Starting phenix.real_space_refine on Sat Aug 23 07:09:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8amf_15525/08_2025/8amf_15525.cif Found real_map, /net/cci-nas-00/data/ceres_data/8amf_15525/08_2025/8amf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8amf_15525/08_2025/8amf_15525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8amf_15525/08_2025/8amf_15525.map" model { file = "/net/cci-nas-00/data/ceres_data/8amf_15525/08_2025/8amf_15525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8amf_15525/08_2025/8amf_15525.cif" } 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-2.0-5787/lib/python3.9/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: 24 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: 24 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: 24 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: 24 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: 2.22, 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: 0.89 Conformation dependent library (CDL) restraints added in 248.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 15 sheets defined 37.4% alpha, 25.0% beta 5 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 1.21 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: 1.10 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=" O1A AGS B 500 " pdb=" PA AGS B 500 " ideal model delta sigma weight residual 1.481 1.582 -0.101 2.70e-02 1.37e+03 1.40e+01 bond pdb=" O2B AGS A 500 " pdb=" PB AGS A 500 " ideal model delta sigma weight residual 1.531 1.472 0.059 1.60e-02 3.91e+03 1.38e+01 bond pdb=" O1A AGS F 500 " pdb=" PA AGS F 500 " ideal model delta sigma weight residual 1.481 1.571 -0.090 2.70e-02 1.37e+03 1.12e+01 bond pdb=" O2B AGS G 500 " pdb=" PB AGS G 500 " ideal model delta sigma weight residual 1.531 1.483 0.048 1.60e-02 3.91e+03 8.81e+00 bond pdb=" O2B AGS B 500 " pdb=" PB AGS B 500 " ideal model delta sigma weight residual 1.531 1.484 0.047 1.60e-02 3.91e+03 8.50e+00 ... (remaining 10674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 13687 1.90 - 3.80: 640 3.80 - 5.70: 75 5.70 - 7.60: 29 7.60 - 9.50: 23 Bond angle restraints: 14454 Sorted by residual: 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 angle pdb=" C ASP B 249 " pdb=" N GLN B 250 " pdb=" CA GLN B 250 " ideal model delta sigma weight residual 121.54 129.39 -7.85 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C ASP A 249 " pdb=" N GLN A 250 " pdb=" CA GLN A 250 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C ASP G 249 " pdb=" N GLN G 250 " pdb=" CA GLN G 250 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 ... (remaining 14449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.38: 6052 28.38 - 56.75: 428 56.75 - 85.13: 51 85.13 - 113.50: 4 113.50 - 141.88: 4 Dihedral angle restraints: 6539 sinusoidal: 2803 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 6536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 1621 0.160 - 0.321: 14 0.321 - 0.481: 0 0.481 - 0.641: 1 0.641 - 0.802: 3 Chirality restraints: 1639 Sorted by residual: chirality pdb=" PB AGS B 500 " pdb=" O2B AGS B 500 " pdb=" O3A AGS B 500 " pdb=" O3B AGS B 500 " both_signs ideal model delta sigma weight residual True 3.18 2.38 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" PB AGS G 500 " pdb=" O2B AGS G 500 " pdb=" O3A AGS G 500 " pdb=" O3B AGS G 500 " both_signs ideal model delta sigma weight residual True 3.18 2.47 0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" PB AGS F 500 " pdb=" O2B AGS F 500 " pdb=" O3A AGS F 500 " pdb=" O3B AGS F 500 " both_signs ideal model delta sigma weight residual True 3.18 2.48 0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 1636 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: 0.010 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: 0.030 Process input model: 9.720 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 0.007 0.143 10691 Z= 0.313 Angle : 0.992 9.496 14454 Z= 0.538 Chirality : 0.065 0.802 1639 Planarity : 0.006 0.075 1800 Dihedral : 18.673 141.876 4163 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 aren 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 covalent geometry : bond 0.00706 (10679) covalent geometry : angle 0.99199 (14454) hydrogen bonds : bond 0.26136 ( 318) hydrogen bonds : angle 8.01262 ( 1031) Misc. bond : bond 0.00693 ( 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 : 0.389 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: 0.5779 (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: 0.7776 (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: 0.0860 time to fit residues: 22.8625 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 : 0.244 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.121457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.088531 restraints weight = 28419.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091355 restraints weight = 13841.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.093166 restraints weight = 9036.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094315 restraints weight = 6989.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.094931 restraints weight = 5998.734| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10691 Z= 0.152 Angle : 0.663 7.787 14454 Z= 0.354 Chirality : 0.047 0.209 1639 Planarity : 0.004 0.052 1800 Dihedral : 17.275 158.643 1717 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.31 % Allowed : 19.81 % Favored : 77.88 % 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 aren not related in a simple way. whole: -2.62 (0.21), residues: 1324 helix: -1.29 (0.26), residues: 348 sheet: -1.41 (0.33), residues: 220 loop : -2.10 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 182 TYR 0.018 0.002 TYR A 78 PHE 0.019 0.001 PHE B 105 TRP 0.013 0.001 TRP G 307 HIS 0.005 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00359 (10679) covalent geometry : angle 0.66279 (14454) hydrogen bonds : bond 0.04503 ( 318) hydrogen bonds : angle 5.62844 ( 1031) Misc. bond : bond 0.00514 ( 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 161 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.9161 (tmm) cc_final: 0.8567 (tmm) REVERT: A 206 ASN cc_start: 0.8637 (t0) cc_final: 0.8081 (t0) REVERT: A 208 LEU cc_start: 0.8834 (tp) cc_final: 0.8437 (tp) REVERT: A 274 GLU cc_start: 0.8862 (pp20) cc_final: 0.8141 (pp20) REVERT: A 283 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8860 (tp30) REVERT: A 315 ILE cc_start: 0.4183 (OUTLIER) cc_final: 0.3732 (mp) REVERT: B 76 GLU cc_start: 0.7210 (pp20) cc_final: 0.6982 (pp20) REVERT: B 141 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8705 (mp) REVERT: B 183 MET cc_start: 0.9030 (tmm) cc_final: 0.8538 (tmm) REVERT: B 184 MET cc_start: 0.9183 (tpp) cc_final: 0.8836 (tpp) REVERT: B 206 ASN cc_start: 0.8623 (t0) cc_final: 0.8382 (t0) REVERT: B 258 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8593 (tm-30) REVERT: F 76 GLU cc_start: 0.7997 (pp20) cc_final: 0.7336 (pp20) REVERT: F 140 GLU cc_start: 0.9108 (tp30) cc_final: 0.8835 (tp30) REVERT: F 183 MET cc_start: 0.9047 (tmm) cc_final: 0.8362 (tmm) REVERT: F 188 MET cc_start: 0.8354 (ttm) cc_final: 0.8101 (ttp) REVERT: F 212 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7966 (p) REVERT: G 183 MET cc_start: 0.8644 (tmm) cc_final: 0.8138 (tmm) REVERT: G 186 GLN cc_start: 0.8750 (tm-30) cc_final: 0.7862 (tp40) REVERT: G 206 ASN cc_start: 0.8817 (t0) cc_final: 0.8388 (t0) REVERT: G 208 LEU cc_start: 0.9192 (mt) cc_final: 0.8953 (mt) REVERT: G 307 TRP cc_start: 0.8328 (m100) cc_final: 0.7382 (m100) outliers start: 24 outliers final: 6 residues processed: 158 average time/residue: 0.0726 time to fit residues: 17.6904 Evaluate side-chains 113 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 141 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 Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 108 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 68 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** F 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** 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 = 0.3783 r_free = 0.3783 target = 0.110026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.080061 restraints weight = 27309.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.082501 restraints weight = 14890.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.084087 restraints weight = 10283.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.085097 restraints weight = 8213.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.085638 restraints weight = 7169.447| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 10691 Z= 0.264 Angle : 0.751 8.912 14454 Z= 0.392 Chirality : 0.048 0.226 1639 Planarity : 0.005 0.046 1800 Dihedral : 17.576 151.722 1717 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.60 % Allowed : 23.17 % Favored : 74.23 % 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 aren not related in a simple way. whole: -1.84 (0.23), residues: 1324 helix: -0.30 (0.29), residues: 324 sheet: -1.15 (0.34), residues: 240 loop : -1.69 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 341 TYR 0.027 0.002 TYR A 231 PHE 0.022 0.002 PHE F 15 TRP 0.012 0.002 TRP F 307 HIS 0.005 0.001 HIS G 329 Details of bonding type rmsd covalent geometry : bond 0.00626 (10679) covalent geometry : angle 0.75118 (14454) hydrogen bonds : bond 0.04846 ( 318) hydrogen bonds : angle 5.49986 ( 1031) Misc. bond : bond 0.00515 ( 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 134 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.9114 (tmm) cc_final: 0.8519 (tmm) REVERT: A 206 ASN cc_start: 0.8641 (t0) cc_final: 0.8195 (t0) REVERT: A 208 LEU cc_start: 0.8845 (tp) cc_final: 0.8488 (tp) REVERT: A 274 GLU cc_start: 0.8976 (pp20) cc_final: 0.8458 (pp20) REVERT: A 280 MET cc_start: 0.9221 (tpp) cc_final: 0.8984 (mmm) REVERT: B 76 GLU cc_start: 0.7543 (pp20) cc_final: 0.7338 (pp20) REVERT: B 183 MET cc_start: 0.9046 (tmm) cc_final: 0.8679 (tmm) REVERT: B 206 ASN cc_start: 0.8837 (t0) cc_final: 0.8611 (t0) REVERT: B 258 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8592 (tm-30) REVERT: F 76 GLU cc_start: 0.8290 (pp20) cc_final: 0.7883 (pp20) REVERT: F 147 ASP cc_start: 0.8131 (p0) cc_final: 0.7489 (t0) REVERT: F 183 MET cc_start: 0.9112 (tmm) cc_final: 0.8256 (tmm) REVERT: F 184 MET cc_start: 0.9058 (tpp) cc_final: 0.8845 (tpp) REVERT: G 183 MET cc_start: 0.8857 (tmm) cc_final: 0.8365 (tmm) REVERT: G 206 ASN cc_start: 0.8825 (t0) cc_final: 0.8541 (t0) REVERT: G 307 TRP cc_start: 0.8630 (m100) cc_final: 0.7835 (m100) REVERT: G 315 ILE cc_start: 0.6631 (OUTLIER) cc_final: 0.6302 (mp) outliers start: 27 outliers final: 15 residues processed: 127 average time/residue: 0.0674 time to fit residues: 13.4993 Evaluate side-chains 109 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 VAL 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 G residue 50 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 69 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 31 optimal weight: 30.0000 chunk 106 optimal weight: 4.9990 chunk 74 optimal weight: 0.0980 chunk 20 optimal weight: 0.4980 chunk 13 optimal weight: 6.9990 chunk 131 optimal weight: 30.0000 chunk 61 optimal weight: 0.0040 chunk 95 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 overall best weight: 2.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** 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 = 0.3846 r_free = 0.3846 target = 0.114137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.084242 restraints weight = 26600.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.086875 restraints weight = 13913.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.088548 restraints weight = 9375.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.089630 restraints weight = 7383.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.090110 restraints weight = 6399.851| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10691 Z= 0.143 Angle : 0.645 9.046 14454 Z= 0.336 Chirality : 0.046 0.197 1639 Planarity : 0.004 0.043 1800 Dihedral : 17.187 154.516 1717 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.98 % Allowed : 23.65 % Favored : 73.37 % 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 aren not related in a simple way. whole: -1.78 (0.23), residues: 1324 helix: -0.38 (0.28), residues: 372 sheet: -0.79 (0.36), residues: 216 loop : -1.77 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 341 TYR 0.015 0.002 TYR A 78 PHE 0.021 0.001 PHE F 15 TRP 0.012 0.001 TRP F 307 HIS 0.006 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00339 (10679) covalent geometry : angle 0.64525 (14454) hydrogen bonds : bond 0.03797 ( 318) hydrogen bonds : angle 5.10278 ( 1031) Misc. bond : bond 0.00471 ( 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 144 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 78 TYR cc_start: 0.9001 (p90) cc_final: 0.8517 (p90) REVERT: A 141 ILE cc_start: 0.9543 (mt) cc_final: 0.9296 (tp) REVERT: A 183 MET cc_start: 0.9173 (tmm) cc_final: 0.8648 (tmm) REVERT: A 206 ASN cc_start: 0.8563 (t0) cc_final: 0.8040 (t0) REVERT: A 208 LEU cc_start: 0.8821 (tp) cc_final: 0.8469 (tp) REVERT: A 274 GLU cc_start: 0.8986 (pp20) cc_final: 0.8530 (pp20) REVERT: A 280 MET cc_start: 0.9208 (tpp) cc_final: 0.8943 (mmm) REVERT: A 283 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8747 (tp30) REVERT: A 307 TRP cc_start: 0.7788 (m100) cc_final: 0.7313 (m100) REVERT: B 29 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9140 (tt) REVERT: B 183 MET cc_start: 0.9093 (tmm) cc_final: 0.8690 (tmm) REVERT: B 184 MET cc_start: 0.9274 (tpp) cc_final: 0.8862 (tpp) REVERT: B 206 ASN cc_start: 0.8740 (t0) cc_final: 0.8490 (t0) REVERT: B 212 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8823 (p) REVERT: B 258 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8511 (tm-30) REVERT: B 310 TYR cc_start: 0.5992 (m-10) cc_final: 0.5753 (m-10) REVERT: F 147 ASP cc_start: 0.8027 (p0) cc_final: 0.7509 (t0) REVERT: F 183 MET cc_start: 0.9174 (tmm) cc_final: 0.8495 (tmm) REVERT: F 212 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8120 (p) REVERT: G 171 ASP cc_start: 0.8309 (t0) cc_final: 0.8026 (t0) REVERT: G 183 MET cc_start: 0.8928 (tmm) cc_final: 0.8343 (tmm) REVERT: G 206 ASN cc_start: 0.8753 (t0) cc_final: 0.8474 (t0) REVERT: G 307 TRP cc_start: 0.8627 (m100) cc_final: 0.7850 (m100) REVERT: G 315 ILE cc_start: 0.6279 (OUTLIER) cc_final: 0.5950 (mp) outliers start: 31 outliers final: 11 residues processed: 135 average time/residue: 0.0640 time to fit residues: 13.8099 Evaluate side-chains 116 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 212 VAL 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 263 VAL 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 315 ILE Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 30.0000 chunk 83 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 105 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 94 optimal weight: 0.0030 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 overall best weight: 3.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** 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 = 0.3828 r_free = 0.3828 target = 0.113247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.083157 restraints weight = 26869.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.085889 restraints weight = 13760.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.087654 restraints weight = 9157.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.088761 restraints weight = 7157.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.089464 restraints weight = 6169.539| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10691 Z= 0.153 Angle : 0.638 8.224 14454 Z= 0.334 Chirality : 0.046 0.195 1639 Planarity : 0.004 0.046 1800 Dihedral : 16.996 154.539 1717 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.08 % Allowed : 24.71 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.23), residues: 1324 helix: 0.21 (0.29), residues: 352 sheet: -0.63 (0.36), residues: 216 loop : -1.55 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 189 TYR 0.014 0.002 TYR A 78 PHE 0.017 0.001 PHE A 105 TRP 0.013 0.001 TRP F 307 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00370 (10679) covalent geometry : angle 0.63828 (14454) hydrogen bonds : bond 0.03589 ( 318) hydrogen bonds : angle 4.98381 ( 1031) Misc. bond : bond 0.00466 ( 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 143 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.326 Fit side-chains REVERT: A 141 ILE cc_start: 0.9492 (mt) cc_final: 0.9271 (tp) REVERT: A 183 MET cc_start: 0.9228 (tmm) cc_final: 0.8603 (tmm) REVERT: A 206 ASN cc_start: 0.8580 (t0) cc_final: 0.8097 (t0) REVERT: A 208 LEU cc_start: 0.8811 (tp) cc_final: 0.8447 (tp) REVERT: A 274 GLU cc_start: 0.8999 (pp20) cc_final: 0.8543 (pp20) REVERT: A 283 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8792 (tp30) REVERT: A 307 TRP cc_start: 0.7921 (m100) cc_final: 0.7466 (m100) REVERT: B 183 MET cc_start: 0.9144 (tmm) cc_final: 0.8698 (tmm) REVERT: B 184 MET cc_start: 0.9300 (tpp) cc_final: 0.8840 (tpp) REVERT: B 206 ASN cc_start: 0.8797 (t0) cc_final: 0.8556 (t0) REVERT: B 258 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8467 (tm-30) REVERT: B 307 TRP cc_start: 0.8279 (m-90) cc_final: 0.7917 (m100) REVERT: F 40 MET cc_start: 0.8040 (mtp) cc_final: 0.7808 (ttm) REVERT: F 64 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8408 (tt) REVERT: F 140 GLU cc_start: 0.8917 (tp30) cc_final: 0.8453 (tp30) REVERT: F 147 ASP cc_start: 0.8087 (p0) cc_final: 0.7546 (t0) REVERT: F 183 MET cc_start: 0.9140 (tmm) cc_final: 0.8414 (tmm) REVERT: F 206 ASN cc_start: 0.9007 (t0) cc_final: 0.8319 (m-40) REVERT: F 251 LYS cc_start: 0.8214 (tptt) cc_final: 0.7800 (tptt) REVERT: G 171 ASP cc_start: 0.8402 (t0) cc_final: 0.8034 (t0) REVERT: G 183 MET cc_start: 0.8956 (tmm) cc_final: 0.8345 (tmm) REVERT: G 206 ASN cc_start: 0.8879 (t0) cc_final: 0.8504 (t0) REVERT: G 274 GLU cc_start: 0.8853 (pp20) cc_final: 0.8489 (pp20) REVERT: G 307 TRP cc_start: 0.8707 (m100) cc_final: 0.7961 (m100) REVERT: G 315 ILE cc_start: 0.6259 (OUTLIER) cc_final: 0.5901 (mp) outliers start: 32 outliers final: 17 residues processed: 135 average time/residue: 0.0683 time to fit residues: 14.6734 Evaluate side-chains 123 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 139 LEU 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 263 VAL 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 Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 111 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 60 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** 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 = 0.3866 r_free = 0.3866 target = 0.115449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.085508 restraints weight = 26354.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.088157 restraints weight = 13724.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.089882 restraints weight = 9225.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.090963 restraints weight = 7250.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.091589 restraints weight = 6279.562| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10691 Z= 0.144 Angle : 0.625 7.555 14454 Z= 0.326 Chirality : 0.045 0.209 1639 Planarity : 0.004 0.044 1800 Dihedral : 16.920 156.379 1717 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.27 % Allowed : 25.19 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.23), residues: 1324 helix: 0.54 (0.30), residues: 348 sheet: -0.61 (0.35), residues: 220 loop : -1.46 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 235 TYR 0.013 0.001 TYR A 78 PHE 0.015 0.001 PHE B 105 TRP 0.013 0.001 TRP F 307 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00345 (10679) covalent geometry : angle 0.62538 (14454) hydrogen bonds : bond 0.03399 ( 318) hydrogen bonds : angle 4.85504 ( 1031) Misc. bond : bond 0.00465 ( 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 146 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.9483 (mt) cc_final: 0.9271 (tp) REVERT: A 183 MET cc_start: 0.9246 (tmm) cc_final: 0.8623 (tmm) REVERT: A 206 ASN cc_start: 0.8534 (t0) cc_final: 0.8105 (t0) REVERT: A 208 LEU cc_start: 0.8818 (tp) cc_final: 0.8461 (tp) REVERT: A 274 GLU cc_start: 0.8970 (pp20) cc_final: 0.8543 (pp20) REVERT: A 307 TRP cc_start: 0.7934 (m100) cc_final: 0.7518 (m100) REVERT: B 29 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9148 (tt) REVERT: B 183 MET cc_start: 0.9153 (tmm) cc_final: 0.8763 (tmm) REVERT: B 258 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8145 (tm-30) REVERT: B 307 TRP cc_start: 0.8234 (m-90) cc_final: 0.7759 (m100) REVERT: F 64 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8398 (tt) REVERT: F 140 GLU cc_start: 0.8901 (tp30) cc_final: 0.8440 (tp30) REVERT: F 183 MET cc_start: 0.9128 (tmm) cc_final: 0.8303 (tmm) REVERT: F 206 ASN cc_start: 0.8969 (t0) cc_final: 0.8666 (t0) REVERT: F 212 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8403 (p) REVERT: G 171 ASP cc_start: 0.8381 (t0) cc_final: 0.8077 (t0) REVERT: G 183 MET cc_start: 0.9009 (tmm) cc_final: 0.8432 (tmm) REVERT: G 206 ASN cc_start: 0.8895 (t0) cc_final: 0.8585 (m-40) REVERT: G 274 GLU cc_start: 0.8856 (pp20) cc_final: 0.8441 (pp20) REVERT: G 307 TRP cc_start: 0.8776 (m100) cc_final: 0.8083 (m100) REVERT: G 315 ILE cc_start: 0.6304 (OUTLIER) cc_final: 0.5775 (mp) outliers start: 34 outliers final: 20 residues processed: 140 average time/residue: 0.0669 time to fit residues: 14.8326 Evaluate side-chains 130 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 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 81 GLU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 131 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 91 optimal weight: 0.0980 chunk 123 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 0.0040 chunk 104 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 29 optimal weight: 40.0000 overall best weight: 2.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.115731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.085975 restraints weight = 26113.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.088629 restraints weight = 13612.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.090359 restraints weight = 9140.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.091467 restraints weight = 7170.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.092183 restraints weight = 6182.945| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10691 Z= 0.138 Angle : 0.625 9.704 14454 Z= 0.327 Chirality : 0.046 0.230 1639 Planarity : 0.004 0.043 1800 Dihedral : 16.894 158.557 1717 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.27 % Allowed : 25.10 % Favored : 71.63 % 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 aren not related in a simple way. whole: -1.06 (0.23), residues: 1324 helix: 0.59 (0.29), residues: 356 sheet: -0.59 (0.35), residues: 220 loop : -1.42 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 235 TYR 0.012 0.002 TYR A 78 PHE 0.012 0.001 PHE G 105 TRP 0.014 0.001 TRP F 307 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00332 (10679) covalent geometry : angle 0.62518 (14454) hydrogen bonds : bond 0.03350 ( 318) hydrogen bonds : angle 4.90548 ( 1031) Misc. bond : bond 0.00478 ( 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 149 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.9269 (tmm) cc_final: 0.8651 (tmm) REVERT: A 206 ASN cc_start: 0.8535 (t0) cc_final: 0.8171 (t0) REVERT: A 208 LEU cc_start: 0.8814 (tp) cc_final: 0.8471 (tp) REVERT: A 274 GLU cc_start: 0.9002 (pp20) cc_final: 0.8586 (pp20) REVERT: A 307 TRP cc_start: 0.7923 (m100) cc_final: 0.7540 (m100) REVERT: A 315 ILE cc_start: 0.4397 (OUTLIER) cc_final: 0.3463 (mp) REVERT: B 29 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9115 (tt) REVERT: B 183 MET cc_start: 0.9165 (tmm) cc_final: 0.8793 (tmm) REVERT: B 258 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8140 (tm-30) REVERT: F 64 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8439 (tt) REVERT: F 109 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7912 (mt-10) REVERT: F 183 MET cc_start: 0.9140 (tmm) cc_final: 0.8413 (tmm) REVERT: F 212 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8426 (p) REVERT: G 171 ASP cc_start: 0.8381 (t0) cc_final: 0.8060 (t0) REVERT: G 183 MET cc_start: 0.9024 (tmm) cc_final: 0.8460 (tmm) REVERT: G 206 ASN cc_start: 0.8910 (t0) cc_final: 0.8694 (m-40) REVERT: G 243 GLN cc_start: 0.8744 (pm20) cc_final: 0.8456 (pm20) REVERT: G 245 LYS cc_start: 0.9061 (mttp) cc_final: 0.8837 (mttm) REVERT: G 274 GLU cc_start: 0.8889 (pp20) cc_final: 0.8470 (pp20) REVERT: G 307 TRP cc_start: 0.8790 (m100) cc_final: 0.8145 (m100) REVERT: G 315 ILE cc_start: 0.6290 (OUTLIER) cc_final: 0.5732 (mp) outliers start: 34 outliers final: 20 residues processed: 141 average time/residue: 0.0649 time to fit residues: 14.5431 Evaluate side-chains 130 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 120 LEU 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 64 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 78 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 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** 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 = 0.3803 r_free = 0.3803 target = 0.111397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.081126 restraints weight = 26856.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083756 restraints weight = 13881.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.085447 restraints weight = 9299.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.086527 restraints weight = 7322.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.086978 restraints weight = 6338.263| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 10691 Z= 0.224 Angle : 0.708 8.904 14454 Z= 0.368 Chirality : 0.047 0.251 1639 Planarity : 0.004 0.045 1800 Dihedral : 17.193 154.686 1717 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.37 % Allowed : 25.96 % 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 aren not related in a simple way. whole: -1.11 (0.23), residues: 1324 helix: 0.55 (0.29), residues: 356 sheet: -0.67 (0.34), residues: 240 loop : -1.43 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 209 TYR 0.013 0.002 TYR A 78 PHE 0.019 0.002 PHE G 105 TRP 0.012 0.001 TRP F 307 HIS 0.005 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00539 (10679) covalent geometry : angle 0.70813 (14454) hydrogen bonds : bond 0.04058 ( 318) hydrogen bonds : angle 5.21119 ( 1031) Misc. bond : bond 0.00519 ( 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 138 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 110 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.7983 (m-70) REVERT: A 183 MET cc_start: 0.9208 (tmm) cc_final: 0.8651 (tmm) REVERT: A 206 ASN cc_start: 0.8591 (t0) cc_final: 0.8137 (t0) REVERT: A 208 LEU cc_start: 0.8816 (tp) cc_final: 0.8410 (tp) REVERT: A 274 GLU cc_start: 0.9091 (pp20) cc_final: 0.8583 (pp20) REVERT: A 283 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8694 (tp30) REVERT: A 307 TRP cc_start: 0.8083 (m100) cc_final: 0.7659 (m100) REVERT: A 315 ILE cc_start: 0.4712 (OUTLIER) cc_final: 0.3715 (mp) REVERT: B 29 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9111 (tt) REVERT: B 183 MET cc_start: 0.9213 (tmm) cc_final: 0.8856 (tmm) REVERT: B 258 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8492 (tm-30) REVERT: F 109 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8035 (mt-10) REVERT: F 183 MET cc_start: 0.9111 (tmm) cc_final: 0.8242 (tmm) REVERT: G 171 ASP cc_start: 0.8450 (t0) cc_final: 0.8158 (t0) REVERT: G 183 MET cc_start: 0.8989 (tmm) cc_final: 0.8372 (tmm) REVERT: G 206 ASN cc_start: 0.8881 (t0) cc_final: 0.8636 (m-40) REVERT: G 274 GLU cc_start: 0.8992 (pp20) cc_final: 0.8510 (pp20) REVERT: G 280 MET cc_start: 0.9039 (mmm) cc_final: 0.8710 (mmm) REVERT: G 307 TRP cc_start: 0.8916 (m100) cc_final: 0.8291 (m100) REVERT: G 315 ILE cc_start: 0.6309 (OUTLIER) cc_final: 0.5775 (mp) outliers start: 35 outliers final: 24 residues processed: 130 average time/residue: 0.0741 time to fit residues: 15.0311 Evaluate side-chains 126 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 315 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 120 LEU 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 134 SER 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 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 159 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 58 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 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** ** F 254 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 = 0.3806 r_free = 0.3806 target = 0.111623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.081402 restraints weight = 26845.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.084043 restraints weight = 13838.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.085776 restraints weight = 9278.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086838 restraints weight = 7267.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.087508 restraints weight = 6320.002| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 10691 Z= 0.210 Angle : 0.716 12.955 14454 Z= 0.372 Chirality : 0.047 0.288 1639 Planarity : 0.004 0.048 1800 Dihedral : 17.292 158.319 1717 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.69 % Allowed : 27.02 % 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 aren not related in a simple way. whole: -1.09 (0.23), residues: 1324 helix: 0.52 (0.29), residues: 360 sheet: -0.57 (0.35), residues: 220 loop : -1.44 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 226 TYR 0.018 0.002 TYR A 231 PHE 0.017 0.002 PHE G 105 TRP 0.012 0.001 TRP F 307 HIS 0.005 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00509 (10679) covalent geometry : angle 0.71623 (14454) hydrogen bonds : bond 0.03953 ( 318) hydrogen bonds : angle 5.21371 ( 1031) Misc. bond : bond 0.00513 ( 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 128 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.8010 (m-70) REVERT: A 183 MET cc_start: 0.9224 (tmm) cc_final: 0.8676 (tmm) REVERT: A 206 ASN cc_start: 0.8582 (t0) cc_final: 0.8113 (t0) REVERT: A 208 LEU cc_start: 0.8812 (tp) cc_final: 0.8414 (tp) REVERT: A 274 GLU cc_start: 0.9076 (pp20) cc_final: 0.8628 (pp20) REVERT: A 307 TRP cc_start: 0.8023 (m100) cc_final: 0.7613 (m100) REVERT: A 315 ILE cc_start: 0.4773 (OUTLIER) cc_final: 0.3806 (mp) REVERT: B 29 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9092 (tt) REVERT: B 183 MET cc_start: 0.9208 (tmm) cc_final: 0.8836 (tmm) REVERT: B 258 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8479 (tm-30) REVERT: F 107 ASP cc_start: 0.7078 (t0) cc_final: 0.6843 (t0) REVERT: F 183 MET cc_start: 0.9122 (tmm) cc_final: 0.8238 (tmm) REVERT: G 183 MET cc_start: 0.8985 (tmm) cc_final: 0.8369 (tmm) REVERT: G 206 ASN cc_start: 0.8905 (t0) cc_final: 0.8667 (m-40) REVERT: G 255 VAL cc_start: 0.8262 (OUTLIER) cc_final: 0.7977 (p) REVERT: G 274 GLU cc_start: 0.9010 (pp20) cc_final: 0.8539 (pp20) REVERT: G 307 TRP cc_start: 0.8919 (m100) cc_final: 0.8324 (m100) REVERT: G 315 ILE cc_start: 0.6344 (OUTLIER) cc_final: 0.5920 (mp) outliers start: 28 outliers final: 22 residues processed: 121 average time/residue: 0.0681 time to fit residues: 12.9211 Evaluate side-chains 120 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER 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 222 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 120 LEU 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 134 SER 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 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 159 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 127 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** 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 176 HIS ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.119741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.087805 restraints weight = 26453.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.091015 restraints weight = 14418.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.092383 restraints weight = 8603.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.093314 restraints weight = 7117.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.093344 restraints weight = 6584.854| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 10691 Z= 0.174 Angle : 0.693 12.378 14454 Z= 0.357 Chirality : 0.046 0.248 1639 Planarity : 0.004 0.047 1800 Dihedral : 17.080 156.711 1717 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.17 % Allowed : 26.54 % 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 aren not related in a simple way. whole: -1.03 (0.24), residues: 1324 helix: 0.66 (0.29), residues: 360 sheet: -0.59 (0.35), residues: 220 loop : -1.42 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 189 TYR 0.023 0.002 TYR F 231 PHE 0.014 0.001 PHE G 105 TRP 0.013 0.001 TRP F 307 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00422 (10679) covalent geometry : angle 0.69270 (14454) hydrogen bonds : bond 0.03654 ( 318) hydrogen bonds : angle 5.05478 ( 1031) Misc. bond : bond 0.00512 ( 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 135 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.7999 (m-70) REVERT: A 183 MET cc_start: 0.9274 (tmm) cc_final: 0.8651 (tmm) REVERT: A 206 ASN cc_start: 0.8563 (t0) cc_final: 0.8106 (t0) REVERT: A 208 LEU cc_start: 0.8792 (tp) cc_final: 0.8386 (tp) REVERT: A 274 GLU cc_start: 0.9032 (pp20) cc_final: 0.8566 (pp20) REVERT: A 307 TRP cc_start: 0.8305 (m100) cc_final: 0.7874 (m100) REVERT: A 315 ILE cc_start: 0.4906 (OUTLIER) cc_final: 0.3906 (mp) REVERT: B 29 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9106 (tt) REVERT: B 183 MET cc_start: 0.9223 (tmm) cc_final: 0.8860 (tmm) REVERT: B 243 GLN cc_start: 0.9315 (pm20) cc_final: 0.9051 (pm20) REVERT: B 258 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8449 (tm-30) REVERT: F 107 ASP cc_start: 0.7048 (t0) cc_final: 0.6823 (t0) REVERT: F 183 MET cc_start: 0.9170 (tmm) cc_final: 0.8403 (tmm) REVERT: G 183 MET cc_start: 0.9034 (tmm) cc_final: 0.8444 (tmm) REVERT: G 243 GLN cc_start: 0.8848 (pm20) cc_final: 0.8123 (pp30) REVERT: G 254 ASN cc_start: 0.5493 (m-40) cc_final: 0.5267 (m-40) REVERT: G 255 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7803 (p) REVERT: G 274 GLU cc_start: 0.9008 (pp20) cc_final: 0.8546 (pp20) REVERT: G 307 TRP cc_start: 0.8949 (m100) cc_final: 0.8357 (m100) REVERT: G 315 ILE cc_start: 0.6297 (OUTLIER) cc_final: 0.5860 (mp) outliers start: 33 outliers final: 23 residues processed: 127 average time/residue: 0.0648 time to fit residues: 13.0442 Evaluate side-chains 124 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER 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 222 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 120 LEU 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 134 SER Chi-restraints excluded: chain F residue 163 VAL 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 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 159 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 71 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 97 optimal weight: 50.0000 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 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 = 0.3837 r_free = 0.3837 target = 0.113611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083653 restraints weight = 26771.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.086257 restraints weight = 14063.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.087938 restraints weight = 9526.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.089001 restraints weight = 7520.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089528 restraints weight = 6535.156| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10691 Z= 0.175 Angle : 0.701 10.991 14454 Z= 0.359 Chirality : 0.046 0.232 1639 Planarity : 0.004 0.046 1800 Dihedral : 17.050 157.004 1717 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.60 % Allowed : 27.31 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.24), residues: 1324 helix: 0.70 (0.29), residues: 360 sheet: -0.60 (0.35), residues: 220 loop : -1.39 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 226 TYR 0.026 0.002 TYR A 325 PHE 0.016 0.001 PHE G 15 TRP 0.013 0.001 TRP F 307 HIS 0.005 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00425 (10679) covalent geometry : angle 0.70119 (14454) hydrogen bonds : bond 0.03628 ( 318) hydrogen bonds : angle 5.04642 ( 1031) Misc. bond : bond 0.00503 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1461.47 seconds wall clock time: 26 minutes 0.04 seconds (1560.04 seconds total)