.309 Chirality : 0.044 0.175 1611 Planarity : 0.004 0.037 1796 Dihedral : 13.726 94.003 1562 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 5.48 % Allowed : 22.69 % Favored : 71.83 % 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: -2.94 (0.21), residues: 1324 helix: -1.02 (0.27), residues: 348 sheet: -1.72 (0.35), residues: 200 loop : -2.57 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 19 TYR 0.021 0.002 TYR B 78 PHE 0.013 0.001 PHE G 105 TRP 0.007 0.001 TRP A 307 HIS 0.004 0.001 HIS B 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10532) covalent geometry : angle 0.58220 / 0.31 (14232) hydrogen bonds : bond 0.02637 / 1.65 ( 259) hydrogen bonds : angle 4.95491 / 3.29 ( 711) Misc. bond : bond 0.00149 / 0.08 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6380 (pm20) REVERT: A 95 GLN cc_start: 0.8744 (tp40) cc_final: 0.8106 (tp-100) REVERT: A 107 ASP cc_start: 0.8179 (t0) cc_final: 0.7797 (t0) REVERT: A 167 GLU cc_start: 0.8993 (pp20) cc_final: 0.8565 (tm-30) REVERT: A 188 MET cc_start: 0.8006 (tpp) cc_final: 0.7560 (tpt) REVERT: A 197 LYS cc_start: 0.9128 (mtmt) cc_final: 0.8485 (tttt) REVERT: A 211 LYS cc_start: 0.8382 (mtmm) cc_final: 0.8070 (ptpp) REVERT: A 254 ASN cc_start: 0.8238 (m-40) cc_final: 0.7960 (m-40) REVERT: A 325 TYR cc_start: 0.8432 (t80) cc_final: 0.8099 (t80) REVERT: B 76 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.5824 (pm20) REVERT: B 125 ASP cc_start: 0.8597 (p0) cc_final: 0.8343 (p0) REVERT: B 183 MET cc_start: 0.8656 (ttp) cc_final: 0.8386 (ttt) REVERT: B 186 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: B 258 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6698 (tm-30) REVERT: B 266 ASN cc_start: 0.8946 (t0) cc_final: 0.8571 (t0) REVERT: F 40 MET cc_start: 0.6660 (ptm) cc_final: 0.6255 (ptp) REVERT: F 53 MET cc_start: 0.8916 (tmm) cc_final: 0.8018 (tmm) REVERT: F 183 MET cc_start: 0.8858 (tmm) cc_final: 0.8332 (tmm) REVERT: F 206 ASN cc_start: 0.9088 (t0) cc_final: 0.8818 (t0) REVERT: F 266 ASN cc_start: 0.8717 (t0) cc_final: 0.8447 (t0) REVERT: F 277 VAL cc_start: 0.8611 (t) cc_final: 0.8225 (p) REVERT: F 280 MET cc_start: 0.8478 (mtt) cc_final: 0.8161 (mtt) REVERT: F 290 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8665 (tm-30) REVERT: F 325 TYR cc_start: 0.7981 (t80) cc_final: 0.7611 (t80) REVERT: G 40 MET cc_start: 0.8367 (ptp) cc_final: 0.7844 (pmm) REVERT: G 41 ARG cc_start: 0.7926 (mpt-90) cc_final: 0.6232 (tpt170) REVERT: G 53 MET cc_start: 0.8558 (ttp) cc_final: 0.8277 (ttt) REVERT: G 76 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.6178 (pm20) REVERT: G 182 ARG cc_start: 0.8704 (ttp-110) cc_final: 0.7128 (mpt180) REVERT: G 183 MET cc_start: 0.8874 (tmm) cc_final: 0.8487 (tmm) REVERT: G 215 MET cc_start: 0.7944 (pmm) cc_final: 0.7446 (pmm) REVERT: G 252 GLU cc_start: 0.6975 (mp0) cc_final: 0.6144 (pm20) REVERT: G 310 TYR cc_start: 0.6514 (t80) cc_final: 0.6255 (t80) REVERT: G 319 SER cc_start: 0.7948 (t) cc_final: 0.7648 (m) REVERT: G 325 TYR cc_start: 0.7690 (t80) cc_final: 0.7367 (t80) outliers start: 57 outliers final: 42 residues processed: 204 average time/residue: 0.0880 time to fit residues: 26.9240 Evaluate side-chains 201 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 285 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 90 optimal weight: 0.7980 chunk 63 optimal weight: 30.0000 chunk 111 optimal weight: 0.0020 chunk 28 optimal weight: 8.9990 chunk 112 optimal weight: 0.0170 chunk 42 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 overall best weight: 1.7630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN F 196 ASN F 241 ASN G 207 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.136345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.101374 restraints weight = 19440.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104830 restraints weight = 10420.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.107135 restraints weight = 6956.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.108639 restraints weight = 5378.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109229 restraints weight = 4574.963| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10548 Z= 0.118 Angle : 0.586 8.643 14232 Z= 0.312 Chirality : 0.044 0.173 1611 Planarity : 0.004 0.038 1796 Dihedral : 13.703 94.666 1562 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.90 % Allowed : 23.85 % Favored : 71.25 % 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: -2.89 (0.21), residues: 1324 helix: -1.02 (0.27), residues: 352 sheet: -1.67 (0.35), residues: 200 loop : -2.52 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 235 TYR 0.032 0.002 TYR B 78 PHE 0.014 0.001 PHE A 105 TRP 0.008 0.001 TRP A 307 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (10532) covalent geometry : angle 0.58570 / 0.31 (14232) hydrogen bonds : bond 0.02596 / 1.62 ( 259) hydrogen bonds : angle 4.89266 / 3.25 ( 711) Misc. bond : bond 0.00147 / 0.07 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8352 (pttm) cc_final: 0.7892 (tppt) REVERT: A 76 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6333 (pm20) REVERT: A 95 GLN cc_start: 0.8762 (tp40) cc_final: 0.8362 (tp40) REVERT: A 107 ASP cc_start: 0.8091 (t0) cc_final: 0.7772 (t0) REVERT: A 167 GLU cc_start: 0.8977 (pp20) cc_final: 0.8581 (tm-30) REVERT: A 188 MET cc_start: 0.7963 (tpp) cc_final: 0.7525 (tpt) REVERT: A 197 LYS cc_start: 0.9128 (mtmt) cc_final: 0.8470 (tttt) REVERT: A 211 LYS cc_start: 0.8369 (mtmm) cc_final: 0.8075 (ptpp) REVERT: A 254 ASN cc_start: 0.8234 (m-40) cc_final: 0.7951 (m-40) REVERT: A 325 TYR cc_start: 0.8420 (t80) cc_final: 0.8093 (t80) REVERT: B 76 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.5684 (pm20) REVERT: B 125 ASP cc_start: 0.8523 (p0) cc_final: 0.8306 (p0) REVERT: B 183 MET cc_start: 0.8646 (ttp) cc_final: 0.8421 (ttt) REVERT: B 258 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6693 (tm-30) REVERT: B 266 ASN cc_start: 0.8955 (t0) cc_final: 0.8571 (t0) REVERT: F 40 MET cc_start: 0.6619 (ptm) cc_final: 0.6217 (ptp) REVERT: F 53 MET cc_start: 0.8928 (tmm) cc_final: 0.8003 (tmm) REVERT: F 183 MET cc_start: 0.8892 (tmm) cc_final: 0.8387 (tmm) REVERT: F 206 ASN cc_start: 0.8929 (t0) cc_final: 0.8659 (t0) REVERT: F 266 ASN cc_start: 0.8703 (t0) cc_final: 0.8440 (t0) REVERT: F 277 VAL cc_start: 0.8602 (t) cc_final: 0.8209 (p) REVERT: F 280 MET cc_start: 0.8448 (mtt) cc_final: 0.8139 (mtt) REVERT: F 290 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8646 (tm-30) REVERT: F 325 TYR cc_start: 0.7962 (t80) cc_final: 0.7601 (t80) REVERT: G 40 MET cc_start: 0.8363 (ptp) cc_final: 0.7920 (pmm) REVERT: G 41 ARG cc_start: 0.7961 (mpt-90) cc_final: 0.6292 (tpt170) REVERT: G 53 MET cc_start: 0.8552 (ttp) cc_final: 0.8302 (ttt) REVERT: G 76 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6141 (pm20) REVERT: G 182 ARG cc_start: 0.8707 (ttp-110) cc_final: 0.7089 (mpt180) REVERT: G 183 MET cc_start: 0.8892 (tmm) cc_final: 0.8492 (tmm) REVERT: G 207 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7636 (mm-40) REVERT: G 215 MET cc_start: 0.7946 (pmm) cc_final: 0.7457 (pmm) REVERT: G 252 GLU cc_start: 0.6892 (mp0) cc_final: 0.6104 (pm20) REVERT: G 319 SER cc_start: 0.7949 (t) cc_final: 0.7690 (m) REVERT: G 325 TYR cc_start: 0.7628 (t80) cc_final: 0.7310 (t80) outliers start: 51 outliers final: 39 residues processed: 203 average time/residue: 0.0895 time to fit residues: 27.1345 Evaluate side-chains 197 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 264 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 102 optimal weight: 20.0000 chunk 63 optimal weight: 0.3980 chunk 99 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN B 196 ASN F 24 ASN ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.135732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.100310 restraints weight = 19703.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103774 restraints weight = 10490.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106046 restraints weight = 7012.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107454 restraints weight = 5452.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108460 restraints weight = 4670.869| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10548 Z= 0.128 Angle : 0.596 8.620 14232 Z= 0.316 Chirality : 0.045 0.175 1611 Planarity : 0.004 0.039 1796 Dihedral : 13.724 95.540 1562 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.81 % Allowed : 24.33 % Favored : 70.87 % 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: -2.81 (0.21), residues: 1324 helix: -0.86 (0.28), residues: 348 sheet: -1.63 (0.35), residues: 200 loop : -2.51 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 209 TYR 0.038 0.002 TYR G 310 PHE 0.016 0.001 PHE F 272 TRP 0.010 0.002 TRP G 307 HIS 0.003 0.001 HIS F 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (10532) covalent geometry : angle 0.59555 / 0.32 (14232) hydrogen bonds : bond 0.02648 / 1.66 ( 259) hydrogen bonds : angle 4.91113 / 3.25 ( 711) Misc. bond : bond 0.00154 / 0.08 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8351 (pttm) cc_final: 0.7918 (tppt) REVERT: A 76 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6332 (pm20) REVERT: A 95 GLN cc_start: 0.8740 (tp40) cc_final: 0.8343 (tp40) REVERT: A 107 ASP cc_start: 0.8138 (t0) cc_final: 0.7810 (t0) REVERT: A 167 GLU cc_start: 0.8971 (pp20) cc_final: 0.8597 (tm-30) REVERT: A 188 MET cc_start: 0.7965 (tpp) cc_final: 0.7533 (tpt) REVERT: A 197 LYS cc_start: 0.9141 (mtmt) cc_final: 0.8476 (tttt) REVERT: A 211 LYS cc_start: 0.8373 (mtmm) cc_final: 0.8058 (ptpp) REVERT: A 254 ASN cc_start: 0.8215 (m-40) cc_final: 0.7941 (m-40) REVERT: A 325 TYR cc_start: 0.8414 (t80) cc_final: 0.8085 (t80) REVERT: B 76 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.5859 (pm20) REVERT: B 125 ASP cc_start: 0.8530 (p0) cc_final: 0.8319 (p0) REVERT: B 183 MET cc_start: 0.8618 (ttp) cc_final: 0.8386 (ttt) REVERT: B 258 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6702 (tm-30) REVERT: B 266 ASN cc_start: 0.8956 (t0) cc_final: 0.8576 (t0) REVERT: F 40 MET cc_start: 0.6626 (ptm) cc_final: 0.6225 (ptp) REVERT: F 53 MET cc_start: 0.8916 (tmm) cc_final: 0.7951 (tmm) REVERT: F 183 MET cc_start: 0.8892 (tmm) cc_final: 0.8631 (tmm) REVERT: F 206 ASN cc_start: 0.8903 (t0) cc_final: 0.8623 (t0) REVERT: F 266 ASN cc_start: 0.8703 (t0) cc_final: 0.8446 (t0) REVERT: F 277 VAL cc_start: 0.8609 (t) cc_final: 0.8217 (p) REVERT: F 280 MET cc_start: 0.8480 (mtt) cc_final: 0.8177 (mtt) REVERT: F 290 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8645 (tm-30) REVERT: F 325 TYR cc_start: 0.7990 (t80) cc_final: 0.7631 (t80) REVERT: G 40 MET cc_start: 0.8336 (ptp) cc_final: 0.7890 (pmm) REVERT: G 41 ARG cc_start: 0.7933 (mpt-90) cc_final: 0.6271 (tpt170) REVERT: G 53 MET cc_start: 0.8552 (ttp) cc_final: 0.8303 (ttt) REVERT: G 75 ILE cc_start: 0.8491 (pt) cc_final: 0.8074 (pt) REVERT: G 76 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6142 (pm20) REVERT: G 157 ASP cc_start: 0.7659 (t0) cc_final: 0.7300 (t70) REVERT: G 182 ARG cc_start: 0.8710 (ttp-110) cc_final: 0.7098 (mpt180) REVERT: G 183 MET cc_start: 0.8904 (tmm) cc_final: 0.8465 (tmm) REVERT: G 215 MET cc_start: 0.7921 (pmm) cc_final: 0.7452 (pmm) REVERT: G 252 GLU cc_start: 0.6892 (mp0) cc_final: 0.6095 (pm20) REVERT: G 319 SER cc_start: 0.7917 (t) cc_final: 0.7659 (m) REVERT: G 325 TYR cc_start: 0.7619 (t80) cc_final: 0.7376 (t80) outliers start: 50 outliers final: 41 residues processed: 201 average time/residue: 0.0907 time to fit residues: 27.2040 Evaluate side-chains 203 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 264 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 104 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 64 optimal weight: 0.0070 chunk 97 optimal weight: 20.0000 chunk 131 optimal weight: 0.0170 chunk 26 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN G 137 GLN G 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.136876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.101370 restraints weight = 19318.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.104836 restraints weight = 10336.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.107098 restraints weight = 6922.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.108569 restraints weight = 5397.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109445 restraints weight = 4622.308| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10548 Z= 0.117 Angle : 0.602 9.524 14232 Z= 0.319 Chirality : 0.044 0.170 1611 Planarity : 0.004 0.038 1796 Dihedral : 13.675 95.734 1562 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.62 % Allowed : 24.52 % Favored : 70.87 % 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: -2.75 (0.21), residues: 1324 helix: -0.83 (0.28), residues: 352 sheet: -1.56 (0.35), residues: 200 loop : -2.47 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 165 TYR 0.030 0.002 TYR B 78 PHE 0.019 0.001 PHE G 105 TRP 0.015 0.002 TRP G 307 HIS 0.003 0.001 HIS F 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (10532) covalent geometry : angle 0.60210 / 0.32 (14232) hydrogen bonds : bond 0.02571 / 1.59 ( 259) hydrogen bonds : angle 4.87371 / 3.21 ( 711) Misc. bond : bond 0.00142 / 0.07 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8386 (pttm) cc_final: 0.7993 (tppt) REVERT: A 76 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6182 (pm20) REVERT: A 95 GLN cc_start: 0.8739 (tp40) cc_final: 0.8292 (tp40) REVERT: A 107 ASP cc_start: 0.8143 (t0) cc_final: 0.7845 (t0) REVERT: A 167 GLU cc_start: 0.8952 (pp20) cc_final: 0.8607 (tm-30) REVERT: A 188 MET cc_start: 0.8033 (tpp) cc_final: 0.7581 (tpt) REVERT: A 197 LYS cc_start: 0.9134 (mtmt) cc_final: 0.8463 (tttt) REVERT: A 210 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7570 (mp0) REVERT: A 211 LYS cc_start: 0.8340 (mtmm) cc_final: 0.8049 (ptpp) REVERT: A 254 ASN cc_start: 0.8206 (m-40) cc_final: 0.7924 (m-40) REVERT: B 76 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.5669 (pm20) REVERT: B 125 ASP cc_start: 0.8521 (p0) cc_final: 0.8262 (p0) REVERT: B 183 MET cc_start: 0.8641 (ttp) cc_final: 0.8379 (ttt) REVERT: B 258 GLU cc_start: 0.7248 (tm-30) cc_final: 0.6710 (tm-30) REVERT: B 266 ASN cc_start: 0.8975 (t0) cc_final: 0.8558 (t0) REVERT: F 40 MET cc_start: 0.6628 (ptm) cc_final: 0.6239 (ptp) REVERT: F 53 MET cc_start: 0.8920 (tmm) cc_final: 0.7987 (tmm) REVERT: F 183 MET cc_start: 0.8921 (tmm) cc_final: 0.8692 (tmm) REVERT: F 206 ASN cc_start: 0.8901 (t0) cc_final: 0.8618 (t0) REVERT: F 266 ASN cc_start: 0.8738 (t0) cc_final: 0.8418 (t0) REVERT: F 277 VAL cc_start: 0.8589 (t) cc_final: 0.8194 (p) REVERT: F 280 MET cc_start: 0.8452 (mtt) cc_final: 0.8150 (mtt) REVERT: F 290 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8625 (tm-30) REVERT: F 325 TYR cc_start: 0.7976 (t80) cc_final: 0.7608 (t80) REVERT: G 40 MET cc_start: 0.8334 (ptp) cc_final: 0.7909 (pmm) REVERT: G 41 ARG cc_start: 0.7952 (mpt-90) cc_final: 0.6284 (tpt170) REVERT: G 53 MET cc_start: 0.8526 (ttp) cc_final: 0.8314 (ttt) REVERT: G 60 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8407 (tt) REVERT: G 75 ILE cc_start: 0.8503 (pt) cc_final: 0.8088 (pt) REVERT: G 76 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6131 (pm20) REVERT: G 157 ASP cc_start: 0.7694 (t0) cc_final: 0.7320 (t70) REVERT: G 182 ARG cc_start: 0.8699 (ttp-110) cc_final: 0.7130 (mpt180) REVERT: G 207 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7575 (mm-40) REVERT: G 215 MET cc_start: 0.7913 (pmm) cc_final: 0.7420 (pmm) REVERT: G 252 GLU cc_start: 0.6795 (mp0) cc_final: 0.6058 (pm20) REVERT: G 319 SER cc_start: 0.7890 (t) cc_final: 0.7603 (m) REVERT: G 325 TYR cc_start: 0.7621 (t80) cc_final: 0.7372 (t80) outliers start: 48 outliers final: 37 residues processed: 198 average time/residue: 0.0883 time to fit residues: 26.1733 Evaluate side-chains 202 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 264 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 45 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 102 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 ASN F 241 ASN G 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.136872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.101307 restraints weight = 19783.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104742 restraints weight = 10602.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107015 restraints weight = 7118.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108465 restraints weight = 5522.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109248 restraints weight = 4735.670| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10548 Z= 0.119 Angle : 0.601 8.567 14232 Z= 0.319 Chirality : 0.044 0.170 1611 Planarity : 0.004 0.038 1796 Dihedral : 13.654 96.062 1562 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.42 % Allowed : 24.71 % Favored : 70.87 % 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: -2.68 (0.21), residues: 1324 helix: -0.77 (0.28), residues: 348 sheet: -1.52 (0.35), residues: 200 loop : -2.43 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 235 TYR 0.030 0.002 TYR B 78 PHE 0.022 0.001 PHE G 105 TRP 0.013 0.002 TRP G 307 HIS 0.003 0.001 HIS F 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10532) covalent geometry : angle 0.60102 / 0.32 (14232) hydrogen bonds : bond 0.02545 / 1.58 ( 259) hydrogen bonds : angle 4.83127 / 3.19 ( 711) Misc. bond : bond 0.00147 / 0.08 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1822.22 seconds wall clock time: 32 minutes 23.25 seconds (1943.25 seconds total)