Starting phenix.real_space_refine on Wed Aug 5 15:27:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8amf_15525/08_2026/8amf_15525.cif Found real_map, /net/cci-nas-00/data/ceres_data/8amf_15525/08_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_15525/08_2026/8amf_15525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8amf_15525/08_2026/8amf_15525.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8amf_15525/08_2026/8amf_15525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8amf_15525/08_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-2.2rc3-6140/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: 2.23, per 1000 atoms: 0.21 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: 0.86 Conformation dependent library (CDL) restraints added in 344.8 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: 0.74 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: 1.57 Time building geometry restraints manager: 1.12 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.470 Find NCS groups from input model: 0.180 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.320 ------------------------------------------------------------------------------- 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= 0.595 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 1.09241 / 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 : 0.271 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: 0.0830 time to fit residues: 22.2338 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 : 0.263 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.121189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.087475 restraints weight = 28304.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.090279 restraints weight = 13953.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.092035 restraints weight = 9182.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093114 restraints weight = 7163.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.093843 restraints weight = 6188.562| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 10691 Z= 0.171 Angle : 0.759 10.582 14454 Z= 0.395 Chirality : 0.049 0.263 1631 Planarity : 0.005 0.050 1800 Dihedral : 21.499 168.291 1765 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.92 % Allowed : 20.87 % Favored : 77.21 % 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: -2.83 (0.21), residues: 1324 helix: -1.61 (0.25), residues: 348 sheet: -1.45 (0.32), residues: 240 loop : -2.19 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 41 TYR 0.025 0.002 TYR F 325 PHE 0.023 0.002 PHE A 105 TRP 0.015 0.002 TRP G 307 HIS 0.005 0.001 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (10679) covalent geometry : angle 0.75923 / 0.40 (14454) hydrogen bonds : bond 0.05496 / 3.57 ( 318) hydrogen bonds : angle 6.27566 / 4.30 ( 1031) Misc. bond : bond 0.00681 / 0.38 ( 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 149 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 183 MET cc_start: 0.9099 (tmm) cc_final: 0.8597 (tmm) REVERT: A 208 LEU cc_start: 0.8797 (tp) cc_final: 0.8376 (tp) REVERT: A 258 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8128 (tm-30) REVERT: A 274 GLU cc_start: 0.8840 (pp20) cc_final: 0.8092 (pp20) REVERT: A 283 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8774 (tp30) REVERT: A 307 TRP cc_start: 0.8501 (m-90) cc_final: 0.8276 (m100) REVERT: A 315 ILE cc_start: 0.3811 (OUTLIER) cc_final: 0.2752 (mt) REVERT: B 183 MET cc_start: 0.8954 (tmm) cc_final: 0.8544 (tmm) REVERT: B 215 MET cc_start: 0.5859 (mmm) cc_final: 0.5647 (mmm) REVERT: B 258 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8705 (tm-30) REVERT: F 76 GLU cc_start: 0.8190 (pp20) cc_final: 0.7679 (pp20) REVERT: F 140 GLU cc_start: 0.8911 (tp30) cc_final: 0.8607 (tp30) REVERT: F 183 MET cc_start: 0.9075 (tmm) cc_final: 0.8453 (tmm) REVERT: F 188 MET cc_start: 0.8341 (ttm) cc_final: 0.8000 (ttp) REVERT: F 212 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8155 (p) REVERT: G 47 GLU cc_start: 0.8900 (pm20) cc_final: 0.8660 (pm20) REVERT: G 183 MET cc_start: 0.8752 (tmm) cc_final: 0.8229 (tmm) REVERT: G 186 GLN cc_start: 0.8725 (tm-30) cc_final: 0.7797 (tp40) REVERT: G 307 TRP cc_start: 0.8124 (m100) cc_final: 0.7377 (m100) REVERT: G 333 PHE cc_start: 0.7843 (m-10) cc_final: 0.7634 (m-80) outliers start: 20 outliers final: 6 residues processed: 146 average time/residue: 0.0840 time to fit residues: 18.6434 Evaluate side-chains 110 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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: 4.9990 chunk 79 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 105 optimal weight: 30.0000 chunk 68 optimal weight: 40.0000 chunk 30 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.117241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.084329 restraints weight = 28840.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.087016 restraints weight = 14181.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.088711 restraints weight = 9352.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.089793 restraints weight = 7293.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.090257 restraints weight = 6300.461| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 10691 Z= 0.271 Angle : 0.803 11.899 14454 Z= 0.412 Chirality : 0.049 0.392 1631 Planarity : 0.005 0.046 1800 Dihedral : 21.131 169.938 1765 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.60 % Allowed : 23.08 % Favored : 74.33 % 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: -0.87 (0.27), residues: 348 sheet: -1.23 (0.33), residues: 240 loop : -1.93 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 19 TYR 0.037 0.003 TYR F 325 PHE 0.014 0.002 PHE G 105 TRP 0.009 0.001 TRP F 307 HIS 0.005 0.001 HIS G 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.27 (10679) covalent geometry : angle 0.80306 / 0.41 (14454) hydrogen bonds : bond 0.05289 / 3.51 ( 318) hydrogen bonds : angle 6.00791 / 4.11 ( 1031) Misc. bond : bond 0.00432 / 0.24 ( 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 131 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 183 MET cc_start: 0.9119 (tmm) cc_final: 0.8463 (tmm) REVERT: A 206 ASN cc_start: 0.8604 (t0) cc_final: 0.8228 (t0) REVERT: A 208 LEU cc_start: 0.8834 (tp) cc_final: 0.8459 (tp) REVERT: A 258 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 274 GLU cc_start: 0.8874 (pp20) cc_final: 0.8189 (pp20) REVERT: A 280 MET cc_start: 0.9279 (tpp) cc_final: 0.8958 (mmm) REVERT: A 283 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8842 (tp30) REVERT: A 307 TRP cc_start: 0.8504 (m-90) cc_final: 0.8184 (m-90) REVERT: A 315 ILE cc_start: 0.4068 (OUTLIER) cc_final: 0.3535 (mp) REVERT: B 183 MET cc_start: 0.9053 (tmm) cc_final: 0.8609 (tmm) REVERT: B 258 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8685 (tm-30) REVERT: F 140 GLU cc_start: 0.8929 (tp30) cc_final: 0.8614 (tp30) REVERT: F 183 MET cc_start: 0.9093 (tmm) cc_final: 0.8258 (tmm) REVERT: F 188 MET cc_start: 0.8483 (ttm) cc_final: 0.7912 (ttp) REVERT: F 251 LYS cc_start: 0.8402 (tptt) cc_final: 0.8153 (tptp) REVERT: G 186 GLN cc_start: 0.8713 (tm-30) cc_final: 0.7823 (tp40) REVERT: G 307 TRP cc_start: 0.8270 (m100) cc_final: 0.7323 (m100) outliers start: 27 outliers final: 14 residues processed: 125 average time/residue: 0.0685 time to fit residues: 13.5459 Evaluate side-chains 111 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 B residue 179 LEU 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 93 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: 8.9990 chunk 114 optimal weight: 0.0470 chunk 31 optimal weight: 30.0000 chunk 106 optimal weight: 7.9990 chunk 74 optimal weight: 0.0050 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 131 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 overall best weight: 2.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3927 r_free = 0.3927 target = 0.115648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.087706 restraints weight = 27520.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.090447 restraints weight = 13300.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.092188 restraints weight = 8665.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.093312 restraints weight = 6699.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.093860 restraints weight = 5743.211| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10691 Z= 0.140 Angle : 0.671 9.543 14454 Z= 0.351 Chirality : 0.046 0.188 1631 Planarity : 0.004 0.043 1800 Dihedral : 20.492 177.826 1765 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % 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: -2.03 (0.22), residues: 1324 helix: -0.63 (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 235 TYR 0.030 0.002 TYR F 325 PHE 0.016 0.001 PHE B 105 TRP 0.012 0.001 TRP F 307 HIS 0.009 0.002 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (10679) covalent geometry : angle 0.67083 / 0.35 (14454) hydrogen bonds : bond 0.04176 / 2.76 ( 318) hydrogen bonds : angle 5.49660 / 3.72 ( 1031) Misc. bond : bond 0.00459 / 0.25 ( 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 149 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8987 (p90) cc_final: 0.8319 (p90) REVERT: A 183 MET cc_start: 0.9132 (tmm) cc_final: 0.8541 (tmm) REVERT: A 191 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9249 (mp) REVERT: A 206 ASN cc_start: 0.8525 (t0) cc_final: 0.8053 (t0) REVERT: A 208 LEU cc_start: 0.8836 (tp) cc_final: 0.8447 (tp) REVERT: A 274 GLU cc_start: 0.8920 (pp20) cc_final: 0.8292 (pp20) REVERT: A 283 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8747 (tp30) REVERT: A 315 ILE cc_start: 0.4288 (OUTLIER) cc_final: 0.3982 (mp) REVERT: B 183 MET cc_start: 0.9079 (tmm) cc_final: 0.8683 (tmm) REVERT: B 258 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8600 (tm-30) REVERT: F 64 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8452 (tt) REVERT: F 76 GLU cc_start: 0.8111 (pp20) cc_final: 0.7671 (pp20) REVERT: F 140 GLU cc_start: 0.8940 (tp30) cc_final: 0.8662 (tp30) REVERT: F 183 MET cc_start: 0.9146 (tmm) cc_final: 0.8456 (tmm) REVERT: F 212 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8104 (p) REVERT: G 183 MET cc_start: 0.8664 (tmm) cc_final: 0.8133 (tmm) REVERT: G 186 GLN cc_start: 0.8604 (tm-30) cc_final: 0.7620 (tp40) REVERT: G 215 MET cc_start: 0.7503 (mmm) cc_final: 0.7193 (mmm) REVERT: G 307 TRP cc_start: 0.8325 (m100) cc_final: 0.7240 (m100) outliers start: 35 outliers final: 15 residues processed: 144 average time/residue: 0.0730 time to fit residues: 16.8516 Evaluate side-chains 120 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 191 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 201 ILE 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: 6.9990 chunk 63 optimal weight: 20.0000 chunk 83 optimal weight: 0.0870 chunk 129 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 94 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.9364 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.113840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.084043 restraints weight = 26520.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.086660 restraints weight = 13797.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.088343 restraints weight = 9275.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.089414 restraints weight = 7310.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.089964 restraints weight = 6318.645| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10691 Z= 0.150 Angle : 0.665 10.858 14454 Z= 0.347 Chirality : 0.046 0.210 1631 Planarity : 0.004 0.041 1800 Dihedral : 20.187 179.841 1765 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.08 % Allowed : 24.04 % Favored : 72.88 % 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: -1.57 (0.23), residues: 1324 helix: -0.08 (0.29), residues: 348 sheet: -0.80 (0.35), residues: 220 loop : -1.61 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 341 TYR 0.025 0.002 TYR A 308 PHE 0.020 0.002 PHE A 105 TRP 0.012 0.001 TRP F 307 HIS 0.008 0.001 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (10679) covalent geometry : angle 0.66527 / 0.35 (14454) hydrogen bonds : bond 0.03976 / 2.65 ( 318) hydrogen bonds : angle 5.33770 / 3.62 ( 1031) Misc. bond : bond 0.00423 / 0.23 ( 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: 32 poor density : 110 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8994 (p90) cc_final: 0.8372 (p90) REVERT: A 141 ILE cc_start: 0.9530 (mt) cc_final: 0.9285 (tp) REVERT: A 183 MET cc_start: 0.9122 (tmm) cc_final: 0.8575 (tmm) REVERT: A 206 ASN cc_start: 0.8571 (t0) cc_final: 0.8068 (t0) REVERT: A 208 LEU cc_start: 0.8852 (tp) cc_final: 0.8483 (tp) REVERT: A 274 GLU cc_start: 0.8912 (pp20) cc_final: 0.8344 (pp20) REVERT: A 283 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8737 (tp30) REVERT: A 307 TRP cc_start: 0.7745 (m100) cc_final: 0.7266 (m100) REVERT: A 315 ILE cc_start: 0.4244 (OUTLIER) cc_final: 0.3247 (mp) REVERT: B 40 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7539 (mtm) REVERT: B 183 MET cc_start: 0.9082 (tmm) cc_final: 0.8708 (tmm) REVERT: B 184 MET cc_start: 0.9297 (tpp) cc_final: 0.9053 (tpp) REVERT: B 206 ASN cc_start: 0.8899 (t0) cc_final: 0.8634 (t0) REVERT: B 258 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8588 (tm-30) REVERT: F 64 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8474 (tt) REVERT: F 140 GLU cc_start: 0.8865 (tp30) cc_final: 0.8444 (tp30) REVERT: F 183 MET cc_start: 0.9170 (tmm) cc_final: 0.8473 (tmm) REVERT: F 212 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8125 (p) REVERT: F 251 LYS cc_start: 0.8347 (tptt) cc_final: 0.7980 (tptp) REVERT: G 183 MET cc_start: 0.8695 (tmm) cc_final: 0.8266 (tmm) REVERT: G 186 GLN cc_start: 0.8706 (tm-30) cc_final: 0.7689 (tp40) REVERT: G 206 ASN cc_start: 0.8777 (t0) cc_final: 0.8497 (t0) REVERT: G 215 MET cc_start: 0.7596 (mmm) cc_final: 0.7363 (mmm) REVERT: G 243 GLN cc_start: 0.8790 (pm20) cc_final: 0.8154 (pt0) REVERT: G 307 TRP cc_start: 0.8422 (m100) cc_final: 0.7379 (m100) outliers start: 32 outliers final: 18 residues processed: 133 average time/residue: 0.0733 time to fit residues: 15.5349 Evaluate side-chains 123 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 40 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 201 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 111 optimal weight: 8.9990 chunk 125 optimal weight: 30.0000 chunk 31 optimal weight: 30.0000 chunk 106 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 24 optimal weight: 30.0000 chunk 60 optimal weight: 2.9990 chunk 84 optimal weight: 0.0770 chunk 64 optimal weight: 5.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.112327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.082155 restraints weight = 27161.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.084813 restraints weight = 13827.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086535 restraints weight = 9246.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.087662 restraints weight = 7230.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.088099 restraints weight = 6237.665| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 10691 Z= 0.191 Angle : 0.692 10.816 14454 Z= 0.356 Chirality : 0.046 0.207 1631 Planarity : 0.004 0.042 1800 Dihedral : 20.255 178.594 1765 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.46 % Allowed : 24.81 % 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: -1.47 (0.23), residues: 1324 helix: 0.07 (0.29), residues: 348 sheet: -0.64 (0.35), residues: 216 loop : -1.62 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 341 TYR 0.021 0.002 TYR F 325 PHE 0.016 0.002 PHE A 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 0.00444 / 0.19 (10679) covalent geometry : angle 0.69192 / 0.36 (14454) hydrogen bonds : bond 0.04026 / 2.69 ( 318) hydrogen bonds : angle 5.32050 / 3.60 ( 1031) Misc. bond : bond 0.00495 / 0.28 ( 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 141 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.415 Fit side-chains REVERT: A 141 ILE cc_start: 0.9532 (mt) cc_final: 0.9298 (tp) REVERT: A 183 MET cc_start: 0.9141 (tmm) cc_final: 0.8548 (tmm) REVERT: A 184 MET cc_start: 0.9038 (tpp) cc_final: 0.8667 (tpp) REVERT: A 206 ASN cc_start: 0.8600 (t0) cc_final: 0.8107 (t0) REVERT: A 208 LEU cc_start: 0.8853 (tp) cc_final: 0.8491 (tp) REVERT: A 274 GLU cc_start: 0.8933 (pp20) cc_final: 0.8380 (pp20) REVERT: A 280 MET cc_start: 0.9269 (tpp) cc_final: 0.9017 (mmm) REVERT: A 283 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8767 (tp30) REVERT: A 307 TRP cc_start: 0.7622 (m100) cc_final: 0.7137 (m100) REVERT: A 315 ILE cc_start: 0.4413 (OUTLIER) cc_final: 0.3411 (mp) REVERT: B 40 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7556 (mtm) REVERT: B 183 MET cc_start: 0.9113 (tmm) cc_final: 0.8730 (tmm) REVERT: B 258 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8597 (tm-30) REVERT: F 64 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8483 (tt) REVERT: F 140 GLU cc_start: 0.8849 (tp30) cc_final: 0.8395 (tp30) REVERT: F 183 MET cc_start: 0.9141 (tmm) cc_final: 0.8276 (tmm) REVERT: F 212 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8238 (p) REVERT: G 171 ASP cc_start: 0.8145 (t0) cc_final: 0.7923 (t0) REVERT: G 183 MET cc_start: 0.8716 (tmm) cc_final: 0.8378 (tmm) REVERT: G 206 ASN cc_start: 0.8838 (t0) cc_final: 0.8515 (t0) REVERT: G 215 MET cc_start: 0.7618 (mmm) cc_final: 0.7407 (mmm) REVERT: G 307 TRP cc_start: 0.8513 (m100) cc_final: 0.7451 (m100) outliers start: 36 outliers final: 24 residues processed: 132 average time/residue: 0.0748 time to fit residues: 15.7218 Evaluate side-chains 129 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 290 GLU 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 120 LEU Chi-restraints excluded: chain B residue 201 ILE 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 195 ILE Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 290 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 131 optimal weight: 30.0000 chunk 71 optimal weight: 20.0000 chunk 133 optimal weight: 30.0000 chunk 79 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.111278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.081174 restraints weight = 26930.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.083715 restraints weight = 14337.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.085344 restraints weight = 9752.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.086370 restraints weight = 7742.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.086801 restraints weight = 6740.723| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 10691 Z= 0.238 Angle : 0.729 10.068 14454 Z= 0.377 Chirality : 0.047 0.209 1631 Planarity : 0.004 0.044 1800 Dihedral : 20.251 177.560 1765 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.94 % Allowed : 25.10 % 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: -1.39 (0.23), residues: 1324 helix: 0.18 (0.29), residues: 348 sheet: -0.57 (0.35), residues: 216 loop : -1.61 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 341 TYR 0.019 0.002 TYR A 308 PHE 0.016 0.002 PHE G 105 TRP 0.012 0.001 TRP F 307 HIS 0.011 0.001 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.24 (10679) covalent geometry : angle 0.72851 / 0.38 (14454) hydrogen bonds : bond 0.04292 / 2.88 ( 318) hydrogen bonds : angle 5.38241 / 3.66 ( 1031) Misc. bond : bond 0.00439 / 0.24 ( 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 147 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.408 Fit side-chains REVERT: A 141 ILE cc_start: 0.9557 (mt) cc_final: 0.9305 (tp) REVERT: A 183 MET cc_start: 0.9164 (tmm) cc_final: 0.8581 (tmm) REVERT: A 206 ASN cc_start: 0.8650 (t0) cc_final: 0.8135 (t0) REVERT: A 208 LEU cc_start: 0.8843 (tp) cc_final: 0.8491 (tp) REVERT: A 274 GLU cc_start: 0.8989 (pp20) cc_final: 0.8455 (pp20) REVERT: A 283 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8789 (tp30) REVERT: A 307 TRP cc_start: 0.7689 (m100) cc_final: 0.7239 (m100) REVERT: A 315 ILE cc_start: 0.4357 (OUTLIER) cc_final: 0.3489 (mp) REVERT: B 40 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7595 (mtm) REVERT: B 183 MET cc_start: 0.9168 (tmm) cc_final: 0.8765 (tmm) REVERT: B 206 ASN cc_start: 0.8914 (t0) cc_final: 0.8640 (t0) REVERT: B 258 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8612 (tm-30) REVERT: F 64 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8407 (tt) REVERT: F 140 GLU cc_start: 0.8915 (tp30) cc_final: 0.8446 (tp30) REVERT: F 183 MET cc_start: 0.9102 (tmm) cc_final: 0.8224 (tmm) REVERT: F 188 MET cc_start: 0.8603 (ttm) cc_final: 0.7977 (ttp) REVERT: F 251 LYS cc_start: 0.8276 (tptt) cc_final: 0.8005 (tptp) REVERT: F 283 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8140 (tp30) REVERT: G 171 ASP cc_start: 0.8248 (t0) cc_final: 0.7995 (t0) REVERT: G 206 ASN cc_start: 0.8867 (t0) cc_final: 0.8547 (t0) REVERT: G 215 MET cc_start: 0.7729 (mmm) cc_final: 0.7502 (mmm) outliers start: 41 outliers final: 27 residues processed: 137 average time/residue: 0.0730 time to fit residues: 15.6512 Evaluate side-chains 127 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER 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 A residue 290 GLU 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 120 LEU Chi-restraints excluded: chain B residue 201 ILE 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 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 93 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 78 optimal weight: 8.9990 chunk 84 optimal weight: 0.1980 chunk 79 optimal weight: 0.7980 chunk 51 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** 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 = 0.3862 r_free = 0.3862 target = 0.115018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085032 restraints weight = 26421.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.087704 restraints weight = 13819.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089411 restraints weight = 9313.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.090294 restraints weight = 7332.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.091108 restraints weight = 6415.350| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10691 Z= 0.132 Angle : 0.713 14.805 14454 Z= 0.363 Chirality : 0.047 0.288 1631 Planarity : 0.004 0.045 1800 Dihedral : 20.277 176.007 1765 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.98 % Allowed : 25.67 % 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: -1.42 (0.23), residues: 1324 helix: -0.03 (0.28), residues: 376 sheet: -0.48 (0.35), residues: 216 loop : -1.61 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 235 TYR 0.017 0.002 TYR G 325 PHE 0.015 0.001 PHE B 105 TRP 0.014 0.001 TRP F 307 HIS 0.008 0.002 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (10679) covalent geometry : angle 0.71306 / 0.36 (14454) hydrogen bonds : bond 0.03843 / 2.54 ( 318) hydrogen bonds : angle 5.32892 / 3.59 ( 1031) Misc. bond : bond 0.00515 / 0.28 ( 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 145 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.253 Fit side-chains REVERT: A 141 ILE cc_start: 0.9516 (mt) cc_final: 0.9265 (tp) REVERT: A 183 MET cc_start: 0.9142 (tmm) cc_final: 0.8602 (tmm) REVERT: A 206 ASN cc_start: 0.8508 (t0) cc_final: 0.7996 (t0) REVERT: A 208 LEU cc_start: 0.8817 (tp) cc_final: 0.8452 (tp) REVERT: A 274 GLU cc_start: 0.8944 (pp20) cc_final: 0.8432 (pp20) REVERT: A 283 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8751 (tp30) REVERT: A 307 TRP cc_start: 0.7615 (m100) cc_final: 0.7188 (m100) REVERT: A 315 ILE cc_start: 0.4282 (OUTLIER) cc_final: 0.3462 (mp) REVERT: B 40 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7530 (mtm) REVERT: B 183 MET cc_start: 0.9095 (tmm) cc_final: 0.8726 (tmm) REVERT: B 206 ASN cc_start: 0.8738 (t0) cc_final: 0.8477 (t0) REVERT: F 64 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8426 (tt) REVERT: F 140 GLU cc_start: 0.8830 (tp30) cc_final: 0.8376 (tp30) REVERT: F 147 ASP cc_start: 0.7995 (p0) cc_final: 0.7418 (t0) REVERT: F 183 MET cc_start: 0.9167 (tmm) cc_final: 0.8475 (tmm) REVERT: F 212 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8191 (p) REVERT: F 251 LYS cc_start: 0.8350 (tptt) cc_final: 0.7902 (tptp) REVERT: F 283 GLU cc_start: 0.8697 (mm-30) cc_final: 0.7884 (tp30) REVERT: G 40 MET cc_start: 0.8664 (mtp) cc_final: 0.7669 (ttm) REVERT: G 171 ASP cc_start: 0.8240 (t0) cc_final: 0.8001 (t0) REVERT: G 206 ASN cc_start: 0.8775 (t0) cc_final: 0.8456 (t0) REVERT: G 243 GLN cc_start: 0.8811 (pm20) cc_final: 0.8238 (pt0) outliers start: 31 outliers final: 19 residues processed: 138 average time/residue: 0.0765 time to fit residues: 16.7283 Evaluate side-chains 123 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 290 GLU 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 106 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 201 ILE 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 128 LEU Chi-restraints excluded: chain G residue 253 THR 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: 6.9990 chunk 109 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.112569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082709 restraints weight = 26747.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.085284 restraints weight = 14064.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.086942 restraints weight = 9517.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088008 restraints weight = 7535.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088338 restraints weight = 6539.941| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10691 Z= 0.173 Angle : 0.764 27.538 14454 Z= 0.376 Chirality : 0.048 0.320 1631 Planarity : 0.004 0.048 1800 Dihedral : 20.206 177.814 1765 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.98 % Allowed : 26.35 % Favored : 70.67 % 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: -1.19 (0.23), residues: 1324 helix: 0.42 (0.29), residues: 348 sheet: -0.57 (0.35), residues: 220 loop : -1.47 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 341 TYR 0.018 0.002 TYR A 308 PHE 0.014 0.001 PHE B 105 TRP 0.014 0.001 TRP F 307 HIS 0.009 0.001 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (10679) covalent geometry : angle 0.76434 / 0.38 (14454) hydrogen bonds : bond 0.03859 / 2.56 ( 318) hydrogen bonds : angle 5.32200 / 3.60 ( 1031) Misc. bond : bond 0.00600 / 0.34 ( 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 131 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 141 ILE cc_start: 0.9532 (mt) cc_final: 0.9298 (tp) REVERT: A 183 MET cc_start: 0.9178 (tmm) cc_final: 0.8573 (tmm) REVERT: A 206 ASN cc_start: 0.8596 (t0) cc_final: 0.8077 (t0) REVERT: A 208 LEU cc_start: 0.8828 (tp) cc_final: 0.8458 (tp) REVERT: A 274 GLU cc_start: 0.8975 (pp20) cc_final: 0.8479 (pp20) REVERT: A 283 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8784 (tp30) REVERT: A 307 TRP cc_start: 0.7718 (m100) cc_final: 0.7295 (m100) REVERT: A 315 ILE cc_start: 0.4357 (OUTLIER) cc_final: 0.3549 (mp) REVERT: B 40 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7599 (mtm) REVERT: B 183 MET cc_start: 0.9167 (tmm) cc_final: 0.8853 (tmm) REVERT: B 206 ASN cc_start: 0.8753 (t0) cc_final: 0.8430 (t0) REVERT: F 140 GLU cc_start: 0.8900 (tp30) cc_final: 0.8455 (tp30) REVERT: F 147 ASP cc_start: 0.8076 (p0) cc_final: 0.7547 (t0) REVERT: F 183 MET cc_start: 0.9134 (tmm) cc_final: 0.8307 (tmm) REVERT: F 212 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8276 (p) REVERT: F 251 LYS cc_start: 0.8293 (tptt) cc_final: 0.7664 (tptp) REVERT: F 283 GLU cc_start: 0.8733 (mm-30) cc_final: 0.7913 (tp30) REVERT: G 171 ASP cc_start: 0.8246 (t0) cc_final: 0.8001 (t0) REVERT: G 206 ASN cc_start: 0.8826 (t0) cc_final: 0.8475 (t0) outliers start: 31 outliers final: 23 residues processed: 125 average time/residue: 0.0675 time to fit residues: 13.4165 Evaluate side-chains 123 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 A residue 290 GLU Chi-restraints excluded: chain A residue 315 ILE 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 201 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 23 LEU 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 32 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** 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 = 0.3844 r_free = 0.3844 target = 0.113937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.084078 restraints weight = 26270.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.086701 restraints weight = 13818.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.088373 restraints weight = 9321.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.089312 restraints weight = 7381.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.090063 restraints weight = 6463.301| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2877 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= 0.148 Angle : 0.739 21.879 14454 Z= 0.368 Chirality : 0.048 0.278 1631 Planarity : 0.004 0.049 1800 Dihedral : 19.986 179.520 1765 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.88 % Allowed : 26.44 % Favored : 70.67 % 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: -1.12 (0.23), residues: 1324 helix: 0.52 (0.29), residues: 352 sheet: -0.57 (0.35), residues: 220 loop : -1.45 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 341 TYR 0.016 0.002 TYR A 308 PHE 0.025 0.001 PHE A 15 TRP 0.015 0.001 TRP F 307 HIS 0.008 0.001 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (10679) covalent geometry : angle 0.73892 / 0.37 (14454) hydrogen bonds : bond 0.03621 / 2.39 ( 318) hydrogen bonds : angle 5.26946 / 3.56 ( 1031) Misc. bond : bond 0.00574 / 0.32 ( 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 134 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.392 Fit side-chains REVERT: A 141 ILE cc_start: 0.9514 (mt) cc_final: 0.9270 (tp) REVERT: A 183 MET cc_start: 0.9182 (tmm) cc_final: 0.8655 (tmm) REVERT: A 206 ASN cc_start: 0.8563 (t0) cc_final: 0.8037 (t0) REVERT: A 208 LEU cc_start: 0.8824 (tp) cc_final: 0.8486 (tp) REVERT: A 274 GLU cc_start: 0.8943 (pp20) cc_final: 0.8476 (pp20) REVERT: A 283 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8720 (tp30) REVERT: A 307 TRP cc_start: 0.7574 (m100) cc_final: 0.7192 (m100) REVERT: A 315 ILE cc_start: 0.4309 (OUTLIER) cc_final: 0.3533 (mp) REVERT: B 183 MET cc_start: 0.9171 (tmm) cc_final: 0.8893 (tmm) REVERT: F 64 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8432 (tt) REVERT: F 140 GLU cc_start: 0.8790 (tp30) cc_final: 0.8385 (tp30) REVERT: F 147 ASP cc_start: 0.7978 (p0) cc_final: 0.7448 (t0) REVERT: F 183 MET cc_start: 0.9149 (tmm) cc_final: 0.8424 (tmm) REVERT: F 212 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8256 (p) REVERT: F 251 LYS cc_start: 0.8250 (tptt) cc_final: 0.7717 (tptp) REVERT: F 283 GLU cc_start: 0.8661 (mm-30) cc_final: 0.7966 (tp30) REVERT: G 171 ASP cc_start: 0.8216 (t0) cc_final: 0.7974 (t0) REVERT: G 206 ASN cc_start: 0.8863 (t0) cc_final: 0.8538 (t0) outliers start: 30 outliers final: 25 residues processed: 128 average time/residue: 0.0718 time to fit residues: 14.6486 Evaluate side-chains 125 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER 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 264 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 315 ILE 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 201 ILE 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 280 MET 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 195 ILE 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: 9.9990 chunk 83 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 98 optimal weight: 0.0370 chunk 62 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 overall best weight: 6.0066 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.111885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.081834 restraints weight = 27254.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.084374 restraints weight = 14393.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.086011 restraints weight = 9797.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.087050 restraints weight = 7791.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.087398 restraints weight = 6780.841| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 10691 Z= 0.226 Angle : 0.781 19.302 14454 Z= 0.392 Chirality : 0.049 0.318 1631 Planarity : 0.004 0.047 1800 Dihedral : 20.000 178.385 1765 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.98 % Allowed : 26.73 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.24), residues: 1324 helix: 0.55 (0.29), residues: 352 sheet: -0.55 (0.35), residues: 220 loop : -1.45 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 341 TYR 0.018 0.002 TYR B 281 PHE 0.014 0.002 PHE G 105 TRP 0.013 0.001 TRP F 307 HIS 0.009 0.001 HIS F 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.23 (10679) covalent geometry : angle 0.78100 / 0.39 (14454) hydrogen bonds : bond 0.03964 / 2.65 ( 318) hydrogen bonds : angle 5.38171 / 3.63 ( 1031) Misc. bond : bond 0.00576 / 0.31 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1586.13 seconds wall clock time: 28 minutes 11.73 seconds (1691.73 seconds total)