Starting phenix.real_space_refine on Thu Jul 2 21:47:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8amf_15525/07_2026/8amf_15525.cif Found real_map, /net/cci-nas-00/data/ceres_data/8amf_15525/07_2026/8amf_15525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8amf_15525/07_2026/8amf_15525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8amf_15525/07_2026/8amf_15525.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8amf_15525/07_2026/8amf_15525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8amf_15525/07_2026/8amf_15525.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 32 5.16 5 C 6520 2.51 5 N 1798 2.21 5 O 2126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10507 Number of models: 1 Model: "" Number of chains: 10 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: "C" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 207 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} 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: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AGS:plan-1': 1, 'AGS:plan-2': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AGS:plan-1': 1, 'AGS:plan-2': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AGS:plan-1': 1, 'AGS:plan-2': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AGS:plan-1': 1, 'AGS:plan-2': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 2.44, per 1000 atoms: 0.23 Number of scatterers: 10507 At special positions: 0 Unit cell: (126.48, 119.04, 141.36, 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 31 15.00 O 2126 8.00 N 1798 7.00 C 6520 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 375.1 milliseconds 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 15 sheets defined 37.4% alpha, 25.0% beta 5 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 21 through 34 removed outlier: 3.898A pdb=" N ASP A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 49 removed outlier: 5.518A pdb=" N ALA A 46 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLU A 47 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A 48 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 49 " --> pdb=" O ALA A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 49' Processing helix chain 'A' and resid 85 through 98 removed outlier: 3.724A pdb=" N ALA A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 120 Processing helix chain 'A' and resid 134 through 148 removed outlier: 3.774A pdb=" N GLY A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.532A pdb=" N ILE A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 164 through 169' Processing helix chain 'A' and resid 179 through 196 removed outlier: 3.628A pdb=" N MET A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ALA A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 4.182A pdb=" N PHE A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.698A pdb=" N GLN A 250 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.813A pdb=" N LEU A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 327 removed outlier: 3.746A pdb=" N ALA A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.673A pdb=" N ILE A 336 " --> pdb=" O PHE A 333 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP A 337 " --> pdb=" O ASP A 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 333 through 337' Processing helix chain 'B' and resid 21 through 34 removed outlier: 3.804A pdb=" N ASP B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.761A pdb=" N LYS B 49 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 84 through 98 removed outlier: 3.913A pdb=" N ALA B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 134 through 148 removed outlier: 3.989A pdb=" N SER B 148 " --> pdb=" O LYS B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.853A pdb=" N ASP B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 198 removed outlier: 3.825A pdb=" N LYS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALA B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 196 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 removed outlier: 3.920A pdb=" N PHE B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.889A pdb=" N LEU B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 329 through 336 removed outlier: 4.008A pdb=" N ILE B 332 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP B 334 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 335 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 336 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 34 removed outlier: 3.896A pdb=" N ASP F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP F 33 " --> pdb=" O LEU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 49 removed outlier: 3.756A pdb=" N LYS F 49 " --> pdb=" O ALA F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 64 removed outlier: 3.716A pdb=" N ASP F 61 " --> pdb=" O SER F 57 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 98 removed outlier: 4.024A pdb=" N ALA F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 120 Processing helix chain 'F' and resid 134 through 149 removed outlier: 3.619A pdb=" N ASP F 147 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER F 148 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 169 removed outlier: 3.811A pdb=" N ASP F 169 " --> pdb=" O ARG F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 198 removed outlier: 3.961A pdb=" N ARG F 182 " --> pdb=" O GLY F 178 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS F 190 " --> pdb=" O GLN F 186 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA F 193 " --> pdb=" O ARG F 189 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE F 195 " --> pdb=" O LEU F 191 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN F 196 " --> pdb=" O GLY F 192 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 232 removed outlier: 3.877A pdb=" N PHE F 230 " --> pdb=" O ARG F 226 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR F 231 " --> pdb=" O ALA F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 251 removed outlier: 3.692A pdb=" N GLN F 250 " --> pdb=" O THR F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 298 removed outlier: 3.617A pdb=" N LEU F 292 " --> pdb=" O THR F 288 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS F 293 " --> pdb=" O GLY F 289 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP F 297 " --> pdb=" O LYS F 293 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU F 298 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 327 Processing helix chain 'F' and resid 329 through 336 removed outlier: 3.765A pdb=" N ILE F 332 " --> pdb=" O HIS F 329 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE F 333 " --> pdb=" O PRO F 330 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP F 334 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU F 335 " --> pdb=" O ILE F 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.944A pdb=" N ASP G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA G 26 " --> pdb=" O ALA G 22 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 49 removed outlier: 3.623A pdb=" N GLN G 48 " --> pdb=" O ARG G 45 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS G 49 " --> pdb=" O ALA G 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 49' Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 84 through 98 removed outlier: 3.852A pdb=" N ALA G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 120 removed outlier: 3.567A pdb=" N ALA G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU G 120 " --> pdb=" O TYR G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 149 removed outlier: 4.385A pdb=" N SER G 148 " --> pdb=" O LYS G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 162 Processing helix chain 'G' and resid 164 through 169 removed outlier: 3.864A pdb=" N ASP G 169 " --> pdb=" O ARG G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 196 removed outlier: 3.996A pdb=" N LYS G 190 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ALA G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER G 194 " --> pdb=" O LYS G 190 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN G 196 " --> pdb=" O GLY G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 232 removed outlier: 3.906A pdb=" N PHE G 230 " --> pdb=" O ARG G 226 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR G 231 " --> pdb=" O ALA G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 298 removed outlier: 4.014A pdb=" N LEU G 292 " --> pdb=" O THR G 288 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS G 293 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP G 297 " --> pdb=" O LYS G 293 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU G 298 " --> pdb=" O ILE G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 327 removed outlier: 3.845A pdb=" N ALA G 327 " --> pdb=" O LYS G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 332 removed outlier: 3.662A pdb=" N ILE G 332 " --> pdb=" O HIS G 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 329 through 332' Processing helix chain 'G' and resid 333 through 338 removed outlier: 3.873A pdb=" N ASP G 337 " --> pdb=" O PHE G 333 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS G 338 " --> pdb=" O ASP G 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 333 through 338' Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 3.857A pdb=" N SER B 130 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL B 154 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE B 205 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL B 156 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 234 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 265 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP B 237 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL B 263 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY B 248 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN B 254 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY B 246 " --> pdb=" O ASN B 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 3.857A pdb=" N SER B 130 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL B 154 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE B 205 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL B 156 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 234 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 265 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP B 237 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL B 263 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 277 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 130 removed outlier: 3.883A pdb=" N SER A 130 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 74 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N LEU A 236 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU A 76 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL A 238 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TYR A 78 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG A 235 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 130 removed outlier: 3.883A pdb=" N SER A 130 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 74 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N LEU A 236 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU A 76 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL A 238 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TYR A 78 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG A 235 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 209 through 210 Processing sheet with id=AA7, first strand: chain 'B' and resid 40 through 41 removed outlier: 3.588A pdb=" N MET B 40 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER F 130 " --> pdb=" O PHE F 105 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE F 75 " --> pdb=" O PHE F 204 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE F 74 " --> pdb=" O VAL F 234 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU F 236 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU F 76 " --> pdb=" O LEU F 236 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL F 238 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR F 78 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS F 265 " --> pdb=" O ARG F 235 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP F 237 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL F 263 " --> pdb=" O ASP F 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 40 through 41 removed outlier: 3.588A pdb=" N MET B 40 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER F 130 " --> pdb=" O PHE F 105 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE F 75 " --> pdb=" O PHE F 204 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE F 74 " --> pdb=" O VAL F 234 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU F 236 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU F 76 " --> pdb=" O LEU F 236 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL F 238 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR F 78 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS F 265 " --> pdb=" O ARG F 235 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP F 237 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL F 263 " --> pdb=" O ASP F 237 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AB1, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.729A pdb=" N MET F 40 " --> pdb=" O LEU G 129 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU G 129 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER G 130 " --> pdb=" O PHE G 105 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA G 104 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE G 74 " --> pdb=" O VAL G 234 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N LEU G 236 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU G 76 " --> pdb=" O LEU G 236 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL G 238 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR G 78 " --> pdb=" O VAL G 238 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG G 235 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU G 252 " --> pdb=" O GLY G 248 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLY G 248 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN G 254 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY G 246 " --> pdb=" O ASN G 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.729A pdb=" N MET F 40 " --> pdb=" O LEU G 129 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU G 129 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER G 130 " --> pdb=" O PHE G 105 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA G 104 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE G 74 " --> pdb=" O VAL G 234 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N LEU G 236 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU G 76 " --> pdb=" O LEU G 236 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL G 238 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR G 78 " --> pdb=" O VAL G 238 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG G 235 " --> pdb=" O VAL G 264 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 52 through 53 Processing sheet with id=AB4, first strand: chain 'F' and resid 209 through 210 Processing sheet with id=AB5, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AB6, first strand: chain 'G' and resid 209 through 210 361 hydrogen bonds defined for protein. 1011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 3475 1.35 - 1.50: 2611 1.50 - 1.65: 4533 1.65 - 1.80: 45 1.80 - 1.95: 15 Bond restraints: 10679 Sorted by residual: bond pdb=" O3B AGS B 500 " pdb=" PB AGS B 500 " ideal model delta sigma weight residual 1.673 1.554 0.119 2.00e-02 2.50e+03 3.51e+01 bond pdb=" O3B AGS F 500 " pdb=" PB AGS F 500 " ideal model delta sigma weight residual 1.673 1.555 0.118 2.00e-02 2.50e+03 3.51e+01 bond pdb=" O3B AGS G 500 " pdb=" PB AGS G 500 " ideal model delta sigma weight residual 1.673 1.556 0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" O3B AGS A 500 " pdb=" PB AGS A 500 " ideal model delta sigma weight residual 1.673 1.562 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" O3A AGS A 500 " pdb=" PA AGS A 500 " ideal model delta sigma weight residual 1.664 1.563 0.101 2.00e-02 2.50e+03 2.56e+01 ... (remaining 10674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 14252 3.52 - 7.05: 165 7.05 - 10.57: 28 10.57 - 14.09: 6 14.09 - 17.62: 3 Bond angle restraints: 14454 Sorted by residual: angle pdb=" PB AGS B 500 " pdb=" O3B AGS B 500 " pdb=" PG AGS B 500 " ideal model delta sigma weight residual 129.21 111.59 17.62 3.00e+00 1.11e-01 3.45e+01 angle pdb=" PB AGS F 500 " pdb=" O3B AGS F 500 " pdb=" PG AGS F 500 " ideal model delta sigma weight residual 129.21 112.51 16.70 3.00e+00 1.11e-01 3.10e+01 angle pdb=" PB AGS G 500 " pdb=" O3B AGS G 500 " pdb=" PG AGS G 500 " ideal model delta sigma weight residual 129.21 112.71 16.50 3.00e+00 1.11e-01 3.02e+01 angle pdb=" C LYS B 85 " pdb=" N THR B 86 " pdb=" CA THR B 86 " ideal model delta sigma weight residual 120.68 112.00 8.68 1.70e+00 3.46e-01 2.61e+01 angle pdb=" C LYS F 85 " pdb=" N THR F 86 " pdb=" CA THR F 86 " ideal model delta sigma weight residual 121.52 112.43 9.09 1.84e+00 2.95e-01 2.44e+01 ... (remaining 14449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.16: 6219 34.16 - 68.33: 310 68.33 - 102.49: 50 102.49 - 136.66: 0 136.66 - 170.82: 8 Dihedral angle restraints: 6587 sinusoidal: 2851 harmonic: 3736 Sorted by residual: dihedral pdb=" CA LYS B 14 " pdb=" C LYS B 14 " pdb=" N PHE B 15 " pdb=" CA PHE B 15 " ideal model delta harmonic sigma weight residual 180.00 141.87 38.13 0 5.00e+00 4.00e-02 5.82e+01 dihedral pdb=" CA GLY G 84 " pdb=" C GLY G 84 " pdb=" N LYS G 85 " pdb=" CA LYS G 85 " ideal model delta harmonic sigma weight residual 180.00 152.61 27.39 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA GLY F 84 " pdb=" C GLY F 84 " pdb=" N LYS F 85 " pdb=" CA LYS F 85 " ideal model delta harmonic sigma weight residual 180.00 152.67 27.33 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 6584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1308 0.069 - 0.138: 279 0.138 - 0.208: 37 0.208 - 0.277: 4 0.277 - 0.346: 3 Chirality restraints: 1631 Sorted by residual: chirality pdb=" C3' AGS B 500 " pdb=" C2' AGS B 500 " pdb=" C4' AGS B 500 " pdb=" O3' AGS B 500 " both_signs ideal model delta sigma weight residual False -2.37 -2.72 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C3' AGS F 500 " pdb=" C2' AGS F 500 " pdb=" C4' AGS F 500 " pdb=" O3' AGS F 500 " both_signs ideal model delta sigma weight residual False -2.37 -2.71 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" C3' AGS G 500 " pdb=" C2' AGS G 500 " pdb=" C4' AGS G 500 " pdb=" O3' AGS G 500 " both_signs ideal model delta sigma weight residual False -2.37 -2.70 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 1628 not shown) Planarity restraints: 1800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 269 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.89e+00 pdb=" N PRO B 270 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 269 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.61e+00 pdb=" N PRO F 270 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 270 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 270 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 269 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO G 270 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO G 270 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 270 " -0.036 5.00e-02 4.00e+02 ... (remaining 1797 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3041 2.80 - 3.33: 9499 3.33 - 3.85: 17033 3.85 - 4.38: 17939 4.38 - 4.90: 30428 Nonbonded interactions: 77940 Sorted by model distance: nonbonded pdb=" OG1 THR A 198 " pdb=" OG1 THR A 200 " model vdw 2.281 3.040 nonbonded pdb=" O1B AGS A 500 " pdb=" O2G AGS A 500 " model vdw 2.315 3.040 nonbonded pdb=" OG1 THR B 198 " pdb=" OG1 THR B 200 " model vdw 2.319 3.040 nonbonded pdb=" O SER A 83 " pdb=" OG SER A 83 " model vdw 2.326 3.040 nonbonded pdb=" OE1 GLU G 31 " pdb=" OG SER G 38 " model vdw 2.327 3.040 ... (remaining 77935 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: 0.260 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.820 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 : 0.008 0.143 10691 Z= 0.421 Angle : 1.092 17.619 14454 Z= 0.594 Chirality : 0.059 0.346 1631 Planarity : 0.006 0.075 1800 Dihedral : 20.539 170.824 4211 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.77 % Allowed : 14.52 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.18), residues: 1324 helix: -2.93 (0.21), residues: 328 sheet: -1.99 (0.31), residues: 212 loop : -2.66 (0.18), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 226 TYR 0.021 0.003 TYR B 78 PHE 0.021 0.003 PHE B 105 TRP 0.010 0.001 TRP G 307 HIS 0.007 0.001 HIS F 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00802 / 0.42 (10679) covalent geometry : angle 1.09236 / 0.59 (14454) hydrogen bonds : bond 0.26136 / 16.72 ( 318) hydrogen bonds : angle 8.01262 / 5.54 ( 1031) Misc. bond : bond 0.00693 / 0.37 ( 12) *********************** 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 187 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.9408 (mt) cc_final: 0.8961 (mt) REVERT: A 176 HIS cc_start: 0.7897 (m-70) cc_final: 0.7670 (m90) REVERT: A 183 MET cc_start: 0.9020 (tmm) cc_final: 0.8594 (tmm) REVERT: A 258 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8127 (tm-30) REVERT: A 307 TRP cc_start: 0.8704 (m-90) cc_final: 0.8279 (m-90) REVERT: B 76 GLU cc_start: 0.8000 (pp20) cc_final: 0.7762 (pp20) REVERT: B 183 MET cc_start: 0.8690 (tmm) cc_final: 0.8295 (tmm) REVERT: B 215 MET cc_start: 0.5997 (mmm) cc_final: 0.5778 (mmm) REVERT: B 258 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8016 (tm-30) REVERT: B 274 GLU cc_start: 0.8732 (pp20) cc_final: 0.7907 (pp20) REVERT: F 140 GLU cc_start: 0.8905 (tp30) cc_final: 0.8598 (tp30) REVERT: F 141 ILE cc_start: 0.9301 (mt) cc_final: 0.8909 (mm) REVERT: F 183 MET cc_start: 0.8956 (tmm) cc_final: 0.8332 (tmm) REVERT: F 258 GLU cc_start: 0.8855 (tm-30) cc_final: 0.7791 (tm-30) REVERT: F 274 GLU cc_start: 0.8797 (pp20) cc_final: 0.8490 (pp20) REVERT: F 307 TRP cc_start: 0.8749 (m-90) cc_final: 0.8540 (m-90) REVERT: G 47 GLU cc_start: 0.8930 (pm20) cc_final: 0.8663 (pm20) REVERT: G 183 MET cc_start: 0.8708 (tmm) cc_final: 0.8128 (tmm) REVERT: G 186 GLN cc_start: 0.8691 (tm-30) cc_final: 0.7775 (tp40) REVERT: G 333 PHE cc_start: 0.8006 (m-10) cc_final: 0.7660 (m-80) outliers start: 8 outliers final: 2 residues processed: 187 average time/residue: 0.1038 time to fit residues: 27.8171 Evaluate side-chains 111 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 50 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.0040 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 0.0000 chunk 55 optimal weight: 6.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 GLN B 176 HIS B 196 ASN B 329 HIS F 176 HIS ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.121352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.087827 restraints weight = 28304.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.090614 restraints weight = 13889.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.092389 restraints weight = 9142.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093508 restraints weight = 7125.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.094090 restraints weight = 6134.645| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 10691 Z= 0.168 Angle : 0.757 10.652 14454 Z= 0.394 Chirality : 0.049 0.250 1631 Planarity : 0.005 0.050 1800 Dihedral : 21.439 168.792 1765 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.02 % Allowed : 20.67 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.21), residues: 1324 helix: -1.59 (0.25), residues: 348 sheet: -1.46 (0.32), residues: 240 loop : -2.18 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 41 TYR 0.024 0.002 TYR F 325 PHE 0.023 0.002 PHE A 105 TRP 0.016 0.002 TRP G 307 HIS 0.004 0.001 HIS F 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (10679) covalent geometry : angle 0.75737 / 0.39 (14454) hydrogen bonds : bond 0.05327 / 3.46 ( 318) hydrogen bonds : angle 6.23217 / 4.27 ( 1031) Misc. bond : bond 0.00594 / 0.34 ( 12) *********************** 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 154 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 183 MET cc_start: 0.9113 (tmm) cc_final: 0.8601 (tmm) REVERT: A 208 LEU cc_start: 0.8800 (tp) cc_final: 0.8387 (tp) REVERT: A 258 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 274 GLU cc_start: 0.8838 (pp20) cc_final: 0.8088 (pp20) REVERT: A 283 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8774 (tp30) REVERT: A 307 TRP cc_start: 0.8506 (m-90) cc_final: 0.8296 (m100) REVERT: A 315 ILE cc_start: 0.3836 (OUTLIER) cc_final: 0.2783 (mt) REVERT: B 183 MET cc_start: 0.8953 (tmm) cc_final: 0.8533 (tmm) REVERT: B 215 MET cc_start: 0.5862 (mmm) cc_final: 0.5655 (mmm) REVERT: B 258 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8706 (tm-30) REVERT: F 64 LEU cc_start: 0.8873 (mp) cc_final: 0.8343 (tt) REVERT: F 76 GLU cc_start: 0.8171 (pp20) cc_final: 0.7662 (pp20) REVERT: F 140 GLU cc_start: 0.8916 (tp30) cc_final: 0.8614 (tp30) REVERT: F 183 MET cc_start: 0.9078 (tmm) cc_final: 0.8455 (tmm) REVERT: F 188 MET cc_start: 0.8289 (ttm) cc_final: 0.7995 (ttp) REVERT: F 212 VAL cc_start: 0.8382 (OUTLIER) cc_final: 0.8144 (p) REVERT: G 47 GLU cc_start: 0.8903 (pm20) cc_final: 0.8659 (pm20) REVERT: G 183 MET cc_start: 0.8771 (tmm) cc_final: 0.8250 (tmm) REVERT: G 186 GLN cc_start: 0.8725 (tm-30) cc_final: 0.7781 (tp40) REVERT: G 307 TRP cc_start: 0.8153 (m100) cc_final: 0.7397 (m100) REVERT: G 333 PHE cc_start: 0.7847 (m-10) cc_final: 0.7639 (m-80) outliers start: 21 outliers final: 6 residues processed: 151 average time/residue: 0.0863 time to fit residues: 19.8488 Evaluate side-chains 111 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain G residue 50 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 108 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 105 optimal weight: 30.0000 chunk 68 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.117801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.084682 restraints weight = 28803.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.087371 restraints weight = 14162.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.089084 restraints weight = 9336.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.090167 restraints weight = 7285.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.090725 restraints weight = 6292.443| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 10691 Z= 0.250 Angle : 0.798 13.598 14454 Z= 0.409 Chirality : 0.050 0.412 1631 Planarity : 0.004 0.045 1800 Dihedral : 21.092 170.200 1765 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.69 % Allowed : 23.17 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.22), residues: 1324 helix: -0.85 (0.27), residues: 348 sheet: -1.25 (0.33), residues: 240 loop : -1.94 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 182 TYR 0.041 0.003 TYR F 325 PHE 0.013 0.002 PHE G 105 TRP 0.009 0.001 TRP F 307 HIS 0.006 0.001 HIS G 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.25 (10679) covalent geometry : angle 0.79826 / 0.41 (14454) hydrogen bonds : bond 0.05204 / 3.46 ( 318) hydrogen bonds : angle 5.97801 / 4.07 ( 1031) Misc. bond : bond 0.00925 / 0.52 ( 12) *********************** 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 135 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.418 Fit side-chains REVERT: A 183 MET cc_start: 0.9125 (tmm) cc_final: 0.8502 (tmm) REVERT: A 206 ASN cc_start: 0.8582 (t0) cc_final: 0.8204 (t0) REVERT: A 208 LEU cc_start: 0.8839 (tp) cc_final: 0.8456 (tp) REVERT: A 258 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8134 (tm-30) REVERT: A 274 GLU cc_start: 0.8865 (pp20) cc_final: 0.8178 (pp20) REVERT: A 280 MET cc_start: 0.9274 (tpp) cc_final: 0.8975 (mmm) REVERT: A 283 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8828 (tp30) REVERT: A 307 TRP cc_start: 0.8536 (m-90) cc_final: 0.8235 (m-90) REVERT: A 315 ILE cc_start: 0.4026 (OUTLIER) cc_final: 0.3446 (mp) REVERT: B 183 MET cc_start: 0.9052 (tmm) cc_final: 0.8604 (tmm) REVERT: B 258 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8674 (tm-30) REVERT: F 140 GLU cc_start: 0.8905 (tp30) cc_final: 0.8600 (tp30) REVERT: F 183 MET cc_start: 0.9098 (tmm) cc_final: 0.8266 (tmm) REVERT: F 251 LYS cc_start: 0.8385 (tptt) cc_final: 0.8136 (tptp) REVERT: G 183 MET cc_start: 0.8770 (tmm) cc_final: 0.8268 (tmm) REVERT: G 186 GLN cc_start: 0.8731 (tm-30) cc_final: 0.7813 (tp40) REVERT: G 307 TRP cc_start: 0.8272 (m100) cc_final: 0.7254 (m100) outliers start: 28 outliers final: 13 residues processed: 129 average time/residue: 0.0830 time to fit residues: 16.6267 Evaluate side-chains 109 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 253 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 69 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 31 optimal weight: 30.0000 chunk 106 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 131 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.114985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.087139 restraints weight = 27676.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.089843 restraints weight = 13420.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.091568 restraints weight = 8744.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.092671 restraints weight = 6775.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.093237 restraints weight = 5800.246| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10691 Z= 0.157 Angle : 0.698 9.707 14454 Z= 0.361 Chirality : 0.047 0.302 1631 Planarity : 0.004 0.043 1800 Dihedral : 20.740 176.657 1765 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.37 % Allowed : 23.37 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.22), residues: 1324 helix: -0.68 (0.27), residues: 372 sheet: -1.05 (0.33), residues: 240 loop : -1.86 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 341 TYR 0.031 0.002 TYR F 325 PHE 0.016 0.002 PHE A 105 TRP 0.011 0.001 TRP F 307 HIS 0.010 0.002 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (10679) covalent geometry : angle 0.69794 / 0.36 (14454) hydrogen bonds : bond 0.04345 / 2.89 ( 318) hydrogen bonds : angle 5.63380 / 3.81 ( 1031) Misc. bond : bond 0.00545 / 0.31 ( 12) *********************** 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 145 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8977 (p90) cc_final: 0.8202 (p90) REVERT: A 183 MET cc_start: 0.9148 (tmm) cc_final: 0.8553 (tmm) REVERT: A 191 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9246 (mp) REVERT: A 206 ASN cc_start: 0.8520 (t0) cc_final: 0.8052 (t0) REVERT: A 208 LEU cc_start: 0.8844 (tp) cc_final: 0.8453 (tp) REVERT: A 274 GLU cc_start: 0.8925 (pp20) cc_final: 0.8303 (pp20) REVERT: A 283 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8754 (tp30) REVERT: A 307 TRP cc_start: 0.8469 (m-90) cc_final: 0.8234 (m-90) REVERT: A 315 ILE cc_start: 0.4223 (OUTLIER) cc_final: 0.3775 (mp) REVERT: B 183 MET cc_start: 0.9064 (tmm) cc_final: 0.8671 (tmm) REVERT: B 258 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8605 (tm-30) REVERT: F 64 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8438 (tt) REVERT: F 76 GLU cc_start: 0.8100 (pp20) cc_final: 0.7652 (pp20) REVERT: F 140 GLU cc_start: 0.8958 (tp30) cc_final: 0.8672 (tp30) REVERT: F 183 MET cc_start: 0.9131 (tmm) cc_final: 0.8421 (tmm) REVERT: F 212 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8128 (p) REVERT: F 251 LYS cc_start: 0.8294 (tptt) cc_final: 0.8079 (tptp) REVERT: G 183 MET cc_start: 0.8797 (tmm) cc_final: 0.8243 (tmm) REVERT: G 186 GLN cc_start: 0.8599 (tm-30) cc_final: 0.7619 (tp40) REVERT: G 215 MET cc_start: 0.7331 (mmm) cc_final: 0.7001 (mmm) REVERT: G 243 GLN cc_start: 0.8757 (pm20) cc_final: 0.8164 (pt0) REVERT: G 307 TRP cc_start: 0.8328 (m100) cc_final: 0.7217 (m100) outliers start: 35 outliers final: 12 residues processed: 140 average time/residue: 0.0762 time to fit residues: 16.9433 Evaluate side-chains 114 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 253 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 30.0000 chunk 83 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.120624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.087776 restraints weight = 28156.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.090590 restraints weight = 13725.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.092376 restraints weight = 8964.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.093524 restraints weight = 6952.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.094084 restraints weight = 5965.553| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10691 Z= 0.144 Angle : 0.679 10.980 14454 Z= 0.349 Chirality : 0.047 0.239 1631 Planarity : 0.004 0.041 1800 Dihedral : 20.273 179.903 1765 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.88 % Allowed : 24.13 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.23), residues: 1324 helix: -0.38 (0.28), residues: 372 sheet: -0.82 (0.35), residues: 220 loop : -1.72 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 235 TYR 0.022 0.002 TYR A 231 PHE 0.019 0.001 PHE G 105 TRP 0.011 0.001 TRP F 307 HIS 0.008 0.001 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (10679) covalent geometry : angle 0.67947 / 0.35 (14454) hydrogen bonds : bond 0.03973 / 2.65 ( 318) hydrogen bonds : angle 5.44196 / 3.66 ( 1031) Misc. bond : bond 0.00468 / 0.26 ( 12) *********************** 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 142 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8962 (p90) cc_final: 0.8264 (p90) REVERT: A 141 ILE cc_start: 0.9495 (mt) cc_final: 0.9274 (tp) REVERT: A 183 MET cc_start: 0.9144 (tmm) cc_final: 0.8576 (tmm) REVERT: A 191 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9232 (mp) REVERT: A 206 ASN cc_start: 0.8547 (t0) cc_final: 0.8000 (t0) REVERT: A 208 LEU cc_start: 0.8837 (tp) cc_final: 0.8429 (tp) REVERT: A 274 GLU cc_start: 0.8909 (pp20) cc_final: 0.8294 (pp20) REVERT: A 283 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8766 (tp30) REVERT: A 307 TRP cc_start: 0.8600 (m-90) cc_final: 0.8367 (m-90) REVERT: A 315 ILE cc_start: 0.4368 (OUTLIER) cc_final: 0.3964 (mp) REVERT: B 40 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7571 (mtm) REVERT: B 183 MET cc_start: 0.9079 (tmm) cc_final: 0.8667 (tmm) REVERT: B 258 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8559 (tm-30) REVERT: B 310 TYR cc_start: 0.6435 (m-10) cc_final: 0.4965 (t80) REVERT: F 64 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8443 (tt) REVERT: F 140 GLU cc_start: 0.8953 (tp30) cc_final: 0.8534 (tp30) REVERT: F 183 MET cc_start: 0.9147 (tmm) cc_final: 0.8450 (tmm) REVERT: F 212 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8046 (p) REVERT: G 183 MET cc_start: 0.8810 (tmm) cc_final: 0.8261 (tmm) REVERT: G 186 GLN cc_start: 0.8588 (tm-30) cc_final: 0.7542 (tp40) REVERT: G 206 ASN cc_start: 0.8772 (t0) cc_final: 0.8454 (t0) REVERT: G 215 MET cc_start: 0.7557 (mmm) cc_final: 0.7312 (mmm) REVERT: G 307 TRP cc_start: 0.8381 (m100) cc_final: 0.7236 (m100) outliers start: 30 outliers final: 19 residues processed: 136 average time/residue: 0.0799 time to fit residues: 17.0360 Evaluate side-chains 124 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 253 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 111 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 24 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 64 optimal weight: 0.0870 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.119484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.086502 restraints weight = 28442.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089264 restraints weight = 13943.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.091028 restraints weight = 9160.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.092158 restraints weight = 7121.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.092849 restraints weight = 6124.636| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10691 Z= 0.174 Angle : 0.681 10.739 14454 Z= 0.351 Chirality : 0.047 0.252 1631 Planarity : 0.004 0.043 1800 Dihedral : 19.916 178.856 1765 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.17 % Allowed : 25.10 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.23), residues: 1324 helix: -0.20 (0.28), residues: 372 sheet: -0.66 (0.35), residues: 216 loop : -1.73 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 226 TYR 0.022 0.002 TYR F 325 PHE 0.015 0.001 PHE G 105 TRP 0.012 0.001 TRP F 307 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (10679) covalent geometry : angle 0.68100 / 0.35 (14454) hydrogen bonds : bond 0.03948 / 2.63 ( 318) hydrogen bonds : angle 5.36417 / 3.61 ( 1031) Misc. bond : bond 0.00480 / 0.27 ( 12) *********************** 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 143 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.418 Fit side-chains REVERT: A 78 TYR cc_start: 0.8983 (p90) cc_final: 0.8303 (p90) REVERT: A 141 ILE cc_start: 0.9506 (mt) cc_final: 0.9291 (tp) REVERT: A 183 MET cc_start: 0.9162 (tmm) cc_final: 0.8550 (tmm) REVERT: A 191 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9258 (mp) REVERT: A 206 ASN cc_start: 0.8575 (t0) cc_final: 0.8029 (t0) REVERT: A 208 LEU cc_start: 0.8863 (tp) cc_final: 0.8477 (tp) REVERT: A 274 GLU cc_start: 0.8932 (pp20) cc_final: 0.8329 (pp20) REVERT: A 280 MET cc_start: 0.9295 (tpp) cc_final: 0.9010 (mmm) REVERT: A 283 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8786 (tp30) REVERT: A 315 ILE cc_start: 0.4390 (OUTLIER) cc_final: 0.4048 (mp) REVERT: B 40 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7568 (mtm) REVERT: B 183 MET cc_start: 0.9125 (tmm) cc_final: 0.8678 (tmm) REVERT: B 206 ASN cc_start: 0.8902 (t0) cc_final: 0.8627 (t0) REVERT: B 258 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8561 (tm-30) REVERT: B 310 TYR cc_start: 0.6394 (m-10) cc_final: 0.4988 (t80) REVERT: F 64 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8433 (tt) REVERT: F 140 GLU cc_start: 0.8990 (tp30) cc_final: 0.8547 (tp30) REVERT: F 183 MET cc_start: 0.9164 (tmm) cc_final: 0.8420 (tmm) REVERT: F 212 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8154 (p) REVERT: F 251 LYS cc_start: 0.8286 (tptt) cc_final: 0.7906 (tptp) REVERT: G 171 ASP cc_start: 0.8278 (t0) cc_final: 0.8047 (t0) REVERT: G 183 MET cc_start: 0.8854 (tmm) cc_final: 0.8386 (tmm) REVERT: G 206 ASN cc_start: 0.8827 (t0) cc_final: 0.8443 (t0) REVERT: G 215 MET cc_start: 0.7586 (mmm) cc_final: 0.7381 (mmm) REVERT: G 243 GLN cc_start: 0.8903 (pm20) cc_final: 0.8417 (pt0) REVERT: G 280 MET cc_start: 0.9064 (tpp) cc_final: 0.8826 (mmm) REVERT: G 307 TRP cc_start: 0.8514 (m100) cc_final: 0.7439 (m100) outliers start: 33 outliers final: 21 residues processed: 136 average time/residue: 0.0788 time to fit residues: 17.0728 Evaluate side-chains 131 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 253 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 131 optimal weight: 0.0370 chunk 71 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 29 optimal weight: 30.0000 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.112942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.083123 restraints weight = 26558.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.085697 restraints weight = 14025.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.087368 restraints weight = 9504.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.088430 restraints weight = 7473.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.088886 restraints weight = 6471.905| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10691 Z= 0.176 Angle : 0.681 11.000 14454 Z= 0.353 Chirality : 0.047 0.228 1631 Planarity : 0.004 0.045 1800 Dihedral : 19.822 177.246 1765 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.27 % Allowed : 25.19 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.23), residues: 1324 helix: 0.17 (0.29), residues: 352 sheet: -0.59 (0.35), residues: 216 loop : -1.61 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 341 TYR 0.016 0.002 TYR F 325 PHE 0.023 0.002 PHE A 105 TRP 0.013 0.002 TRP F 307 HIS 0.009 0.001 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (10679) covalent geometry : angle 0.68095 / 0.35 (14454) hydrogen bonds : bond 0.03955 / 2.64 ( 318) hydrogen bonds : angle 5.32358 / 3.60 ( 1031) Misc. bond : bond 0.00526 / 0.30 ( 12) *********************** 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 144 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.412 Fit side-chains REVERT: A 78 TYR cc_start: 0.9025 (p90) cc_final: 0.8480 (p90) REVERT: A 141 ILE cc_start: 0.9519 (mt) cc_final: 0.9303 (tp) REVERT: A 183 MET cc_start: 0.9155 (tmm) cc_final: 0.8555 (tmm) REVERT: A 184 MET cc_start: 0.9051 (tpp) cc_final: 0.8679 (tpp) REVERT: A 206 ASN cc_start: 0.8598 (t0) cc_final: 0.8087 (t0) REVERT: A 208 LEU cc_start: 0.8866 (tp) cc_final: 0.8498 (tp) REVERT: A 274 GLU cc_start: 0.8929 (pp20) cc_final: 0.8390 (pp20) REVERT: A 283 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8773 (tp30) REVERT: B 40 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7516 (mtm) REVERT: B 183 MET cc_start: 0.9145 (tmm) cc_final: 0.8729 (tmm) REVERT: B 258 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8558 (tm-30) REVERT: F 64 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8481 (tt) REVERT: F 140 GLU cc_start: 0.8901 (tp30) cc_final: 0.8423 (tp30) REVERT: F 183 MET cc_start: 0.9173 (tmm) cc_final: 0.8445 (tmm) REVERT: F 212 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8272 (p) REVERT: G 171 ASP cc_start: 0.8260 (t0) cc_final: 0.8007 (t0) REVERT: G 183 MET cc_start: 0.8884 (tmm) cc_final: 0.8434 (tmm) REVERT: G 206 ASN cc_start: 0.8810 (t0) cc_final: 0.8467 (t0) outliers start: 34 outliers final: 20 residues processed: 137 average time/residue: 0.0810 time to fit residues: 17.4051 Evaluate side-chains 124 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 253 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 78 optimal weight: 9.9990 chunk 84 optimal weight: 0.0570 chunk 79 optimal weight: 5.9990 chunk 51 optimal weight: 0.0470 chunk 17 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 10 optimal weight: 0.0050 chunk 113 optimal weight: 7.9990 overall best weight: 1.6214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.115774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086074 restraints weight = 26011.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.088706 restraints weight = 13591.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.090417 restraints weight = 9153.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.091525 restraints weight = 7172.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.092103 restraints weight = 6183.704| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10691 Z= 0.134 Angle : 0.704 11.562 14454 Z= 0.359 Chirality : 0.047 0.233 1631 Planarity : 0.004 0.046 1800 Dihedral : 19.658 175.101 1765 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.88 % Allowed : 25.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.23), residues: 1324 helix: -0.10 (0.28), residues: 376 sheet: -0.62 (0.35), residues: 220 loop : -1.62 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 341 TYR 0.017 0.002 TYR G 325 PHE 0.016 0.001 PHE B 15 TRP 0.014 0.002 TRP F 307 HIS 0.009 0.002 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (10679) covalent geometry : angle 0.70375 / 0.36 (14454) hydrogen bonds : bond 0.03728 / 2.46 ( 318) hydrogen bonds : angle 5.38115 / 3.61 ( 1031) Misc. bond : bond 0.00585 / 0.31 ( 12) *********************** 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 142 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8966 (p90) cc_final: 0.8481 (p90) REVERT: A 141 ILE cc_start: 0.9484 (mt) cc_final: 0.9265 (tp) REVERT: A 183 MET cc_start: 0.9162 (tmm) cc_final: 0.8594 (tmm) REVERT: A 184 MET cc_start: 0.9061 (tpp) cc_final: 0.8679 (tpp) REVERT: A 206 ASN cc_start: 0.8500 (t0) cc_final: 0.8011 (t0) REVERT: A 208 LEU cc_start: 0.8837 (tp) cc_final: 0.8483 (tp) REVERT: A 274 GLU cc_start: 0.8925 (pp20) cc_final: 0.8422 (pp20) REVERT: A 283 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8757 (tp30) REVERT: A 307 TRP cc_start: 0.7871 (m-90) cc_final: 0.7658 (m100) REVERT: B 40 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7550 (mtm) REVERT: B 183 MET cc_start: 0.9122 (tmm) cc_final: 0.8717 (tmm) REVERT: B 258 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8511 (tm-30) REVERT: F 64 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8494 (tt) REVERT: F 140 GLU cc_start: 0.8868 (tp30) cc_final: 0.8405 (tp30) REVERT: F 147 ASP cc_start: 0.7995 (p0) cc_final: 0.7455 (t0) REVERT: F 183 MET cc_start: 0.9160 (tmm) cc_final: 0.8460 (tmm) REVERT: F 212 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8090 (p) REVERT: F 251 LYS cc_start: 0.8237 (tptt) cc_final: 0.7973 (tptp) REVERT: F 280 MET cc_start: 0.8887 (mmm) cc_final: 0.8531 (mmm) REVERT: G 40 MET cc_start: 0.8662 (mtp) cc_final: 0.7704 (ttm) REVERT: G 171 ASP cc_start: 0.8209 (t0) cc_final: 0.7975 (t0) REVERT: G 183 MET cc_start: 0.8898 (tmm) cc_final: 0.8360 (tmm) REVERT: G 206 ASN cc_start: 0.8775 (t0) cc_final: 0.8425 (t0) REVERT: G 307 TRP cc_start: 0.8844 (m100) cc_final: 0.7575 (m100) REVERT: G 315 ILE cc_start: 0.6652 (OUTLIER) cc_final: 0.5901 (mp) outliers start: 30 outliers final: 19 residues processed: 136 average time/residue: 0.0795 time to fit residues: 17.1404 Evaluate side-chains 129 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 58 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 1 optimal weight: 0.0170 chunk 121 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 98 optimal weight: 0.1980 chunk 124 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 overall best weight: 1.8424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN B 254 ASN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** 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 = 0.3869 r_free = 0.3869 target = 0.115597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.085944 restraints weight = 26227.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.088598 restraints weight = 13716.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.090318 restraints weight = 9234.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.091446 restraints weight = 7239.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.091947 restraints weight = 6235.580| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10691 Z= 0.130 Angle : 0.685 12.453 14454 Z= 0.350 Chirality : 0.047 0.237 1631 Planarity : 0.004 0.045 1800 Dihedral : 19.404 176.624 1765 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.40 % Allowed : 26.25 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.23), residues: 1324 helix: 0.13 (0.28), residues: 376 sheet: -0.57 (0.35), residues: 220 loop : -1.51 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 189 TYR 0.016 0.002 TYR G 325 PHE 0.020 0.002 PHE F 15 TRP 0.017 0.002 TRP F 307 HIS 0.009 0.001 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (10679) covalent geometry : angle 0.68530 / 0.35 (14454) hydrogen bonds : bond 0.03464 / 2.27 ( 318) hydrogen bonds : angle 5.22558 / 3.52 ( 1031) Misc. bond : bond 0.00486 / 0.26 ( 12) *********************** 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 141 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.423 Fit side-chains REVERT: A 78 TYR cc_start: 0.8933 (p90) cc_final: 0.8408 (p90) REVERT: A 141 ILE cc_start: 0.9472 (mt) cc_final: 0.9244 (tp) REVERT: A 183 MET cc_start: 0.9206 (tmm) cc_final: 0.8619 (tmm) REVERT: A 184 MET cc_start: 0.9060 (tpp) cc_final: 0.8604 (tpp) REVERT: A 206 ASN cc_start: 0.8515 (t0) cc_final: 0.8092 (t0) REVERT: A 208 LEU cc_start: 0.8848 (tp) cc_final: 0.8496 (tp) REVERT: A 274 GLU cc_start: 0.8906 (pp20) cc_final: 0.8415 (pp20) REVERT: A 283 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8751 (tp30) REVERT: B 183 MET cc_start: 0.9134 (tmm) cc_final: 0.8741 (tmm) REVERT: B 184 MET cc_start: 0.9310 (tpp) cc_final: 0.8990 (tpp) REVERT: B 220 GLU cc_start: 0.8670 (pm20) cc_final: 0.8461 (pt0) REVERT: F 140 GLU cc_start: 0.8883 (tp30) cc_final: 0.8394 (tp30) REVERT: F 147 ASP cc_start: 0.8004 (p0) cc_final: 0.7503 (t0) REVERT: F 183 MET cc_start: 0.9166 (tmm) cc_final: 0.8456 (tmm) REVERT: F 206 ASN cc_start: 0.8926 (t0) cc_final: 0.8198 (m-40) REVERT: F 212 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8145 (p) REVERT: F 251 LYS cc_start: 0.8172 (tptt) cc_final: 0.7616 (tptp) REVERT: G 171 ASP cc_start: 0.8189 (t0) cc_final: 0.7948 (t0) REVERT: G 183 MET cc_start: 0.8926 (tmm) cc_final: 0.8453 (tmm) REVERT: G 206 ASN cc_start: 0.8837 (t0) cc_final: 0.8484 (m-40) outliers start: 25 outliers final: 19 residues processed: 137 average time/residue: 0.0783 time to fit residues: 16.9871 Evaluate side-chains 127 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.0470 chunk 128 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.113681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.083913 restraints weight = 26304.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.086494 restraints weight = 13871.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088167 restraints weight = 9412.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.089238 restraints weight = 7438.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.089903 restraints weight = 6452.628| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 10691 Z= 0.192 Angle : 0.775 26.740 14454 Z= 0.384 Chirality : 0.048 0.281 1631 Planarity : 0.004 0.044 1800 Dihedral : 19.694 176.774 1765 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.12 % Allowed : 26.83 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.24), residues: 1324 helix: 0.52 (0.29), residues: 356 sheet: -0.56 (0.35), residues: 220 loop : -1.44 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 341 TYR 0.023 0.002 TYR A 231 PHE 0.017 0.002 PHE B 15 TRP 0.019 0.002 TRP A 307 HIS 0.009 0.001 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (10679) covalent geometry : angle 0.77479 / 0.38 (14454) hydrogen bonds : bond 0.03719 / 2.45 ( 318) hydrogen bonds : angle 5.29934 / 3.57 ( 1031) Misc. bond : bond 0.00553 / 0.31 ( 12) ********************** 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 121 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 110 HIS cc_start: 0.8562 (OUTLIER) cc_final: 0.8033 (m-70) REVERT: A 141 ILE cc_start: 0.9473 (mt) cc_final: 0.9251 (tp) REVERT: A 183 MET cc_start: 0.9244 (tmm) cc_final: 0.8653 (tmm) REVERT: A 206 ASN cc_start: 0.8572 (t0) cc_final: 0.8089 (t0) REVERT: A 208 LEU cc_start: 0.8833 (tp) cc_final: 0.8451 (tp) REVERT: A 274 GLU cc_start: 0.8980 (pp20) cc_final: 0.8450 (pp20) REVERT: A 283 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8785 (tp30) REVERT: A 307 TRP cc_start: 0.8162 (m-90) cc_final: 0.7779 (m-90) REVERT: B 183 MET cc_start: 0.9193 (tmm) cc_final: 0.8742 (tmm) REVERT: F 76 GLU cc_start: 0.7836 (pp20) cc_final: 0.7592 (pp20) REVERT: F 140 GLU cc_start: 0.9060 (tp30) cc_final: 0.8599 (tp30) REVERT: F 147 ASP cc_start: 0.8232 (p0) cc_final: 0.7683 (t0) REVERT: F 183 MET cc_start: 0.9097 (tmm) cc_final: 0.8258 (tmm) REVERT: F 212 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8265 (p) REVERT: F 251 LYS cc_start: 0.8277 (tptt) cc_final: 0.7730 (tptp) REVERT: G 171 ASP cc_start: 0.8293 (t0) cc_final: 0.8040 (t0) REVERT: G 183 MET cc_start: 0.8873 (tmm) cc_final: 0.8474 (tmm) REVERT: G 206 ASN cc_start: 0.8895 (t0) cc_final: 0.8642 (m-40) outliers start: 22 outliers final: 19 residues processed: 119 average time/residue: 0.0835 time to fit residues: 15.6827 Evaluate side-chains 120 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 253 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 71 optimal weight: 0.0970 chunk 83 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 59 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.114884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.084958 restraints weight = 26573.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.087615 restraints weight = 13883.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.089309 restraints weight = 9325.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.090260 restraints weight = 7342.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.091031 restraints weight = 6417.045| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10691 Z= 0.181 Angle : 0.760 22.844 14454 Z= 0.380 Chirality : 0.048 0.270 1631 Planarity : 0.004 0.045 1800 Dihedral : 19.683 178.319 1765 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.31 % Allowed : 26.73 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.24), residues: 1324 helix: 0.54 (0.29), residues: 356 sheet: -0.48 (0.35), residues: 220 loop : -1.46 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 341 TYR 0.021 0.002 TYR A 231 PHE 0.014 0.002 PHE A 105 TRP 0.014 0.002 TRP F 307 HIS 0.009 0.001 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (10679) covalent geometry : angle 0.76014 / 0.38 (14454) hydrogen bonds : bond 0.03712 / 2.45 ( 318) hydrogen bonds : angle 5.25331 / 3.53 ( 1031) Misc. bond : bond 0.00635 / 0.35 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1769.08 seconds wall clock time: 31 minutes 34.00 seconds (1894.00 seconds total)