Starting phenix.real_space_refine on Mon Jul 28 14:53:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8amd_15524/07_2025/8amd_15524.cif Found real_map, /net/cci-nas-00/data/ceres_data/8amd_15524/07_2025/8amd_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_15524/07_2025/8amd_15524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8amd_15524/07_2025/8amd_15524.map" model { file = "/net/cci-nas-00/data/ceres_data/8amd_15524/07_2025/8amd_15524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8amd_15524/07_2025/8amd_15524.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.40, per 1000 atoms: 0.62 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: 2.58 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.09 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: 2.73 Time building geometry restraints manager: 3.10 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: 0.370 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.040 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.170 ------------------------------------------------------------------------------- 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 : 5.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.002 TRP A 307 HIS 0.008 0.002 HIS F 329 PHE 0.020 0.002 PHE B 34 TYR 0.031 0.004 TYR G 116 ARG 0.004 0.001 ARG F 209 Details of bonding type rmsd hydrogen bonds : bond 0.23050 ( 259) hydrogen bonds : angle 7.71449 ( 711) covalent geometry : bond 0.00609 (10532) covalent geometry : angle 0.96269 (14232) 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 : 1.061 Fit side-chains 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: 0.7889 (t0) REVERT: A 167 GLU cc_start: 0.8904 (pp20) cc_final: 0.8253 (tm-30) REVERT: A 197 LYS cc_start: 0.9104 (mtmt) cc_final: 0.8595 (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: 0.8314 (p0) REVERT: B 157 ASP cc_start: 0.7836 (p0) cc_final: 0.7572 (p0) REVERT: B 183 MET cc_start: 0.8670 (ttp) cc_final: 0.8434 (ttt) REVERT: F 157 ASP cc_start: 0.8084 (t0) cc_final: 0.7616 (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: 0.6637 (tmt170) REVERT: G 197 LYS cc_start: 0.9201 (mtmt) cc_final: 0.8962 (ttmm) REVERT: G 205 ILE cc_start: 0.9193 (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: 0.2147 time to fit residues: 66.2090 Evaluate side-chains 158 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 112 optimal weight: 0.0070 chunk 100 optimal weight: 20.0000 chunk 55 optimal weight: 0.0770 chunk 34 optimal weight: 40.0000 chunk 67 optimal weight: 40.0000 chunk 53 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 overall best weight: 2.0162 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.134603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097271 restraints weight = 20425.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100994 restraints weight = 10379.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.103504 restraints weight = 6788.820| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10548 Z= 0.137 Angle : 0.662 9.548 14232 Z= 0.358 Chirality : 0.046 0.195 1611 Planarity : 0.004 0.045 1796 Dihedral : 14.715 91.780 1608 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 3.37 % Allowed : 19.52 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.18), residues: 1324 helix: -3.11 (0.21), residues: 344 sheet: -2.62 (0.33), residues: 192 loop : -3.00 (0.17), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 307 HIS 0.006 0.001 HIS B 329 PHE 0.014 0.001 PHE G 105 TYR 0.033 0.003 TYR B 78 ARG 0.007 0.000 ARG F 235 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 259) hydrogen bonds : angle 5.95591 ( 711) covalent geometry : bond 0.00296 (10532) covalent geometry : angle 0.66235 (14232) Misc. bond : bond 0.00157 ( 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 213 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.6819 (pm20) REVERT: A 95 GLN cc_start: 0.8746 (tp40) cc_final: 0.8306 (tp40) REVERT: A 107 ASP cc_start: 0.8269 (t0) cc_final: 0.7897 (t0) REVERT: A 167 GLU cc_start: 0.8981 (pp20) cc_final: 0.8388 (tm-30) REVERT: A 197 LYS cc_start: 0.9190 (mtmt) cc_final: 0.8663 (tttt) REVERT: A 254 ASN cc_start: 0.8487 (m-40) cc_final: 0.8254 (m-40) REVERT: B 18 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7002 (mm-30) REVERT: B 53 MET cc_start: 0.8258 (tmm) cc_final: 0.7928 (tmm) REVERT: B 76 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.6293 (pm20) REVERT: B 78 TYR cc_start: 0.8309 (p90) cc_final: 0.7875 (p90) REVERT: B 125 ASP cc_start: 0.8694 (p0) cc_final: 0.8400 (p0) REVERT: B 183 MET cc_start: 0.8695 (ttp) cc_final: 0.7911 (tmm) REVERT: B 186 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: B 266 ASN cc_start: 0.8796 (t0) cc_final: 0.8421 (t0) REVERT: F 40 MET cc_start: 0.6638 (ptm) cc_final: 0.6237 (ptp) REVERT: F 53 MET cc_start: 0.8951 (tmm) cc_final: 0.8022 (tmm) REVERT: F 76 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7063 (pm20) REVERT: F 183 MET cc_start: 0.8615 (ttp) cc_final: 0.8205 (tmm) REVERT: F 266 ASN cc_start: 0.8508 (t0) cc_final: 0.8214 (t0) REVERT: F 280 MET cc_start: 0.8696 (mtt) cc_final: 0.8378 (mpp) REVERT: F 325 TYR cc_start: 0.8024 (t80) cc_final: 0.7679 (t80) REVERT: G 40 MET cc_start: 0.8618 (ptp) cc_final: 0.8161 (pmm) REVERT: G 41 ARG cc_start: 0.8007 (mpt-90) cc_final: 0.6448 (tmt170) REVERT: G 76 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.6327 (pm20) REVERT: G 183 MET cc_start: 0.8845 (ttp) cc_final: 0.8439 (tmm) REVERT: G 197 LYS cc_start: 0.9179 (mtmt) cc_final: 0.8968 (ttmm) REVERT: G 207 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8522 (mm-40) REVERT: G 252 GLU cc_start: 0.7302 (mp0) cc_final: 0.6297 (pm20) outliers start: 35 outliers final: 23 residues processed: 200 average time/residue: 0.1972 time to fit residues: 57.2334 Evaluate side-chains 186 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain G residue 285 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 12 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 67 optimal weight: 40.0000 chunk 51 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 97 optimal weight: 0.4980 chunk 69 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 110 optimal weight: 0.0570 chunk 47 optimal weight: 0.0570 overall best weight: 2.9220 ------------------------------------------------------------------------------- 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 G 207 GLN G 243 GLN G 339 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.098381 restraints weight = 20084.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.101796 restraints weight = 10780.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104072 restraints weight = 7252.933| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10548 Z= 0.158 Angle : 0.638 8.807 14232 Z= 0.342 Chirality : 0.045 0.188 1611 Planarity : 0.004 0.042 1796 Dihedral : 14.634 96.941 1606 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 5.29 % Allowed : 19.62 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.19), residues: 1324 helix: -2.38 (0.23), residues: 368 sheet: -2.31 (0.33), residues: 192 loop : -2.98 (0.18), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 307 HIS 0.004 0.001 HIS B 329 PHE 0.014 0.001 PHE G 105 TYR 0.028 0.002 TYR B 78 ARG 0.003 0.000 ARG F 235 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 259) hydrogen bonds : angle 5.57022 ( 711) covalent geometry : bond 0.00356 (10532) covalent geometry : angle 0.63771 (14232) Misc. bond : bond 0.00180 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 169 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6823 (pm20) REVERT: A 78 TYR cc_start: 0.8076 (p90) cc_final: 0.7838 (p90) REVERT: A 95 GLN cc_start: 0.8635 (tp40) cc_final: 0.8266 (tp40) REVERT: A 107 ASP cc_start: 0.8219 (t0) cc_final: 0.7873 (t0) REVERT: A 167 GLU cc_start: 0.9006 (pp20) cc_final: 0.8517 (tm-30) REVERT: A 197 LYS cc_start: 0.9173 (mtmt) cc_final: 0.8666 (tttt) REVERT: A 254 ASN cc_start: 0.8331 (m-40) cc_final: 0.8054 (m-40) REVERT: A 281 TYR cc_start: 0.7591 (m-80) cc_final: 0.7390 (m-80) REVERT: A 325 TYR cc_start: 0.8439 (t80) cc_final: 0.7994 (t80) REVERT: B 18 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7064 (mm-30) REVERT: B 53 MET cc_start: 0.8181 (tmm) cc_final: 0.6979 (tmm) REVERT: B 76 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.6117 (pm20) REVERT: B 125 ASP cc_start: 0.8702 (p0) cc_final: 0.8431 (p0) REVERT: B 183 MET cc_start: 0.8692 (ttp) cc_final: 0.8323 (tmm) REVERT: B 186 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: B 266 ASN cc_start: 0.8764 (t0) cc_final: 0.8385 (t0) REVERT: B 280 MET cc_start: 0.8402 (mpp) cc_final: 0.8201 (mpp) REVERT: F 40 MET cc_start: 0.6575 (ptm) cc_final: 0.6206 (ptp) REVERT: F 53 MET cc_start: 0.8921 (tmm) cc_final: 0.8059 (tmm) REVERT: F 183 MET cc_start: 0.8638 (ttp) cc_final: 0.8260 (tmm) REVERT: F 266 ASN cc_start: 0.8658 (t0) cc_final: 0.8365 (t0) REVERT: F 277 VAL cc_start: 0.8720 (t) cc_final: 0.8427 (p) REVERT: F 280 MET cc_start: 0.8668 (mtt) cc_final: 0.8370 (mtt) REVERT: F 290 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8868 (tm-30) REVERT: F 325 TYR cc_start: 0.7998 (t80) cc_final: 0.7645 (t80) REVERT: G 40 MET cc_start: 0.8517 (ptp) cc_final: 0.7794 (pmm) REVERT: G 41 ARG cc_start: 0.8025 (mpt-90) cc_final: 0.6374 (tpt170) REVERT: G 76 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.6430 (pm20) REVERT: G 183 MET cc_start: 0.8831 (ttp) cc_final: 0.8421 (tmm) REVERT: G 197 LYS cc_start: 0.9183 (mtmt) cc_final: 0.8976 (ttmm) REVERT: G 207 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8396 (mm-40) REVERT: G 252 GLU cc_start: 0.7373 (mp0) cc_final: 0.6336 (pm20) REVERT: G 278 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7948 (mt-10) REVERT: G 325 TYR cc_start: 0.7769 (t80) cc_final: 0.7414 (t80) outliers start: 55 outliers final: 36 residues processed: 207 average time/residue: 0.1940 time to fit residues: 58.0261 Evaluate side-chains 198 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 113 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 154 VAL 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 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 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 277 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 72 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 67 optimal weight: 40.0000 chunk 86 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 196 ASN F 241 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.130754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.094318 restraints weight = 20587.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.097880 restraints weight = 10613.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100230 restraints weight = 6994.515| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10548 Z= 0.255 Angle : 0.701 8.931 14232 Z= 0.371 Chirality : 0.047 0.182 1611 Planarity : 0.004 0.048 1796 Dihedral : 14.994 104.505 1606 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 5.77 % Allowed : 21.15 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.19), residues: 1324 helix: -2.16 (0.24), residues: 348 sheet: -2.35 (0.33), residues: 196 loop : -2.75 (0.18), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 307 HIS 0.006 0.002 HIS B 329 PHE 0.016 0.002 PHE G 105 TYR 0.035 0.003 TYR B 78 ARG 0.004 0.000 ARG G 235 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 259) hydrogen bonds : angle 5.66831 ( 711) covalent geometry : bond 0.00576 (10532) covalent geometry : angle 0.70125 (14232) Misc. bond : bond 0.00240 ( 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 220 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 160 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: A 95 GLN cc_start: 0.8628 (tp40) cc_final: 0.8386 (tp40) REVERT: A 107 ASP cc_start: 0.8224 (t0) cc_final: 0.7946 (t0) REVERT: A 167 GLU cc_start: 0.8940 (pp20) cc_final: 0.8505 (tm-30) REVERT: A 197 LYS cc_start: 0.9218 (mtmt) cc_final: 0.8676 (tttt) REVERT: A 254 ASN cc_start: 0.8333 (m-40) cc_final: 0.8031 (m-40) REVERT: A 281 TYR cc_start: 0.7675 (m-80) cc_final: 0.7378 (m-80) REVERT: A 325 TYR cc_start: 0.8467 (t80) cc_final: 0.7999 (t80) REVERT: B 18 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7143 (mm-30) REVERT: B 53 MET cc_start: 0.8322 (tmm) cc_final: 0.7021 (tmm) REVERT: B 76 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.6181 (pm20) REVERT: B 125 ASP cc_start: 0.8597 (p0) cc_final: 0.8327 (p0) REVERT: B 183 MET cc_start: 0.8698 (ttp) cc_final: 0.8422 (tmm) REVERT: B 186 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7797 (tm-30) REVERT: B 266 ASN cc_start: 0.8852 (t0) cc_final: 0.8520 (t0) REVERT: B 280 MET cc_start: 0.8441 (mpp) cc_final: 0.8232 (mpp) REVERT: F 40 MET cc_start: 0.6788 (ptm) cc_final: 0.6305 (ptp) REVERT: F 53 MET cc_start: 0.8946 (tmm) cc_final: 0.8042 (tmm) REVERT: F 76 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: F 157 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7552 (m-30) REVERT: F 266 ASN cc_start: 0.8551 (t0) cc_final: 0.8281 (t0) REVERT: F 277 VAL cc_start: 0.8871 (t) cc_final: 0.8624 (p) REVERT: F 280 MET cc_start: 0.8574 (mtt) cc_final: 0.8310 (mtt) REVERT: F 290 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8878 (tm-30) REVERT: F 325 TYR cc_start: 0.7911 (t80) cc_final: 0.7631 (t80) REVERT: G 40 MET cc_start: 0.8414 (ptp) cc_final: 0.7980 (pmm) REVERT: G 41 ARG cc_start: 0.8062 (mpt-90) cc_final: 0.6450 (tpt170) REVERT: G 76 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.6664 (pm20) REVERT: G 183 MET cc_start: 0.8876 (ttp) cc_final: 0.8558 (tmm) REVERT: G 207 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8672 (mm-40) REVERT: G 252 GLU cc_start: 0.7421 (mp0) cc_final: 0.5605 (pp20) REVERT: G 325 TYR cc_start: 0.7893 (t80) cc_final: 0.7499 (t80) outliers start: 60 outliers final: 42 residues processed: 203 average time/residue: 0.2097 time to fit residues: 62.3297 Evaluate side-chains 204 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 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 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 205 ILE 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 83 optimal weight: 9.9990 chunk 131 optimal weight: 0.0980 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 90 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 115 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.133808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.098832 restraints weight = 19765.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.102128 restraints weight = 10844.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104358 restraints weight = 7377.425| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10548 Z= 0.131 Angle : 0.605 8.685 14232 Z= 0.322 Chirality : 0.045 0.178 1611 Planarity : 0.004 0.052 1796 Dihedral : 14.612 100.578 1606 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 5.67 % Allowed : 21.73 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.20), residues: 1324 helix: -1.87 (0.26), residues: 344 sheet: -2.06 (0.34), residues: 196 loop : -2.64 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 307 HIS 0.003 0.001 HIS B 329 PHE 0.012 0.001 PHE G 105 TYR 0.036 0.003 TYR F 310 ARG 0.002 0.000 ARG G 235 Details of bonding type rmsd hydrogen bonds : bond 0.02933 ( 259) hydrogen bonds : angle 5.32224 ( 711) covalent geometry : bond 0.00291 (10532) covalent geometry : angle 0.60482 (14232) Misc. bond : bond 0.00167 ( 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 224 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 165 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6819 (pm20) REVERT: A 95 GLN cc_start: 0.8637 (tp40) cc_final: 0.8167 (tp40) REVERT: A 107 ASP cc_start: 0.8201 (t0) cc_final: 0.7844 (t0) REVERT: A 167 GLU cc_start: 0.9054 (pp20) cc_final: 0.8529 (tm-30) REVERT: A 197 LYS cc_start: 0.9147 (mtmt) cc_final: 0.8586 (tttt) REVERT: A 254 ASN cc_start: 0.8274 (m-40) cc_final: 0.7941 (m-40) REVERT: A 281 TYR cc_start: 0.7538 (m-80) cc_final: 0.7238 (m-80) REVERT: A 325 TYR cc_start: 0.8455 (t80) cc_final: 0.8051 (t80) REVERT: B 18 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7161 (mm-30) REVERT: B 76 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.5883 (pm20) REVERT: B 125 ASP cc_start: 0.8638 (p0) cc_final: 0.8392 (p0) REVERT: B 183 MET cc_start: 0.8733 (ttp) cc_final: 0.8442 (tmm) REVERT: B 186 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: B 266 ASN cc_start: 0.8900 (t0) cc_final: 0.8488 (t0) REVERT: B 280 MET cc_start: 0.8429 (mpp) cc_final: 0.8169 (mpp) REVERT: F 40 MET cc_start: 0.6668 (ptm) cc_final: 0.6241 (ptp) REVERT: F 53 MET cc_start: 0.8878 (tmm) cc_final: 0.7919 (tmm) REVERT: F 76 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: F 183 MET cc_start: 0.8848 (tmm) cc_final: 0.8213 (tmm) REVERT: F 266 ASN cc_start: 0.8641 (t0) cc_final: 0.8320 (t0) REVERT: F 277 VAL cc_start: 0.8665 (t) cc_final: 0.8308 (p) REVERT: F 280 MET cc_start: 0.8544 (mtt) cc_final: 0.8071 (mtp) REVERT: F 290 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8828 (tm-30) REVERT: F 325 TYR cc_start: 0.7997 (t80) cc_final: 0.7627 (t80) REVERT: G 40 MET cc_start: 0.8394 (ptp) cc_final: 0.7927 (pmm) REVERT: G 41 ARG cc_start: 0.7914 (mpt-90) cc_final: 0.6274 (tpt170) REVERT: G 53 MET cc_start: 0.8684 (ttp) cc_final: 0.8338 (ttt) REVERT: G 76 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.6304 (pm20) REVERT: G 183 MET cc_start: 0.8839 (ttp) cc_final: 0.8496 (tmm) REVERT: G 207 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8266 (mm-40) REVERT: G 252 GLU cc_start: 0.7059 (mp0) cc_final: 0.6175 (pm20) REVERT: G 319 SER cc_start: 0.8274 (t) cc_final: 0.7903 (m) REVERT: G 325 TYR cc_start: 0.7774 (t80) cc_final: 0.7431 (t80) outliers start: 59 outliers final: 39 residues processed: 206 average time/residue: 0.1898 time to fit residues: 57.7988 Evaluate side-chains 201 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 153 LEU 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 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 163 VAL 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 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 264 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 56 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 79 optimal weight: 0.0980 chunk 47 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 99 optimal weight: 40.0000 chunk 25 optimal weight: 0.7980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN F 254 ASN G 207 GLN G 243 GLN G 254 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.133610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.098615 restraints weight = 19912.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.102024 restraints weight = 10698.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104246 restraints weight = 7182.735| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10548 Z= 0.144 Angle : 0.605 8.749 14232 Z= 0.320 Chirality : 0.045 0.177 1611 Planarity : 0.004 0.049 1796 Dihedral : 14.549 100.230 1606 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 6.15 % Allowed : 21.63 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.20), residues: 1324 helix: -1.33 (0.27), residues: 344 sheet: -1.92 (0.34), residues: 196 loop : -2.66 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 307 HIS 0.004 0.001 HIS B 329 PHE 0.013 0.001 PHE G 105 TYR 0.032 0.002 TYR B 78 ARG 0.002 0.000 ARG F 235 Details of bonding type rmsd hydrogen bonds : bond 0.02902 ( 259) hydrogen bonds : angle 5.24525 ( 711) covalent geometry : bond 0.00324 (10532) covalent geometry : angle 0.60459 (14232) Misc. bond : bond 0.00178 ( 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 221 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 157 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6844 (pm20) REVERT: A 95 GLN cc_start: 0.8650 (tp40) cc_final: 0.8199 (tp40) REVERT: A 107 ASP cc_start: 0.8229 (t0) cc_final: 0.7868 (t0) REVERT: A 167 GLU cc_start: 0.9033 (pp20) cc_final: 0.8532 (tm-30) REVERT: A 197 LYS cc_start: 0.9135 (mtmt) cc_final: 0.8484 (tttt) REVERT: A 254 ASN cc_start: 0.8300 (m-40) cc_final: 0.7968 (m-40) REVERT: A 281 TYR cc_start: 0.7610 (m-80) cc_final: 0.7360 (m-80) REVERT: A 325 TYR cc_start: 0.8461 (t80) cc_final: 0.8066 (t80) REVERT: B 18 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7220 (mm-30) REVERT: B 76 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.5993 (pm20) REVERT: B 125 ASP cc_start: 0.8549 (p0) cc_final: 0.8302 (p0) REVERT: B 183 MET cc_start: 0.8683 (ttp) cc_final: 0.8426 (ttt) REVERT: B 186 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: B 266 ASN cc_start: 0.8897 (t0) cc_final: 0.8481 (t0) REVERT: B 280 MET cc_start: 0.8444 (mpp) cc_final: 0.8190 (mpp) REVERT: F 40 MET cc_start: 0.6800 (ptm) cc_final: 0.6372 (ptp) REVERT: F 53 MET cc_start: 0.8908 (tmm) cc_final: 0.7984 (tmm) REVERT: F 76 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7383 (pm20) REVERT: F 183 MET cc_start: 0.8866 (tmm) cc_final: 0.8264 (tmm) REVERT: F 266 ASN cc_start: 0.8669 (t0) cc_final: 0.8404 (t0) REVERT: F 277 VAL cc_start: 0.8770 (t) cc_final: 0.8424 (p) REVERT: F 280 MET cc_start: 0.8478 (mtt) cc_final: 0.8145 (mtm) REVERT: F 290 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8688 (tm-30) REVERT: F 325 TYR cc_start: 0.7975 (t80) cc_final: 0.7602 (t80) REVERT: G 40 MET cc_start: 0.8396 (ptp) cc_final: 0.7988 (pmm) REVERT: G 41 ARG cc_start: 0.8009 (mpt-90) cc_final: 0.6338 (tpt170) REVERT: G 53 MET cc_start: 0.8678 (ttp) cc_final: 0.8356 (ttt) REVERT: G 76 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.6436 (pm20) REVERT: G 183 MET cc_start: 0.8779 (ttp) cc_final: 0.8545 (tmm) REVERT: G 207 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7803 (mm-40) REVERT: G 252 GLU cc_start: 0.7055 (mp0) cc_final: 0.6117 (pm20) REVERT: G 319 SER cc_start: 0.8068 (t) cc_final: 0.7689 (m) REVERT: G 325 TYR cc_start: 0.7657 (t80) cc_final: 0.7291 (t80) outliers start: 64 outliers final: 45 residues processed: 205 average time/residue: 0.1824 time to fit residues: 55.7868 Evaluate side-chains 203 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 152 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 205 ILE 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 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 110 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN G 137 GLN 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 = 0.3734 r_free = 0.3734 target = 0.130883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.096169 restraints weight = 20311.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.099364 restraints weight = 11127.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.101531 restraints weight = 7561.925| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10548 Z= 0.248 Angle : 0.676 9.003 14232 Z= 0.356 Chirality : 0.047 0.177 1611 Planarity : 0.004 0.051 1796 Dihedral : 14.848 105.186 1606 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 5.87 % Allowed : 22.69 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.20), residues: 1324 helix: -1.48 (0.27), residues: 324 sheet: -2.04 (0.34), residues: 196 loop : -2.45 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 307 HIS 0.005 0.001 HIS B 329 PHE 0.014 0.002 PHE B 105 TYR 0.026 0.003 TYR B 78 ARG 0.004 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 259) hydrogen bonds : angle 5.42572 ( 711) covalent geometry : bond 0.00561 (10532) covalent geometry : angle 0.67596 (14232) Misc. bond : bond 0.00226 ( 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 215 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 154 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7334 (pm20) REVERT: A 95 GLN cc_start: 0.8623 (tp40) cc_final: 0.8295 (tp40) REVERT: A 107 ASP cc_start: 0.8209 (t0) cc_final: 0.7904 (t0) REVERT: A 167 GLU cc_start: 0.9023 (pp20) cc_final: 0.8536 (tm-30) REVERT: A 176 HIS cc_start: 0.8818 (m-70) cc_final: 0.7869 (m170) REVERT: A 197 LYS cc_start: 0.9181 (mtmt) cc_final: 0.8512 (tttt) REVERT: A 254 ASN cc_start: 0.8313 (m-40) cc_final: 0.7999 (m-40) REVERT: A 281 TYR cc_start: 0.7650 (m-80) cc_final: 0.7383 (m-80) REVERT: A 325 TYR cc_start: 0.8476 (t80) cc_final: 0.8059 (t80) REVERT: B 18 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7246 (mm-30) REVERT: B 76 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.6121 (pm20) REVERT: B 125 ASP cc_start: 0.8523 (p0) cc_final: 0.8267 (p0) REVERT: B 183 MET cc_start: 0.8748 (ttp) cc_final: 0.8540 (tmm) REVERT: B 186 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: B 266 ASN cc_start: 0.8886 (t0) cc_final: 0.8547 (t0) REVERT: B 280 MET cc_start: 0.8412 (mpp) cc_final: 0.8150 (mpp) REVERT: F 40 MET cc_start: 0.6859 (ptm) cc_final: 0.6411 (ptp) REVERT: F 53 MET cc_start: 0.8951 (tmm) cc_final: 0.8028 (tmm) REVERT: F 76 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: F 266 ASN cc_start: 0.8633 (t0) cc_final: 0.8357 (t0) REVERT: F 277 VAL cc_start: 0.8861 (t) cc_final: 0.8609 (p) REVERT: F 280 MET cc_start: 0.8482 (mtt) cc_final: 0.8186 (mtt) REVERT: F 290 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8702 (tm-30) REVERT: F 325 TYR cc_start: 0.8009 (t80) cc_final: 0.7606 (t80) REVERT: G 40 MET cc_start: 0.8396 (ptp) cc_final: 0.8031 (pmm) REVERT: G 41 ARG cc_start: 0.8101 (mpt-90) cc_final: 0.6461 (tpt170) REVERT: G 53 MET cc_start: 0.8675 (ttp) cc_final: 0.8290 (ttt) REVERT: G 76 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.6622 (pm20) REVERT: G 183 MET cc_start: 0.8858 (ttp) cc_final: 0.8591 (tmm) REVERT: G 252 GLU cc_start: 0.7103 (mp0) cc_final: 0.6156 (pm20) REVERT: G 319 SER cc_start: 0.8248 (t) cc_final: 0.7843 (m) REVERT: G 325 TYR cc_start: 0.7798 (t80) cc_final: 0.7507 (t80) outliers start: 61 outliers final: 49 residues processed: 200 average time/residue: 0.1859 time to fit residues: 55.4662 Evaluate side-chains 203 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 205 ILE 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 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 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 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 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 34 optimal weight: 40.0000 chunk 127 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN ** F 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN G 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.131889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.095455 restraints weight = 20544.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.099140 restraints weight = 10515.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101550 restraints weight = 6877.785| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10548 Z= 0.172 Angle : 0.629 8.903 14232 Z= 0.333 Chirality : 0.045 0.174 1611 Planarity : 0.004 0.051 1796 Dihedral : 14.694 104.061 1606 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 6.06 % Allowed : 23.56 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.21), residues: 1324 helix: -1.33 (0.28), residues: 324 sheet: -1.92 (0.34), residues: 196 loop : -2.39 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 307 HIS 0.004 0.001 HIS B 329 PHE 0.012 0.001 PHE G 105 TYR 0.038 0.003 TYR F 310 ARG 0.003 0.000 ARG G 235 Details of bonding type rmsd hydrogen bonds : bond 0.03011 ( 259) hydrogen bonds : angle 5.28661 ( 711) covalent geometry : bond 0.00389 (10532) covalent geometry : angle 0.62947 (14232) Misc. bond : bond 0.00196 ( 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 223 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 160 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: A 95 GLN cc_start: 0.8639 (tp40) cc_final: 0.8195 (tp40) REVERT: A 107 ASP cc_start: 0.8208 (t0) cc_final: 0.7924 (t0) REVERT: A 167 GLU cc_start: 0.9001 (pp20) cc_final: 0.8528 (tm-30) REVERT: A 176 HIS cc_start: 0.8850 (m-70) cc_final: 0.7875 (m-70) REVERT: A 197 LYS cc_start: 0.9164 (mtmt) cc_final: 0.8494 (tttt) REVERT: A 254 ASN cc_start: 0.8293 (m-40) cc_final: 0.7970 (m-40) REVERT: A 281 TYR cc_start: 0.7609 (m-80) cc_final: 0.7354 (m-80) REVERT: A 325 TYR cc_start: 0.8472 (t80) cc_final: 0.8058 (t80) REVERT: B 18 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7217 (mm-30) REVERT: B 76 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.5965 (pm20) REVERT: B 125 ASP cc_start: 0.8557 (p0) cc_final: 0.8309 (p0) REVERT: B 183 MET cc_start: 0.8709 (ttp) cc_final: 0.8449 (ttt) REVERT: B 186 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: B 266 ASN cc_start: 0.8885 (t0) cc_final: 0.8509 (t0) REVERT: B 280 MET cc_start: 0.8479 (mpp) cc_final: 0.8220 (mpp) REVERT: B 313 GLU cc_start: 0.1718 (OUTLIER) cc_final: 0.1471 (pp20) REVERT: F 40 MET cc_start: 0.6791 (ptm) cc_final: 0.6347 (ptp) REVERT: F 53 MET cc_start: 0.8908 (tmm) cc_final: 0.8000 (tmm) REVERT: F 76 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7579 (pm20) REVERT: F 266 ASN cc_start: 0.8593 (t0) cc_final: 0.8305 (t0) REVERT: F 277 VAL cc_start: 0.8789 (t) cc_final: 0.8519 (p) REVERT: F 280 MET cc_start: 0.8477 (mtt) cc_final: 0.7966 (mtp) REVERT: F 290 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8695 (tm-30) REVERT: F 325 TYR cc_start: 0.8015 (t80) cc_final: 0.7599 (t80) REVERT: G 40 MET cc_start: 0.8395 (ptp) cc_final: 0.8177 (pmm) REVERT: G 41 ARG cc_start: 0.7902 (mpt-90) cc_final: 0.6245 (tpt170) REVERT: G 53 MET cc_start: 0.8625 (ttp) cc_final: 0.8282 (ttt) REVERT: G 76 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.6510 (pm20) REVERT: G 182 ARG cc_start: 0.8848 (ttp-110) cc_final: 0.7256 (mpt180) REVERT: G 183 MET cc_start: 0.8835 (ttp) cc_final: 0.8555 (tmm) REVERT: G 207 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7930 (mm-40) REVERT: G 252 GLU cc_start: 0.6882 (mp0) cc_final: 0.6010 (pm20) REVERT: G 319 SER cc_start: 0.8064 (t) cc_final: 0.7656 (m) REVERT: G 325 TYR cc_start: 0.7787 (t80) cc_final: 0.7508 (t80) outliers start: 63 outliers final: 51 residues processed: 208 average time/residue: 0.1857 time to fit residues: 56.9463 Evaluate side-chains 212 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 154 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 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 205 ILE 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 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 B residue 313 GLU 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 163 VAL Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 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 48 optimal weight: 0.5980 chunk 88 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 40.0000 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 0.0970 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 F 339 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 = 0.134354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.099356 restraints weight = 19884.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.102703 restraints weight = 10903.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.104926 restraints weight = 7397.263| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2648 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= 0.123 Angle : 0.614 8.693 14232 Z= 0.325 Chirality : 0.045 0.172 1611 Planarity : 0.004 0.051 1796 Dihedral : 14.488 102.315 1606 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 5.58 % Allowed : 24.90 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.21), residues: 1324 helix: -1.12 (0.28), residues: 320 sheet: -1.76 (0.35), residues: 196 loop : -2.38 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 307 HIS 0.003 0.001 HIS B 329 PHE 0.015 0.001 PHE A 105 TYR 0.032 0.002 TYR B 78 ARG 0.003 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.02694 ( 259) hydrogen bonds : angle 5.11426 ( 711) covalent geometry : bond 0.00273 (10532) covalent geometry : angle 0.61353 (14232) Misc. bond : bond 0.00166 ( 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 222 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 164 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8322 (pttm) cc_final: 0.8090 (tppt) REVERT: A 76 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.6902 (pm20) REVERT: A 95 GLN cc_start: 0.8654 (tp40) cc_final: 0.8219 (tp40) REVERT: A 107 ASP cc_start: 0.8172 (t0) cc_final: 0.7915 (t0) REVERT: A 167 GLU cc_start: 0.9002 (pp20) cc_final: 0.8545 (tm-30) REVERT: A 176 HIS cc_start: 0.8816 (m-70) cc_final: 0.7865 (m-70) REVERT: A 197 LYS cc_start: 0.9139 (mtmt) cc_final: 0.8497 (tttt) REVERT: A 254 ASN cc_start: 0.8296 (m-40) cc_final: 0.7946 (m-40) REVERT: A 281 TYR cc_start: 0.7609 (m-80) cc_final: 0.7353 (m-80) REVERT: A 325 TYR cc_start: 0.8447 (t80) cc_final: 0.8042 (t80) REVERT: B 76 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.5920 (pm20) REVERT: B 125 ASP cc_start: 0.8519 (p0) cc_final: 0.8286 (p0) REVERT: B 183 MET cc_start: 0.8676 (ttp) cc_final: 0.8402 (ttt) REVERT: B 186 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: B 266 ASN cc_start: 0.8949 (t0) cc_final: 0.8660 (t0) REVERT: B 280 MET cc_start: 0.8453 (mpp) cc_final: 0.8228 (mpp) REVERT: F 40 MET cc_start: 0.6784 (ptm) cc_final: 0.6373 (ptp) REVERT: F 53 MET cc_start: 0.8912 (tmm) cc_final: 0.7986 (tmm) REVERT: F 183 MET cc_start: 0.8799 (tmm) cc_final: 0.8124 (tmm) REVERT: F 186 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8287 (tm-30) REVERT: F 206 ASN cc_start: 0.9152 (t0) cc_final: 0.8919 (t0) REVERT: F 266 ASN cc_start: 0.8666 (t0) cc_final: 0.8412 (t0) REVERT: F 277 VAL cc_start: 0.8760 (t) cc_final: 0.8424 (p) REVERT: F 280 MET cc_start: 0.8431 (mtt) cc_final: 0.7917 (mtp) REVERT: F 290 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8680 (tm-30) REVERT: F 325 TYR cc_start: 0.7985 (t80) cc_final: 0.7570 (t80) REVERT: G 53 MET cc_start: 0.8572 (ttp) cc_final: 0.8281 (ttt) REVERT: G 76 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.6444 (pm20) REVERT: G 157 ASP cc_start: 0.7836 (t0) cc_final: 0.7525 (t70) REVERT: G 182 ARG cc_start: 0.8798 (ttp-110) cc_final: 0.7222 (mpt180) REVERT: G 183 MET cc_start: 0.8704 (ttp) cc_final: 0.8387 (tmm) REVERT: G 252 GLU cc_start: 0.6814 (mp0) cc_final: 0.6022 (pm20) REVERT: G 319 SER cc_start: 0.8002 (t) cc_final: 0.7622 (m) REVERT: G 325 TYR cc_start: 0.7797 (t80) cc_final: 0.7503 (t80) outliers start: 58 outliers final: 46 residues processed: 209 average time/residue: 0.1895 time to fit residues: 58.5536 Evaluate side-chains 209 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 159 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 205 ILE 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 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 163 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 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 100 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 117 optimal weight: 0.0370 chunk 81 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 43 optimal weight: 0.3980 chunk 94 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 overall best weight: 2.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.134275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.099042 restraints weight = 19941.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.102406 restraints weight = 10877.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.104637 restraints weight = 7354.546| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10548 Z= 0.136 Angle : 0.624 8.889 14232 Z= 0.328 Chirality : 0.045 0.171 1611 Planarity : 0.004 0.041 1796 Dihedral : 14.409 102.170 1606 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 5.19 % Allowed : 25.38 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.21), residues: 1324 helix: -0.88 (0.28), residues: 344 sheet: -1.69 (0.35), residues: 196 loop : -2.51 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 307 HIS 0.003 0.001 HIS B 329 PHE 0.014 0.001 PHE A 105 TYR 0.033 0.002 TYR B 78 ARG 0.002 0.000 ARG G 235 Details of bonding type rmsd hydrogen bonds : bond 0.02744 ( 259) hydrogen bonds : angle 5.04825 ( 711) covalent geometry : bond 0.00307 (10532) covalent geometry : angle 0.62417 (14232) Misc. bond : bond 0.00171 ( 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 213 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 159 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8356 (pttm) cc_final: 0.8060 (tppt) REVERT: A 76 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6770 (pm20) REVERT: A 95 GLN cc_start: 0.8654 (tp40) cc_final: 0.8220 (tp40) REVERT: A 107 ASP cc_start: 0.8223 (t0) cc_final: 0.7966 (t0) REVERT: A 167 GLU cc_start: 0.9001 (pp20) cc_final: 0.8562 (tm-30) REVERT: A 176 HIS cc_start: 0.8822 (m-70) cc_final: 0.7822 (m170) REVERT: A 197 LYS cc_start: 0.9148 (mtmt) cc_final: 0.8492 (tttt) REVERT: A 254 ASN cc_start: 0.8277 (m-40) cc_final: 0.7929 (m-40) REVERT: A 281 TYR cc_start: 0.7605 (m-80) cc_final: 0.7340 (m-80) REVERT: A 325 TYR cc_start: 0.8399 (t80) cc_final: 0.7987 (t80) REVERT: B 76 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.5923 (pm20) REVERT: B 125 ASP cc_start: 0.8511 (p0) cc_final: 0.8279 (p0) REVERT: B 183 MET cc_start: 0.8669 (ttp) cc_final: 0.8409 (ttt) REVERT: B 186 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: B 266 ASN cc_start: 0.8933 (t0) cc_final: 0.8610 (t0) REVERT: B 280 MET cc_start: 0.8396 (mpp) cc_final: 0.8182 (mpp) REVERT: B 336 ILE cc_start: 0.7864 (mt) cc_final: 0.7305 (mp) REVERT: F 40 MET cc_start: 0.6772 (ptm) cc_final: 0.6364 (ptp) REVERT: F 53 MET cc_start: 0.8908 (tmm) cc_final: 0.7986 (tmm) REVERT: F 183 MET cc_start: 0.8810 (tmm) cc_final: 0.8235 (tmm) REVERT: F 206 ASN cc_start: 0.9124 (t0) cc_final: 0.8878 (t0) REVERT: F 266 ASN cc_start: 0.8716 (t0) cc_final: 0.8500 (t0) REVERT: F 277 VAL cc_start: 0.8759 (t) cc_final: 0.8411 (p) REVERT: F 280 MET cc_start: 0.8454 (mtt) cc_final: 0.7950 (mtp) REVERT: F 290 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8675 (tm-30) REVERT: F 325 TYR cc_start: 0.8044 (t80) cc_final: 0.7620 (t80) REVERT: G 40 MET cc_start: 0.7798 (pmm) cc_final: 0.7517 (pmm) REVERT: G 53 MET cc_start: 0.8589 (ttp) cc_final: 0.8302 (ttt) REVERT: G 76 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.6432 (pm20) REVERT: G 157 ASP cc_start: 0.7844 (t0) cc_final: 0.7520 (t70) REVERT: G 182 ARG cc_start: 0.8793 (ttp-110) cc_final: 0.7229 (mpt180) REVERT: G 183 MET cc_start: 0.8715 (ttp) cc_final: 0.8439 (tmm) REVERT: G 207 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8037 (mm-40) REVERT: G 252 GLU cc_start: 0.6804 (mp0) cc_final: 0.6013 (pm20) REVERT: G 319 SER cc_start: 0.8005 (t) cc_final: 0.7621 (m) REVERT: G 325 TYR cc_start: 0.7840 (t80) cc_final: 0.7532 (t80) outliers start: 54 outliers final: 45 residues processed: 201 average time/residue: 0.1886 time to fit residues: 55.9537 Evaluate side-chains 208 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 ILE 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 106 ILE 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 163 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 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 124 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 22 optimal weight: 0.0270 chunk 31 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 0.0070 chunk 14 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 overall best weight: 1.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN ** G 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.134148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099228 restraints weight = 19734.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.102516 restraints weight = 10811.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.104733 restraints weight = 7365.460| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.213 10548 Z= 0.247 Angle : 1.105 59.195 14232 Z= 0.670 Chirality : 0.050 0.668 1611 Planarity : 0.004 0.041 1796 Dihedral : 14.419 102.180 1606 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 5.48 % Allowed : 25.29 % Favored : 69.23 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.21), residues: 1324 helix: -0.86 (0.28), residues: 344 sheet: -1.68 (0.35), residues: 196 loop : -2.50 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 307 HIS 0.003 0.001 HIS B 329 PHE 0.013 0.001 PHE A 105 TYR 0.031 0.002 TYR B 78 ARG 0.002 0.000 ARG G 235 Details of bonding type rmsd hydrogen bonds : bond 0.02727 ( 259) hydrogen bonds : angle 5.04962 ( 711) covalent geometry : bond 0.00521 (10532) covalent geometry : angle 1.10473 (14232) Misc. bond : bond 0.00166 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3249.79 seconds wall clock time: 57 minutes 10.22 seconds (3430.22 seconds total)