Starting phenix.real_space_refine on Wed Mar 4 03:22:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8amd_15524/03_2026/8amd_15524.cif Found real_map, /net/cci-nas-00/data/ceres_data/8amd_15524/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8amd_15524/03_2026/8amd_15524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8amd_15524/03_2026/8amd_15524.map" model { file = "/net/cci-nas-00/data/ceres_data/8amd_15524/03_2026/8amd_15524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8amd_15524/03_2026/8amd_15524.cif" } 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-dev-5986/lib/python3.9/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: 2.54, per 1000 atoms: 0.24 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: 0.56 Conformation dependent library (CDL) restraints added in 438.5 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: 0.26 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: 1.32 Time building geometry restraints manager: 0.77 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=" N GLN G 250 " pdb=" CA GLN G 250 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.57e+00 bond pdb=" N GLU G 331 " pdb=" CA GLU G 331 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.15e-02 7.56e+03 3.08e+00 bond pdb=" CB GLN F 250 " pdb=" CG GLN F 250 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.94e+00 bond pdb=" CA HIS G 329 " pdb=" CB HIS G 329 " ideal model delta sigma weight residual 1.533 1.565 -0.032 1.99e-02 2.53e+03 2.57e+00 bond pdb=" N GLU A 313 " pdb=" CA GLU A 313 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.58e-02 4.01e+03 2.52e+00 ... (remaining 10527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 13705 2.25 - 4.51: 467 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=" N GLY F 217 " pdb=" CA GLY F 217 " pdb=" C GLY F 217 " ideal model delta sigma weight residual 110.77 118.97 -8.20 1.93e+00 2.68e-01 1.80e+01 ... (remaining 14227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5501 17.86 - 35.73: 673 35.73 - 53.59: 186 53.59 - 71.46: 52 71.46 - 89.32: 16 Dihedral angle restraints: 6428 sinusoidal: 2692 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 6425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1124 0.053 - 0.106: 356 0.106 - 0.159: 106 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.900 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 0.051 10548 Z= 0.281 Angle : 0.963 11.264 14232 Z= 0.552 Chirality : 0.059 0.264 1611 Planarity : 0.006 0.058 1796 Dihedral : 17.828 89.319 4052 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 covalent geometry : bond 0.00609 (10532) covalent geometry : angle 0.96269 (14232) hydrogen bonds : bond 0.23050 ( 259) hydrogen bonds : angle 7.71449 ( 711) Misc. bond : bond 0.00371 ( 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 : 0.287 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: 0.0920 time to fit residues: 28.8202 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 : 0.316 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3794 r_free = 0.3794 target = 0.134743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097249 restraints weight = 20563.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100985 restraints weight = 10459.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.103471 restraints weight = 6842.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.105107 restraints weight = 5250.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.106115 restraints weight = 4441.623| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1588 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 : 0.655 9.207 14232 Z= 0.355 Chirality : 0.046 0.194 1611 Planarity : 0.004 0.043 1796 Dihedral : 14.688 91.475 1608 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.17 % Allowed : 19.81 % Favored : 77.02 % 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: -3.08 (0.21), residues: 344 sheet: -2.73 (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 0.008 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00296 (10532) covalent geometry : angle 0.65499 (14232) hydrogen bonds : bond 0.03718 ( 259) hydrogen bonds : angle 5.87618 ( 711) Misc. bond : bond 0.00141 ( 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 : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6787 (pm20) REVERT: A 95 GLN cc_start: 0.8723 (tp40) cc_final: 0.8283 (tp40) REVERT: A 107 ASP cc_start: 0.8276 (t0) cc_final: 0.7916 (t0) REVERT: A 167 GLU cc_start: 0.8964 (pp20) cc_final: 0.8396 (tm-30) REVERT: A 197 LYS cc_start: 0.9146 (mtmt) cc_final: 0.8682 (tttt) REVERT: A 254 ASN cc_start: 0.8467 (m-40) cc_final: 0.8228 (m-40) REVERT: B 18 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7017 (mm-30) REVERT: B 53 MET cc_start: 0.8234 (tmm) cc_final: 0.7877 (tmm) REVERT: B 76 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.6228 (pm20) REVERT: B 78 TYR cc_start: 0.8309 (p90) cc_final: 0.7912 (p90) REVERT: B 125 ASP cc_start: 0.8630 (p0) cc_final: 0.8332 (p0) REVERT: B 183 MET cc_start: 0.8675 (ttp) cc_final: 0.7896 (tmm) REVERT: B 186 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: B 266 ASN cc_start: 0.8784 (t0) cc_final: 0.8399 (t0) REVERT: F 40 MET cc_start: 0.6664 (ptm) cc_final: 0.6272 (ptp) REVERT: F 53 MET cc_start: 0.8924 (tmm) cc_final: 0.7967 (tmm) REVERT: F 76 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.6989 (pm20) REVERT: F 109 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7894 (mt-10) REVERT: F 183 MET cc_start: 0.8604 (ttp) cc_final: 0.8196 (tmm) REVERT: F 266 ASN cc_start: 0.8527 (t0) cc_final: 0.8238 (t0) REVERT: F 280 MET cc_start: 0.8695 (mtt) cc_final: 0.8367 (mpp) REVERT: F 325 TYR cc_start: 0.8002 (t80) cc_final: 0.7656 (t80) REVERT: G 40 MET cc_start: 0.8614 (ptp) cc_final: 0.7842 (pmm) REVERT: G 41 ARG cc_start: 0.8032 (mpt-90) cc_final: 0.6514 (tmt170) REVERT: G 76 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.6287 (pm20) REVERT: G 183 MET cc_start: 0.8837 (ttp) cc_final: 0.8420 (tmm) REVERT: G 207 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8224 (mm-40) REVERT: G 252 GLU cc_start: 0.7334 (mp0) cc_final: 0.6318 (pm20) outliers start: 33 outliers final: 22 residues processed: 202 average time/residue: 0.0812 time to fit residues: 24.1491 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 : 0.367 ------------------------------------------------------------------------------- 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: 8.9990 chunk 132 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3758 r_free = 0.3758 target = 0.131738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095102 restraints weight = 20654.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098726 restraints weight = 10523.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.101110 restraints weight = 6883.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.102644 restraints weight = 5294.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103625 restraints weight = 4492.197| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10548 Z= 0.219 Angle : 0.686 8.780 14232 Z= 0.366 Chirality : 0.046 0.190 1611 Planarity : 0.004 0.043 1796 Dihedral : 14.881 100.976 1606 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % 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: -3.92 (0.19), residues: 1324 helix: -2.42 (0.24), residues: 344 sheet: -2.38 (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 0.015 0.002 PHE G 105 TRP 0.011 0.002 TRP G 307 HIS 0.005 0.001 HIS G 329 Details of bonding type rmsd covalent geometry : bond 0.00492 (10532) covalent geometry : angle 0.68606 (14232) hydrogen bonds : bond 0.03927 ( 259) hydrogen bonds : angle 5.67352 ( 711) Misc. bond : bond 0.00222 ( 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 228 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 167 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7172 (pm20) REVERT: A 95 GLN cc_start: 0.8615 (tp40) cc_final: 0.8282 (tp40) REVERT: A 107 ASP cc_start: 0.8320 (t0) cc_final: 0.8030 (t0) REVERT: A 167 GLU cc_start: 0.8935 (pp20) cc_final: 0.8488 (tm-30) REVERT: A 197 LYS cc_start: 0.9192 (mtmt) cc_final: 0.8653 (tttt) REVERT: A 208 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8750 (mm) REVERT: A 254 ASN cc_start: 0.8347 (m-40) cc_final: 0.8072 (m-40) REVERT: A 325 TYR cc_start: 0.8442 (t80) cc_final: 0.7961 (t80) REVERT: B 18 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7141 (mm-30) REVERT: B 53 MET cc_start: 0.8280 (tmm) cc_final: 0.7077 (tmm) REVERT: B 76 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.6257 (pm20) REVERT: B 125 ASP cc_start: 0.8600 (p0) cc_final: 0.8300 (p0) REVERT: B 183 MET cc_start: 0.8675 (ttp) cc_final: 0.8339 (tmm) REVERT: B 186 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: B 266 ASN cc_start: 0.8773 (t0) cc_final: 0.8466 (t0) REVERT: F 40 MET cc_start: 0.6769 (ptm) cc_final: 0.6379 (ptp) REVERT: F 53 MET cc_start: 0.8938 (tmm) cc_final: 0.8015 (tmm) REVERT: F 109 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7955 (mt-10) REVERT: F 266 ASN cc_start: 0.8563 (t0) cc_final: 0.8330 (t0) REVERT: F 277 VAL cc_start: 0.8873 (t) cc_final: 0.8613 (p) REVERT: F 280 MET cc_start: 0.8600 (mtt) cc_final: 0.8317 (mtt) REVERT: F 290 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8871 (tm-30) REVERT: F 325 TYR cc_start: 0.8001 (t80) cc_final: 0.7642 (t80) REVERT: G 40 MET cc_start: 0.8535 (ptp) cc_final: 0.7861 (pmm) REVERT: G 41 ARG cc_start: 0.8068 (mpt-90) cc_final: 0.6401 (tpt170) REVERT: G 76 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.6589 (pm20) REVERT: G 183 MET cc_start: 0.8838 (ttp) cc_final: 0.8431 (tmm) REVERT: G 207 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8505 (mm-40) REVERT: G 215 MET cc_start: 0.7958 (pmm) cc_final: 0.7624 (pmm) REVERT: G 252 GLU cc_start: 0.7419 (mp0) cc_final: 0.5892 (pp20) REVERT: G 325 TYR cc_start: 0.7874 (t80) cc_final: 0.7597 (t80) outliers start: 61 outliers final: 41 residues processed: 210 average time/residue: 0.0788 time to fit residues: 24.2890 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 : 0.362 ------------------------------------------------------------------------------- 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: 8.9990 chunk 46 optimal weight: 10.0000 chunk 13 optimal weight: 0.0970 chunk 91 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 80 optimal weight: 0.1980 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.099238 restraints weight = 19973.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102614 restraints weight = 10926.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.104831 restraints weight = 7404.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.106239 restraints weight = 5780.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.106861 restraints weight = 4967.709| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10548 Z= 0.127 Angle : 0.612 8.705 14232 Z= 0.327 Chirality : 0.045 0.180 1611 Planarity : 0.004 0.043 1796 Dihedral : 14.563 99.302 1606 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 5.58 % Allowed : 21.25 % Favored : 73.17 % 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: -3.64 (0.20), residues: 1324 helix: -1.91 (0.25), residues: 372 sheet: -2.20 (0.33), residues: 196 loop : -2.84 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 235 TYR 0.030 0.002 TYR B 78 PHE 0.016 0.001 PHE G 105 TRP 0.008 0.001 TRP G 307 HIS 0.005 0.001 HIS G 329 Details of bonding type rmsd covalent geometry : bond 0.00282 (10532) covalent geometry : angle 0.61168 (14232) hydrogen bonds : bond 0.03012 ( 259) hydrogen bonds : angle 5.31708 ( 711) Misc. bond : bond 0.00164 ( 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 223 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6779 (pm20) REVERT: A 95 GLN cc_start: 0.8614 (tp40) cc_final: 0.8348 (tp40) REVERT: A 107 ASP cc_start: 0.8171 (t0) cc_final: 0.7900 (t0) REVERT: A 167 GLU cc_start: 0.9044 (pp20) cc_final: 0.8485 (tm-30) REVERT: A 197 LYS cc_start: 0.9172 (mtmt) cc_final: 0.8610 (tttt) REVERT: A 254 ASN cc_start: 0.8318 (m-40) cc_final: 0.8018 (m-40) REVERT: A 325 TYR cc_start: 0.8402 (t80) cc_final: 0.7937 (t80) REVERT: B 18 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7216 (mm-30) REVERT: B 53 MET cc_start: 0.8207 (tmm) cc_final: 0.6937 (tmm) REVERT: B 76 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.6026 (pm20) REVERT: B 125 ASP cc_start: 0.8544 (p0) cc_final: 0.8261 (p0) REVERT: B 183 MET cc_start: 0.8654 (ttp) cc_final: 0.8385 (ttt) REVERT: B 186 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: B 266 ASN cc_start: 0.8880 (t0) cc_final: 0.8483 (t0) REVERT: F 40 MET cc_start: 0.6783 (ptm) cc_final: 0.6359 (ptp) REVERT: F 53 MET cc_start: 0.8922 (tmm) cc_final: 0.7972 (tmm) REVERT: F 109 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7871 (mt-10) REVERT: F 183 MET cc_start: 0.8834 (tmm) cc_final: 0.8214 (tmm) REVERT: F 266 ASN cc_start: 0.8640 (t0) cc_final: 0.8367 (t0) REVERT: F 277 VAL cc_start: 0.8787 (t) cc_final: 0.8455 (p) REVERT: F 280 MET cc_start: 0.8585 (mtt) cc_final: 0.8273 (mtt) REVERT: F 290 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8805 (tm-30) REVERT: F 325 TYR cc_start: 0.7930 (t80) cc_final: 0.7600 (t80) REVERT: G 40 MET cc_start: 0.8405 (ptp) cc_final: 0.7949 (pmm) REVERT: G 41 ARG cc_start: 0.8114 (mpt-90) cc_final: 0.6466 (tpt170) REVERT: G 76 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.6384 (pm20) REVERT: G 183 MET cc_start: 0.8769 (ttp) cc_final: 0.8445 (tmm) REVERT: G 207 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8412 (mm-40) REVERT: G 215 MET cc_start: 0.7847 (pmm) cc_final: 0.7495 (pmm) REVERT: G 252 GLU cc_start: 0.7213 (mp0) cc_final: 0.6320 (pm20) REVERT: G 278 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7910 (mt-10) REVERT: G 310 TYR cc_start: 0.6526 (t80) cc_final: 0.6278 (t80) REVERT: G 319 SER cc_start: 0.8200 (t) cc_final: 0.7791 (m) REVERT: G 325 TYR cc_start: 0.7945 (t80) cc_final: 0.7538 (t80) outliers start: 58 outliers final: 43 residues processed: 206 average time/residue: 0.0791 time to fit residues: 24.2985 Evaluate side-chains 209 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET 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 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 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 107 ASP 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 205 ILE Chi-restraints excluded: chain F residue 210 GLU 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 288 THR 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 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 277 VAL 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: 9.9990 chunk 118 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 321 ASN B 196 ASN F 137 GLN F 241 ASN F 243 GLN F 254 ASN G 207 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.093925 restraints weight = 20657.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097504 restraints weight = 10569.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.099851 restraints weight = 6924.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.101382 restraints weight = 5283.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.102366 restraints weight = 4470.872| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10548 Z= 0.279 Angle : 0.710 8.970 14232 Z= 0.374 Chirality : 0.048 0.182 1611 Planarity : 0.004 0.046 1796 Dihedral : 15.028 106.190 1606 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 6.63 % Allowed : 21.06 % Favored : 72.31 % 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: -3.52 (0.20), residues: 1324 helix: -1.96 (0.25), residues: 344 sheet: -2.28 (0.33), residues: 196 loop : -2.63 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 209 TYR 0.033 0.003 TYR B 78 PHE 0.016 0.002 PHE G 105 TRP 0.009 0.002 TRP A 307 HIS 0.006 0.002 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00633 (10532) covalent geometry : angle 0.71048 (14232) hydrogen bonds : bond 0.03733 ( 259) hydrogen bonds : angle 5.59175 ( 711) Misc. bond : bond 0.00239 ( 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 226 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 157 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: A 95 GLN cc_start: 0.8625 (tp40) cc_final: 0.8381 (tp40) REVERT: A 107 ASP cc_start: 0.8295 (t0) cc_final: 0.7986 (t0) REVERT: A 167 GLU cc_start: 0.9040 (pp20) cc_final: 0.8574 (tm-30) REVERT: A 176 HIS cc_start: 0.8812 (m-70) cc_final: 0.7876 (m170) REVERT: A 197 LYS cc_start: 0.9220 (mtmt) cc_final: 0.8649 (tttt) REVERT: A 254 ASN cc_start: 0.8284 (m-40) cc_final: 0.7996 (m-40) REVERT: A 325 TYR cc_start: 0.8441 (t80) cc_final: 0.7899 (t80) REVERT: B 18 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7179 (mm-30) REVERT: B 53 MET cc_start: 0.8369 (tmm) cc_final: 0.7047 (tmm) REVERT: B 76 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.6181 (pm20) REVERT: B 125 ASP cc_start: 0.8525 (p0) cc_final: 0.8261 (p0) REVERT: B 183 MET cc_start: 0.8709 (ttp) cc_final: 0.8464 (ttt) REVERT: B 186 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: B 266 ASN cc_start: 0.8844 (t0) cc_final: 0.8492 (t0) REVERT: F 40 MET cc_start: 0.6850 (ptm) cc_final: 0.6357 (ptp) REVERT: F 53 MET cc_start: 0.8946 (tmm) cc_final: 0.7974 (tmm) REVERT: F 76 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: F 109 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7951 (mt-10) REVERT: F 266 ASN cc_start: 0.8595 (t0) cc_final: 0.8339 (t0) REVERT: F 277 VAL cc_start: 0.8901 (t) cc_final: 0.8655 (p) REVERT: F 280 MET cc_start: 0.8560 (mtt) cc_final: 0.8096 (mtp) REVERT: F 290 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8852 (tm-30) REVERT: F 325 TYR cc_start: 0.7996 (t80) cc_final: 0.7622 (t80) REVERT: G 40 MET cc_start: 0.8413 (ptp) cc_final: 0.7992 (pmm) REVERT: G 41 ARG cc_start: 0.8090 (mpt-90) cc_final: 0.6465 (tpt170) REVERT: G 76 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.6677 (pm20) REVERT: G 183 MET cc_start: 0.8829 (ttp) cc_final: 0.8518 (tmm) REVERT: G 207 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8445 (mm-40) REVERT: G 215 MET cc_start: 0.7973 (pmm) cc_final: 0.7499 (pmm) REVERT: G 252 GLU cc_start: 0.7424 (mp0) cc_final: 0.5618 (pp20) REVERT: G 325 TYR cc_start: 0.7866 (t80) cc_final: 0.7521 (t80) outliers start: 69 outliers final: 49 residues processed: 208 average time/residue: 0.0766 time to fit residues: 24.0673 Evaluate side-chains 207 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 A residue 294 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 107 ASP 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 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 39 ILE Chi-restraints excluded: chain F residue 76 GLU 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 210 GLU Chi-restraints excluded: chain F residue 214 VAL 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 288 THR Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 298 LEU 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 222 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 264 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 24 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 26 optimal weight: 0.0870 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN F 137 GLN F 241 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 = 0.3788 r_free = 0.3788 target = 0.135333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.099999 restraints weight = 19949.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.103513 restraints weight = 10606.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105778 restraints weight = 7071.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.107296 restraints weight = 5479.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.108153 restraints weight = 4659.372| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10548 Z= 0.109 Angle : 0.595 8.635 14232 Z= 0.317 Chirality : 0.045 0.174 1611 Planarity : 0.004 0.044 1796 Dihedral : 14.455 99.406 1606 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 5.58 % Allowed : 22.60 % 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: -3.16 (0.20), residues: 1324 helix: -1.24 (0.27), residues: 344 sheet: -1.97 (0.34), residues: 196 loop : -2.64 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 235 TYR 0.023 0.002 TYR A 78 PHE 0.013 0.001 PHE G 105 TRP 0.009 0.002 TRP A 307 HIS 0.003 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00237 (10532) covalent geometry : angle 0.59518 (14232) hydrogen bonds : bond 0.02687 ( 259) hydrogen bonds : angle 5.12903 ( 711) Misc. bond : bond 0.00145 ( 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 231 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 173 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6731 (pm20) REVERT: A 107 ASP cc_start: 0.8158 (t0) cc_final: 0.7856 (t0) REVERT: A 167 GLU cc_start: 0.9024 (pp20) cc_final: 0.8554 (tm-30) REVERT: A 197 LYS cc_start: 0.9127 (mtmt) cc_final: 0.8496 (tttt) REVERT: A 211 LYS cc_start: 0.8393 (mtmm) cc_final: 0.7995 (ptpp) REVERT: A 254 ASN cc_start: 0.8227 (m-40) cc_final: 0.7901 (m-40) REVERT: A 325 TYR cc_start: 0.8455 (t80) cc_final: 0.8071 (t80) REVERT: B 18 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7165 (mm-30) REVERT: B 76 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.5636 (pm20) REVERT: B 125 ASP cc_start: 0.8587 (p0) cc_final: 0.8346 (p0) REVERT: B 183 MET cc_start: 0.8710 (ttp) cc_final: 0.8457 (ttt) REVERT: B 186 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: B 266 ASN cc_start: 0.8893 (t0) cc_final: 0.8470 (t0) REVERT: F 40 MET cc_start: 0.6651 (ptm) cc_final: 0.6248 (ptp) REVERT: F 53 MET cc_start: 0.8854 (tmm) cc_final: 0.7922 (tmm) REVERT: F 137 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7778 (pt0) REVERT: F 183 MET cc_start: 0.8769 (tmm) cc_final: 0.8254 (tmm) REVERT: F 206 ASN cc_start: 0.9116 (t0) cc_final: 0.8867 (t0) REVERT: F 266 ASN cc_start: 0.8783 (t0) cc_final: 0.8543 (t0) REVERT: F 277 VAL cc_start: 0.8610 (t) cc_final: 0.8224 (p) REVERT: F 280 MET cc_start: 0.8504 (mtt) cc_final: 0.8151 (mtm) REVERT: F 290 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8685 (tm-30) REVERT: F 325 TYR cc_start: 0.7973 (t80) cc_final: 0.7588 (t80) REVERT: G 40 MET cc_start: 0.8370 (ptp) cc_final: 0.7898 (pmm) REVERT: G 41 ARG cc_start: 0.7914 (mpt-90) cc_final: 0.6265 (tpt170) REVERT: G 53 MET cc_start: 0.8586 (ttp) cc_final: 0.8303 (ttt) REVERT: G 76 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6181 (pm20) REVERT: G 183 MET cc_start: 0.8799 (ttp) cc_final: 0.8464 (tmm) REVERT: G 207 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8309 (mm-40) REVERT: G 215 MET cc_start: 0.8100 (pmm) cc_final: 0.7577 (pmm) REVERT: G 252 GLU cc_start: 0.7001 (mp0) cc_final: 0.6150 (pm20) REVERT: G 319 SER cc_start: 0.8040 (t) cc_final: 0.7671 (m) REVERT: G 325 TYR cc_start: 0.7891 (t80) cc_final: 0.7507 (t80) outliers start: 58 outliers final: 40 residues processed: 211 average time/residue: 0.0799 time to fit residues: 25.4995 Evaluate side-chains 203 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 222 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 153 LEU 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 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 137 GLN Chi-restraints excluded: chain F residue 139 LEU 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 214 VAL Chi-restraints excluded: chain F residue 222 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 120 optimal weight: 6.9990 chunk 132 optimal weight: 0.0000 chunk 99 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 overall best weight: 2.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN F 137 GLN F 241 ASN G 137 GLN G 207 GLN G 243 GLN G 254 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.099488 restraints weight = 19749.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.102867 restraints weight = 10718.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105118 restraints weight = 7216.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.106561 restraints weight = 5615.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.107501 restraints weight = 4801.226| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2552 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 : 0.605 8.652 14232 Z= 0.321 Chirality : 0.045 0.176 1611 Planarity : 0.004 0.041 1796 Dihedral : 14.435 99.473 1606 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 6.15 % Allowed : 22.88 % Favored : 70.96 % 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 (0.21), residues: 1324 helix: -1.17 (0.27), residues: 348 sheet: -1.89 (0.34), residues: 196 loop : -2.60 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 235 TYR 0.040 0.002 TYR F 310 PHE 0.014 0.001 PHE G 105 TRP 0.013 0.002 TRP G 307 HIS 0.004 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00310 (10532) covalent geometry : angle 0.60468 (14232) hydrogen bonds : bond 0.02816 ( 259) hydrogen bonds : angle 5.13427 ( 711) Misc. bond : bond 0.00172 ( 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 226 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 162 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6647 (pm20) REVERT: A 95 GLN cc_start: 0.8738 (tp40) cc_final: 0.8420 (tp40) REVERT: A 107 ASP cc_start: 0.8149 (t0) cc_final: 0.7831 (t0) REVERT: A 167 GLU cc_start: 0.9023 (pp20) cc_final: 0.8578 (tm-30) REVERT: A 188 MET cc_start: 0.7972 (tpp) cc_final: 0.7537 (tpt) REVERT: A 197 LYS cc_start: 0.9144 (mtmt) cc_final: 0.8495 (tttt) REVERT: A 211 LYS cc_start: 0.8434 (mtmm) cc_final: 0.8037 (ptpp) REVERT: A 254 ASN cc_start: 0.8216 (m-40) cc_final: 0.7904 (m-40) REVERT: A 325 TYR cc_start: 0.8469 (t80) cc_final: 0.8094 (t80) REVERT: B 76 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.5802 (pm20) REVERT: B 125 ASP cc_start: 0.8557 (p0) cc_final: 0.8317 (p0) REVERT: B 183 MET cc_start: 0.8681 (ttp) cc_final: 0.8423 (ttt) REVERT: B 186 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: B 266 ASN cc_start: 0.8904 (t0) cc_final: 0.8474 (t0) REVERT: F 40 MET cc_start: 0.6701 (ptm) cc_final: 0.6288 (ptp) REVERT: F 53 MET cc_start: 0.8888 (tmm) cc_final: 0.7930 (tmm) REVERT: F 76 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: F 183 MET cc_start: 0.8822 (tmm) cc_final: 0.8306 (tmm) REVERT: F 206 ASN cc_start: 0.9143 (t0) cc_final: 0.8905 (t0) REVERT: F 266 ASN cc_start: 0.8650 (t0) cc_final: 0.8361 (t0) REVERT: F 277 VAL cc_start: 0.8695 (t) cc_final: 0.8324 (p) REVERT: F 280 MET cc_start: 0.8482 (mtt) cc_final: 0.8166 (mtt) REVERT: F 290 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8684 (tm-30) REVERT: F 325 TYR cc_start: 0.7970 (t80) cc_final: 0.7582 (t80) REVERT: G 40 MET cc_start: 0.8365 (ptp) cc_final: 0.7947 (pmm) REVERT: G 41 ARG cc_start: 0.7938 (mpt-90) cc_final: 0.6282 (tpt170) REVERT: G 53 MET cc_start: 0.8618 (ttp) cc_final: 0.8317 (ttt) REVERT: G 76 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.6282 (pm20) REVERT: G 182 ARG cc_start: 0.8775 (ttp-110) cc_final: 0.7149 (mpt180) REVERT: G 183 MET cc_start: 0.8821 (ttp) cc_final: 0.8484 (tmm) REVERT: G 215 MET cc_start: 0.8103 (pmm) cc_final: 0.7512 (pmm) REVERT: G 252 GLU cc_start: 0.7033 (mp0) cc_final: 0.6174 (pm20) REVERT: G 319 SER cc_start: 0.7990 (t) cc_final: 0.7611 (m) REVERT: G 325 TYR cc_start: 0.7906 (t80) cc_final: 0.7499 (t80) outliers start: 64 outliers final: 47 residues processed: 208 average time/residue: 0.0787 time to fit residues: 24.2111 Evaluate side-chains 205 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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 106 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 153 LEU 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 154 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 205 ILE 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 214 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 264 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 90 optimal weight: 10.0000 chunk 63 optimal weight: 30.0000 chunk 111 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN F 196 ASN F 241 ASN G 207 GLN G 254 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.132014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097357 restraints weight = 19916.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.100632 restraints weight = 10829.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.102809 restraints weight = 7311.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.104186 restraints weight = 5714.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105074 restraints weight = 4902.589| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10548 Z= 0.216 Angle : 0.666 8.912 14232 Z= 0.352 Chirality : 0.046 0.174 1611 Planarity : 0.004 0.044 1796 Dihedral : 14.679 103.744 1606 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 5.77 % Allowed : 23.94 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.03 (0.20), residues: 1324 helix: -1.26 (0.27), residues: 324 sheet: -1.95 (0.34), residues: 196 loop : -2.45 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 235 TYR 0.051 0.003 TYR F 310 PHE 0.014 0.001 PHE G 105 TRP 0.013 0.002 TRP G 307 HIS 0.005 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00492 (10532) covalent geometry : angle 0.66601 (14232) hydrogen bonds : bond 0.03158 ( 259) hydrogen bonds : angle 5.29987 ( 711) Misc. bond : bond 0.00210 ( 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 211 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 151 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: A 95 GLN cc_start: 0.8753 (tp40) cc_final: 0.8280 (tp-100) REVERT: A 107 ASP cc_start: 0.8203 (t0) cc_final: 0.7919 (t0) REVERT: A 167 GLU cc_start: 0.8999 (pp20) cc_final: 0.8551 (tm-30) REVERT: A 176 HIS cc_start: 0.8852 (m-70) cc_final: 0.7827 (m170) REVERT: A 188 MET cc_start: 0.7931 (tpp) cc_final: 0.7516 (tpt) REVERT: A 197 LYS cc_start: 0.9180 (mtmt) cc_final: 0.8501 (tttt) REVERT: A 211 LYS cc_start: 0.8492 (mtmm) cc_final: 0.8100 (ptpp) REVERT: A 254 ASN cc_start: 0.8229 (m-40) cc_final: 0.7931 (m-40) REVERT: B 76 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.5930 (pm20) REVERT: B 125 ASP cc_start: 0.8550 (p0) cc_final: 0.8304 (p0) REVERT: B 183 MET cc_start: 0.8718 (ttp) cc_final: 0.8470 (ttt) REVERT: B 186 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: B 266 ASN cc_start: 0.8844 (t0) cc_final: 0.8433 (t0) REVERT: B 313 GLU cc_start: 0.1569 (OUTLIER) cc_final: 0.1323 (pp20) REVERT: F 40 MET cc_start: 0.6726 (ptm) cc_final: 0.6288 (ptp) REVERT: F 53 MET cc_start: 0.8884 (tmm) cc_final: 0.7965 (tmm) REVERT: F 76 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: F 183 MET cc_start: 0.8836 (tmm) cc_final: 0.8519 (tmm) REVERT: F 266 ASN cc_start: 0.8591 (t0) cc_final: 0.8274 (t0) REVERT: F 277 VAL cc_start: 0.8780 (t) cc_final: 0.8488 (p) REVERT: F 280 MET cc_start: 0.8503 (mtt) cc_final: 0.8195 (mtt) REVERT: F 290 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8696 (tm-30) REVERT: F 325 TYR cc_start: 0.7997 (t80) cc_final: 0.7589 (t80) REVERT: G 40 MET cc_start: 0.8325 (ptp) cc_final: 0.7899 (pmm) REVERT: G 41 ARG cc_start: 0.8014 (mpt-90) cc_final: 0.6387 (tpt170) REVERT: G 53 MET cc_start: 0.8617 (ttp) cc_final: 0.8260 (ttt) REVERT: G 76 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.6410 (pm20) REVERT: G 182 ARG cc_start: 0.8838 (ttp-110) cc_final: 0.7219 (mpt180) REVERT: G 183 MET cc_start: 0.8874 (ttp) cc_final: 0.8562 (tmm) REVERT: G 207 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7721 (mm-40) REVERT: G 215 MET cc_start: 0.8022 (pmm) cc_final: 0.7433 (pmm) REVERT: G 252 GLU cc_start: 0.7065 (mp0) cc_final: 0.6122 (pm20) REVERT: G 266 ASN cc_start: 0.8218 (t0) cc_final: 0.7987 (t0) REVERT: G 319 SER cc_start: 0.8024 (t) cc_final: 0.7634 (m) REVERT: G 325 TYR cc_start: 0.7934 (t80) cc_final: 0.7571 (t80) outliers start: 60 outliers final: 48 residues processed: 195 average time/residue: 0.0788 time to fit residues: 22.7213 Evaluate side-chains 206 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 151 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET 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 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 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 A residue 294 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 153 LEU 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 B residue 313 GLU 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 154 VAL 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 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: 0.0370 chunk 63 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 116 optimal weight: 0.0050 chunk 83 optimal weight: 2.9990 overall best weight: 2.0078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 321 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.134607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.099721 restraints weight = 19644.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103054 restraints weight = 10710.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105285 restraints weight = 7235.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.106672 restraints weight = 5652.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.107496 restraints weight = 4855.426| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10548 Z= 0.128 Angle : 0.610 8.942 14232 Z= 0.324 Chirality : 0.045 0.172 1611 Planarity : 0.004 0.044 1796 Dihedral : 14.418 101.970 1606 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 5.58 % Allowed : 24.13 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.92 (0.21), residues: 1324 helix: -0.94 (0.27), residues: 348 sheet: -1.78 (0.35), residues: 196 loop : -2.57 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 209 TYR 0.047 0.002 TYR F 310 PHE 0.015 0.001 PHE A 105 TRP 0.013 0.002 TRP G 307 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00289 (10532) covalent geometry : angle 0.61007 (14232) hydrogen bonds : bond 0.02677 ( 259) hydrogen bonds : angle 5.08086 ( 711) Misc. bond : bond 0.00168 ( 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 218 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 160 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8419 (pttm) cc_final: 0.7989 (tppt) REVERT: A 76 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6677 (pm20) REVERT: A 95 GLN cc_start: 0.8726 (tp40) cc_final: 0.8406 (tp40) REVERT: A 107 ASP cc_start: 0.8200 (t0) cc_final: 0.7923 (t0) REVERT: A 167 GLU cc_start: 0.8999 (pp20) cc_final: 0.8571 (tm-30) REVERT: A 176 HIS cc_start: 0.8830 (m-70) cc_final: 0.7853 (m-70) REVERT: A 188 MET cc_start: 0.7967 (tpp) cc_final: 0.7558 (tpt) REVERT: A 197 LYS cc_start: 0.9148 (mtmt) cc_final: 0.8495 (tttt) REVERT: A 211 LYS cc_start: 0.8408 (mtmm) cc_final: 0.8041 (ptpp) REVERT: A 254 ASN cc_start: 0.8208 (m-40) cc_final: 0.7888 (m-40) REVERT: B 76 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.5652 (pm20) REVERT: B 125 ASP cc_start: 0.8551 (p0) cc_final: 0.8321 (p0) REVERT: B 183 MET cc_start: 0.8684 (ttp) cc_final: 0.8435 (ttt) REVERT: B 186 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: B 266 ASN cc_start: 0.8962 (t0) cc_final: 0.8640 (t0) REVERT: B 313 GLU cc_start: 0.1640 (OUTLIER) cc_final: 0.1421 (pp20) REVERT: F 40 MET cc_start: 0.6676 (ptm) cc_final: 0.6263 (ptp) REVERT: F 53 MET cc_start: 0.8878 (tmm) cc_final: 0.7939 (tmm) REVERT: F 76 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7126 (pm20) REVERT: F 183 MET cc_start: 0.8829 (tmm) cc_final: 0.8511 (tmm) REVERT: F 206 ASN cc_start: 0.9117 (t0) cc_final: 0.8874 (t0) REVERT: F 266 ASN cc_start: 0.8721 (t0) cc_final: 0.8446 (t0) REVERT: F 277 VAL cc_start: 0.8680 (t) cc_final: 0.8303 (p) REVERT: F 280 MET cc_start: 0.8465 (mtt) cc_final: 0.7941 (mtp) REVERT: F 290 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8672 (tm-30) REVERT: F 325 TYR cc_start: 0.8003 (t80) cc_final: 0.7582 (t80) REVERT: G 32 LYS cc_start: 0.9144 (mmmt) cc_final: 0.8869 (mmtm) REVERT: G 53 MET cc_start: 0.8588 (ttp) cc_final: 0.8301 (ttt) REVERT: G 76 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.6292 (pm20) REVERT: G 157 ASP cc_start: 0.7626 (t0) cc_final: 0.7255 (t70) REVERT: G 182 ARG cc_start: 0.8760 (ttp-110) cc_final: 0.7165 (mpt180) REVERT: G 183 MET cc_start: 0.8748 (ttp) cc_final: 0.8382 (tmm) REVERT: G 215 MET cc_start: 0.8160 (pmm) cc_final: 0.7686 (pmm) REVERT: G 252 GLU cc_start: 0.6844 (mp0) cc_final: 0.6025 (pm20) REVERT: G 319 SER cc_start: 0.8009 (t) cc_final: 0.7644 (m) REVERT: G 325 TYR cc_start: 0.7833 (t80) cc_final: 0.7472 (t80) outliers start: 58 outliers final: 43 residues processed: 200 average time/residue: 0.0756 time to fit residues: 23.0142 Evaluate side-chains 207 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 214 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 153 LEU 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 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 B residue 313 GLU 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 154 VAL 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 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: 0.9980 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 321 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN F 339 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 = 0.3748 r_free = 0.3748 target = 0.131828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.096771 restraints weight = 19909.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100040 restraints weight = 10923.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.102174 restraints weight = 7433.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103524 restraints weight = 5828.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104409 restraints weight = 5023.110| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10548 Z= 0.210 Angle : 0.669 10.478 14232 Z= 0.352 Chirality : 0.046 0.172 1611 Planarity : 0.004 0.044 1796 Dihedral : 14.642 105.432 1606 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 5.48 % Allowed : 24.71 % Favored : 69.81 % 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: -2.87 (0.21), residues: 1324 helix: -1.19 (0.28), residues: 324 sheet: -1.83 (0.34), residues: 196 loop : -2.33 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 235 TYR 0.045 0.003 TYR F 310 PHE 0.014 0.001 PHE B 105 TRP 0.013 0.002 TRP G 307 HIS 0.004 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00477 (10532) covalent geometry : angle 0.66918 (14232) hydrogen bonds : bond 0.03229 ( 259) hydrogen bonds : angle 5.27538 ( 711) Misc. bond : bond 0.00214 ( 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 208 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 151 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8467 (pttm) cc_final: 0.8092 (tppt) REVERT: A 76 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7154 (pm20) REVERT: A 95 GLN cc_start: 0.8724 (tp40) cc_final: 0.8212 (tp-100) REVERT: A 107 ASP cc_start: 0.8179 (t0) cc_final: 0.7905 (t0) REVERT: A 167 GLU cc_start: 0.8991 (pp20) cc_final: 0.8590 (tm-30) REVERT: A 176 HIS cc_start: 0.8856 (m-70) cc_final: 0.7832 (m170) REVERT: A 188 MET cc_start: 0.7920 (tpp) cc_final: 0.7508 (tpt) REVERT: A 197 LYS cc_start: 0.9184 (mtmt) cc_final: 0.8508 (tttt) REVERT: A 211 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8089 (ptpp) REVERT: A 254 ASN cc_start: 0.8226 (m-40) cc_final: 0.7929 (m-40) REVERT: B 76 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.6026 (pm20) REVERT: B 125 ASP cc_start: 0.8520 (p0) cc_final: 0.8292 (p0) REVERT: B 183 MET cc_start: 0.8714 (ttp) cc_final: 0.8459 (ttt) REVERT: B 186 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: B 266 ASN cc_start: 0.8831 (t0) cc_final: 0.8431 (t0) REVERT: F 40 MET cc_start: 0.6732 (ptm) cc_final: 0.6244 (ptp) REVERT: F 53 MET cc_start: 0.8883 (tmm) cc_final: 0.7959 (tmm) REVERT: F 76 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: F 183 MET cc_start: 0.8852 (tmm) cc_final: 0.8545 (tmm) REVERT: F 206 ASN cc_start: 0.9145 (t0) cc_final: 0.8900 (t0) REVERT: F 266 ASN cc_start: 0.8547 (t0) cc_final: 0.8239 (t0) REVERT: F 277 VAL cc_start: 0.8800 (t) cc_final: 0.8518 (p) REVERT: F 280 MET cc_start: 0.8518 (mtt) cc_final: 0.7993 (mtp) REVERT: F 290 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8689 (tm-30) REVERT: F 325 TYR cc_start: 0.8046 (t80) cc_final: 0.7614 (t80) REVERT: G 40 MET cc_start: 0.7726 (pmm) cc_final: 0.7407 (pmm) REVERT: G 53 MET cc_start: 0.8608 (ttp) cc_final: 0.8230 (ttt) REVERT: G 76 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.6465 (pm20) REVERT: G 157 ASP cc_start: 0.7722 (t0) cc_final: 0.7387 (t70) REVERT: G 182 ARG cc_start: 0.8850 (ttp-110) cc_final: 0.7227 (mpt180) REVERT: G 183 MET cc_start: 0.8877 (ttp) cc_final: 0.8605 (tmm) REVERT: G 207 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7784 (mm-40) REVERT: G 215 MET cc_start: 0.8092 (pmm) cc_final: 0.7592 (pmm) REVERT: G 252 GLU cc_start: 0.7005 (mp0) cc_final: 0.5571 (pp20) REVERT: G 266 ASN cc_start: 0.8250 (t0) cc_final: 0.8008 (t0) REVERT: G 319 SER cc_start: 0.8000 (t) cc_final: 0.7639 (m) REVERT: G 325 TYR cc_start: 0.7935 (t80) cc_final: 0.7633 (t80) outliers start: 57 outliers final: 48 residues processed: 196 average time/residue: 0.0790 time to fit residues: 23.2594 Evaluate side-chains 205 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 151 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET 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 137 GLN 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 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 58 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 153 LEU 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 177 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 154 VAL 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 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 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: 0.5980 chunk 109 optimal weight: 10.0000 chunk 88 optimal weight: 0.0030 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 102 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 321 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 GLN ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN G 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.135936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100755 restraints weight = 19747.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104147 restraints weight = 10753.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106409 restraints weight = 7267.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.107840 restraints weight = 5654.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.108630 restraints weight = 4852.932| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10548 Z= 0.115 Angle : 0.627 9.132 14232 Z= 0.332 Chirality : 0.045 0.169 1611 Planarity : 0.004 0.042 1796 Dihedral : 14.288 101.979 1606 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.81 % Allowed : 25.58 % Favored : 69.62 % 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: -2.82 (0.21), residues: 1324 helix: -0.89 (0.27), residues: 352 sheet: -1.59 (0.35), residues: 196 loop : -2.53 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 235 TYR 0.045 0.002 TYR F 310 PHE 0.017 0.001 PHE A 105 TRP 0.013 0.002 TRP G 307 HIS 0.003 0.001 HIS G 110 Details of bonding type rmsd covalent geometry : bond 0.00250 (10532) covalent geometry : angle 0.62665 (14232) hydrogen bonds : bond 0.02600 ( 259) hydrogen bonds : angle 4.99538 ( 711) Misc. bond : bond 0.00148 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1602.05 seconds wall clock time: 28 minutes 25.74 seconds (1705.74 seconds total)