Starting phenix.real_space_refine on Sat Aug 23 14:52:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sk6_40556/08_2025/8sk6_40556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sk6_40556/08_2025/8sk6_40556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sk6_40556/08_2025/8sk6_40556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sk6_40556/08_2025/8sk6_40556.map" model { file = "/net/cci-nas-00/data/ceres_data/8sk6_40556/08_2025/8sk6_40556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sk6_40556/08_2025/8sk6_40556.cif" } resolution = 2.96 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= 0.015 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 8064 2.51 5 N 2262 2.21 5 O 2436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 12858 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2143 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 281, 2137 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 272} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 281, 2137 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 272} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 2162 Chain: "B" Number of atoms: 2143 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 281, 2137 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 272} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 281, 2137 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 272} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 2162 Chain: "C" Number of atoms: 2143 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 281, 2137 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 272} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 281, 2137 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 272} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 2162 Chain: "D" Number of atoms: 2143 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 281, 2137 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 272} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 281, 2137 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 272} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 2162 Chain: "E" Number of atoms: 2143 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 281, 2137 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 272} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 281, 2137 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 272} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 2162 Chain: "F" Number of atoms: 2143 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 281, 2137 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 272} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 281, 2137 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 272} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 2162 Time building chain proxies: 5.46, per 1000 atoms: 0.42 Number of scatterers: 12858 At special positions: 0 Unit cell: (91.575, 94.05, 93.225, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2436 8.00 N 2262 7.00 C 8064 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=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 59.1% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 82 through 99 removed outlier: 3.520A pdb=" N TRP A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 90 " --> pdb=" O TRP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 129 removed outlier: 4.355A pdb=" N SER A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 159 removed outlier: 4.068A pdb=" N PHE A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 removed outlier: 4.268A pdb=" N ASP A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 218 through 229 Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 249 through 267 removed outlier: 3.619A pdb=" N LYS A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 285 removed outlier: 3.561A pdb=" N ASP A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 302 removed outlier: 4.654A pdb=" N SER A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET A 301 " --> pdb=" O TRP A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 removed outlier: 3.968A pdb=" N VAL A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 99 removed outlier: 3.515A pdb=" N TRP B 86 " --> pdb=" O ASN B 82 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 90 " --> pdb=" O TRP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 removed outlier: 4.344A pdb=" N SER B 125 " --> pdb=" O MET B 121 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 159 removed outlier: 4.046A pdb=" N PHE B 153 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 157 " --> pdb=" O PHE B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 removed outlier: 4.260A pdb=" N ASP B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 207 through 216 Proline residue: B 213 - end of helix removed outlier: 3.526A pdb=" N ILE B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 229 Processing helix chain 'B' and resid 234 through 240 Processing helix chain 'B' and resid 249 through 267 removed outlier: 3.623A pdb=" N LYS B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 285 removed outlier: 3.561A pdb=" N ASP B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 302 removed outlier: 4.641A pdb=" N SER B 300 " --> pdb=" O SER B 296 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET B 301 " --> pdb=" O TRP B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 316 removed outlier: 3.973A pdb=" N VAL B 308 " --> pdb=" O THR B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 99 removed outlier: 3.511A pdb=" N TRP C 86 " --> pdb=" O ASN C 82 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 90 " --> pdb=" O TRP C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 129 removed outlier: 4.359A pdb=" N SER C 125 " --> pdb=" O MET C 121 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 159 removed outlier: 4.053A pdb=" N PHE C 153 " --> pdb=" O TYR C 149 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE C 156 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU C 157 " --> pdb=" O PHE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 removed outlier: 4.238A pdb=" N ASP C 177 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 218 through 229 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 249 through 267 removed outlier: 3.635A pdb=" N LYS C 267 " --> pdb=" O GLU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 285 removed outlier: 3.571A pdb=" N ASP C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 302 removed outlier: 4.646A pdb=" N SER C 300 " --> pdb=" O SER C 296 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET C 301 " --> pdb=" O TRP C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.971A pdb=" N VAL C 308 " --> pdb=" O THR C 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.503A pdb=" N TRP D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 90 " --> pdb=" O TRP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 removed outlier: 4.355A pdb=" N SER D 125 " --> pdb=" O MET D 121 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 159 removed outlier: 4.062A pdb=" N PHE D 153 " --> pdb=" O TYR D 149 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE D 156 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 157 " --> pdb=" O PHE D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 removed outlier: 4.261A pdb=" N ASP D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 201 Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 218 through 229 Processing helix chain 'D' and resid 234 through 240 Processing helix chain 'D' and resid 249 through 267 removed outlier: 3.619A pdb=" N LYS D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 285 removed outlier: 3.561A pdb=" N ASP D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 302 removed outlier: 4.650A pdb=" N SER D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET D 301 " --> pdb=" O TRP D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 316 removed outlier: 3.972A pdb=" N VAL D 308 " --> pdb=" O THR D 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 99 removed outlier: 3.517A pdb=" N TRP E 86 " --> pdb=" O ASN E 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG E 87 " --> pdb=" O LYS E 83 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 90 " --> pdb=" O TRP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 129 removed outlier: 4.344A pdb=" N SER E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP E 126 " --> pdb=" O ASP E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 159 removed outlier: 4.057A pdb=" N PHE E 153 " --> pdb=" O TYR E 149 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE E 156 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU E 157 " --> pdb=" O PHE E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 181 removed outlier: 4.265A pdb=" N ASP E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 201 Processing helix chain 'E' and resid 207 through 216 Proline residue: E 213 - end of helix removed outlier: 3.526A pdb=" N ILE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 229 Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 249 through 267 removed outlier: 3.613A pdb=" N LYS E 267 " --> pdb=" O GLU E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 285 removed outlier: 3.560A pdb=" N ASP E 284 " --> pdb=" O LEU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 302 removed outlier: 4.644A pdb=" N SER E 300 " --> pdb=" O SER E 296 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET E 301 " --> pdb=" O TRP E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 316 removed outlier: 3.975A pdb=" N VAL E 308 " --> pdb=" O THR E 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 99 removed outlier: 3.511A pdb=" N TRP F 86 " --> pdb=" O ASN F 82 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 90 " --> pdb=" O TRP F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 129 removed outlier: 4.361A pdb=" N SER F 125 " --> pdb=" O MET F 121 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASP F 126 " --> pdb=" O ASP F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 159 removed outlier: 4.039A pdb=" N PHE F 153 " --> pdb=" O TYR F 149 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE F 156 " --> pdb=" O THR F 152 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU F 157 " --> pdb=" O PHE F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 181 removed outlier: 4.239A pdb=" N ASP F 177 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 201 Processing helix chain 'F' and resid 207 through 212 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 218 through 229 Processing helix chain 'F' and resid 234 through 241 Processing helix chain 'F' and resid 249 through 267 removed outlier: 3.643A pdb=" N LYS F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 285 removed outlier: 3.576A pdb=" N ASP F 284 " --> pdb=" O LEU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 302 removed outlier: 4.647A pdb=" N SER F 300 " --> pdb=" O SER F 296 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET F 301 " --> pdb=" O TRP F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 316 removed outlier: 3.971A pdb=" N VAL F 308 " --> pdb=" O THR F 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 63 removed outlier: 3.888A pdb=" N VAL A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 68 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N SER A 108 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 70 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY A 109 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL A 163 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N TYR A 186 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA A 165 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ALA A 188 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL A 167 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ARG A 185 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N PHE A 247 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS A 187 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.598A pdb=" N CYS A 171 " --> pdb=" O GLN A 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.867A pdb=" N VAL B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 68 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N SER B 108 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 70 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY B 109 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 163 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N TYR B 186 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA B 165 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALA B 188 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL B 167 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ARG B 185 " --> pdb=" O ARG B 245 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N PHE B 247 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N CYS B 187 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 170 through 172 removed outlier: 6.575A pdb=" N CYS B 171 " --> pdb=" O GLN B 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.869A pdb=" N VAL C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY C 109 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL C 163 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR C 186 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA C 165 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ALA C 188 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL C 167 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ARG C 185 " --> pdb=" O ARG C 245 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N PHE C 247 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N CYS C 187 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 170 through 172 Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.886A pdb=" N VAL D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU D 68 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER D 108 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL D 70 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY D 109 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL D 163 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N TYR D 186 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ALA D 165 " --> pdb=" O TYR D 186 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA D 188 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL D 167 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ARG D 185 " --> pdb=" O ARG D 245 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N PHE D 247 " --> pdb=" O ARG D 185 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N CYS D 187 " --> pdb=" O PHE D 247 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.597A pdb=" N CYS D 171 " --> pdb=" O GLN D 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 58 through 63 removed outlier: 3.867A pdb=" N VAL E 67 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU E 68 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N SER E 108 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL E 70 " --> pdb=" O SER E 108 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY E 109 " --> pdb=" O ALA E 166 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 163 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N TYR E 186 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA E 165 " --> pdb=" O TYR E 186 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA E 188 " --> pdb=" O ALA E 165 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL E 167 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ARG E 185 " --> pdb=" O ARG E 245 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N PHE E 247 " --> pdb=" O ARG E 185 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N CYS E 187 " --> pdb=" O PHE E 247 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 170 through 172 removed outlier: 6.570A pdb=" N CYS E 171 " --> pdb=" O GLN E 194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 58 through 63 removed outlier: 3.879A pdb=" N VAL F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY F 109 " --> pdb=" O ALA F 166 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL F 163 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TYR F 186 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ALA F 165 " --> pdb=" O TYR F 186 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA F 188 " --> pdb=" O ALA F 165 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL F 167 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ARG F 185 " --> pdb=" O ARG F 245 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N PHE F 247 " --> pdb=" O ARG F 185 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N CYS F 187 " --> pdb=" O PHE F 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 170 through 172 removed outlier: 6.598A pdb=" N CYS F 171 " --> pdb=" O GLN F 194 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 2022 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4326 1.34 - 1.46: 2447 1.46 - 1.58: 6139 1.58 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 13068 Sorted by residual: bond pdb=" C ALA A 50 " pdb=" N PRO A 51 " ideal model delta sigma weight residual 1.338 1.354 -0.016 1.90e-02 2.77e+03 7.32e-01 bond pdb=" CA ALA F 50 " pdb=" C ALA F 50 " ideal model delta sigma weight residual 1.520 1.531 -0.010 1.23e-02 6.61e+03 7.04e-01 bond pdb=" CA ALA B 50 " pdb=" C ALA B 50 " ideal model delta sigma weight residual 1.520 1.531 -0.010 1.23e-02 6.61e+03 6.98e-01 bond pdb=" C ALA E 50 " pdb=" N PRO E 51 " ideal model delta sigma weight residual 1.338 1.354 -0.016 1.90e-02 2.77e+03 6.94e-01 bond pdb=" C ALA B 50 " pdb=" N PRO B 51 " ideal model delta sigma weight residual 1.338 1.354 -0.016 1.90e-02 2.77e+03 6.92e-01 ... (remaining 13063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 17002 0.94 - 1.88: 564 1.88 - 2.82: 86 2.82 - 3.75: 54 3.75 - 4.69: 12 Bond angle restraints: 17718 Sorted by residual: angle pdb=" C ASN A 73 " pdb=" N ARG A 74 " pdb=" CA ARG A 74 " ideal model delta sigma weight residual 123.15 120.20 2.95 1.21e+00 6.83e-01 5.94e+00 angle pdb=" C ASN E 73 " pdb=" N ARG E 74 " pdb=" CA ARG E 74 " ideal model delta sigma weight residual 123.15 120.21 2.94 1.21e+00 6.83e-01 5.90e+00 angle pdb=" C ASN F 73 " pdb=" N ARG F 74 " pdb=" CA ARG F 74 " ideal model delta sigma weight residual 123.15 120.28 2.87 1.21e+00 6.83e-01 5.64e+00 angle pdb=" C GLU B 49 " pdb=" N ALA B 50 " pdb=" CA ALA B 50 " ideal model delta sigma weight residual 120.26 123.38 -3.12 1.34e+00 5.57e-01 5.43e+00 angle pdb=" C GLU E 49 " pdb=" N ALA E 50 " pdb=" CA ALA E 50 " ideal model delta sigma weight residual 120.26 123.36 -3.10 1.34e+00 5.57e-01 5.36e+00 ... (remaining 17713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.84: 7371 10.84 - 21.68: 492 21.68 - 32.52: 104 32.52 - 43.36: 28 43.36 - 54.20: 9 Dihedral angle restraints: 8004 sinusoidal: 3048 harmonic: 4956 Sorted by residual: dihedral pdb=" CA ARG E 74 " pdb=" CB ARG E 74 " pdb=" CG ARG E 74 " pdb=" CD ARG E 74 " ideal model delta sinusoidal sigma weight residual -180.00 -133.76 -46.24 3 1.50e+01 4.44e-03 8.30e+00 dihedral pdb=" CA ARG F 74 " pdb=" CB ARG F 74 " pdb=" CG ARG F 74 " pdb=" CD ARG F 74 " ideal model delta sinusoidal sigma weight residual -180.00 -134.15 -45.85 3 1.50e+01 4.44e-03 8.24e+00 dihedral pdb=" CA ARG A 74 " pdb=" CB ARG A 74 " pdb=" CG ARG A 74 " pdb=" CD ARG A 74 " ideal model delta sinusoidal sigma weight residual -180.00 -134.32 -45.68 3 1.50e+01 4.44e-03 8.21e+00 ... (remaining 8001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1220 0.024 - 0.048: 481 0.048 - 0.072: 232 0.072 - 0.096: 52 0.096 - 0.120: 97 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CA ILE D 164 " pdb=" N ILE D 164 " pdb=" C ILE D 164 " pdb=" CB ILE D 164 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA ILE A 164 " pdb=" N ILE A 164 " pdb=" C ILE A 164 " pdb=" CB ILE A 164 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA ILE F 164 " pdb=" N ILE F 164 " pdb=" C ILE F 164 " pdb=" CB ILE F 164 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 ... (remaining 2079 not shown) Planarity restraints: 2286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 247 " -0.015 5.00e-02 4.00e+02 2.30e-02 8.47e-01 pdb=" N PRO D 248 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO D 248 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 248 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 247 " 0.015 5.00e-02 4.00e+02 2.27e-02 8.21e-01 pdb=" N PRO A 248 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 247 " 0.015 5.00e-02 4.00e+02 2.26e-02 8.19e-01 pdb=" N PRO F 248 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO F 248 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 248 " 0.013 5.00e-02 4.00e+02 ... (remaining 2283 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2072 2.75 - 3.29: 12900 3.29 - 3.83: 21496 3.83 - 4.36: 28002 4.36 - 4.90: 47065 Nonbonded interactions: 111535 Sorted by model distance: nonbonded pdb=" OG SER F 57 " pdb=" OE1 GLU F 88 " model vdw 2.218 3.040 nonbonded pdb=" OG SER C 57 " pdb=" OE1 GLU C 88 " model vdw 2.218 3.040 nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 88 " model vdw 2.219 3.040 nonbonded pdb=" OG SER B 57 " pdb=" OE1 GLU B 88 " model vdw 2.220 3.040 nonbonded pdb=" OG SER D 57 " pdb=" OE1 GLU D 88 " model vdw 2.224 3.040 ... (remaining 111530 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.410 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.002 0.016 13068 Z= 0.104 Angle : 0.440 4.692 17718 Z= 0.259 Chirality : 0.038 0.120 2082 Planarity : 0.002 0.023 2286 Dihedral : 8.099 54.201 4788 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 0.86 % Allowed : 4.17 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.87 (0.21), residues: 1686 helix: 1.38 (0.17), residues: 912 sheet: 0.43 (0.43), residues: 204 loop : -0.62 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 78 TYR 0.005 0.001 TYR D 186 PHE 0.008 0.001 PHE E 114 TRP 0.002 0.001 TRP E 86 HIS 0.001 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00214 (13068) covalent geometry : angle 0.44049 (17718) hydrogen bonds : bond 0.22192 ( 676) hydrogen bonds : angle 7.09867 ( 2022) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.480 Fit side-chains REVERT: A 55 TYR cc_start: 0.8785 (m-80) cc_final: 0.8341 (m-80) REVERT: A 183 ASP cc_start: 0.8566 (m-30) cc_final: 0.8343 (m-30) REVERT: B 113 MET cc_start: 0.8762 (ptm) cc_final: 0.8457 (ptm) REVERT: C 183 ASP cc_start: 0.8531 (m-30) cc_final: 0.8263 (m-30) REVERT: D 55 TYR cc_start: 0.8787 (m-80) cc_final: 0.8350 (m-80) REVERT: D 183 ASP cc_start: 0.8566 (m-30) cc_final: 0.8343 (m-30) REVERT: E 113 MET cc_start: 0.8766 (ptm) cc_final: 0.8464 (ptm) REVERT: F 183 ASP cc_start: 0.8530 (m-30) cc_final: 0.8265 (m-30) outliers start: 12 outliers final: 6 residues processed: 151 average time/residue: 0.8795 time to fit residues: 141.1102 Evaluate side-chains 92 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 129 GLN A 303 GLN B 71 GLN B 129 GLN B 303 GLN C 71 GLN C 129 GLN C 303 GLN D 71 GLN D 129 GLN D 303 GLN E 71 GLN E 129 GLN E 303 GLN F 129 GLN F 303 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.085224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.068425 restraints weight = 67724.185| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 4.48 r_work: 0.2696 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13068 Z= 0.175 Angle : 0.547 7.020 17718 Z= 0.294 Chirality : 0.043 0.146 2082 Planarity : 0.003 0.022 2286 Dihedral : 4.057 19.979 1836 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.80 % Allowed : 7.33 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.90 (0.20), residues: 1686 helix: 1.55 (0.17), residues: 936 sheet: 0.65 (0.41), residues: 192 loop : -1.05 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 78 TYR 0.032 0.002 TYR A 141 PHE 0.015 0.002 PHE A 93 TRP 0.006 0.001 TRP B 86 HIS 0.002 0.001 HIS D 66 Details of bonding type rmsd covalent geometry : bond 0.00402 (13068) covalent geometry : angle 0.54680 (17718) hydrogen bonds : bond 0.05220 ( 676) hydrogen bonds : angle 4.84184 ( 2022) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.416 Fit side-chains REVERT: A 151 GLU cc_start: 0.8582 (tp30) cc_final: 0.8354 (tp30) REVERT: A 183 ASP cc_start: 0.8985 (m-30) cc_final: 0.8763 (m-30) REVERT: B 113 MET cc_start: 0.9249 (ptm) cc_final: 0.9045 (ptm) REVERT: B 151 GLU cc_start: 0.8549 (tp30) cc_final: 0.8334 (tp30) REVERT: C 183 ASP cc_start: 0.8988 (m-30) cc_final: 0.8647 (m-30) REVERT: C 233 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.7726 (mpt) REVERT: D 151 GLU cc_start: 0.8582 (tp30) cc_final: 0.8357 (tp30) REVERT: D 183 ASP cc_start: 0.8989 (m-30) cc_final: 0.8755 (m-30) REVERT: E 113 MET cc_start: 0.9234 (ptm) cc_final: 0.9022 (ptm) REVERT: E 151 GLU cc_start: 0.8522 (tp30) cc_final: 0.8312 (tp30) REVERT: F 183 ASP cc_start: 0.9000 (m-30) cc_final: 0.8667 (m-30) REVERT: F 233 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.7782 (mpt) outliers start: 39 outliers final: 8 residues processed: 111 average time/residue: 0.6748 time to fit residues: 81.2374 Evaluate side-chains 91 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 144 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.084551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.067397 restraints weight = 81218.113| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 4.85 r_work: 0.2663 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 13068 Z= 0.199 Angle : 0.536 4.998 17718 Z= 0.287 Chirality : 0.043 0.159 2082 Planarity : 0.003 0.024 2286 Dihedral : 4.210 23.136 1836 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.87 % Allowed : 8.91 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.71 (0.20), residues: 1686 helix: 1.47 (0.17), residues: 936 sheet: 0.42 (0.41), residues: 186 loop : -1.20 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 78 TYR 0.027 0.001 TYR A 141 PHE 0.016 0.002 PHE A 93 TRP 0.006 0.001 TRP B 86 HIS 0.002 0.001 HIS F 285 Details of bonding type rmsd covalent geometry : bond 0.00462 (13068) covalent geometry : angle 0.53600 (17718) hydrogen bonds : bond 0.04931 ( 676) hydrogen bonds : angle 4.68102 ( 2022) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8514 (tp30) cc_final: 0.8267 (tp30) REVERT: A 183 ASP cc_start: 0.9005 (m-30) cc_final: 0.8793 (m-30) REVERT: B 113 MET cc_start: 0.9252 (ptm) cc_final: 0.9038 (ptm) REVERT: B 151 GLU cc_start: 0.8499 (tp30) cc_final: 0.8261 (tp30) REVERT: D 151 GLU cc_start: 0.8523 (tp30) cc_final: 0.8272 (tp30) REVERT: D 183 ASP cc_start: 0.9013 (m-30) cc_final: 0.8807 (m-30) REVERT: E 113 MET cc_start: 0.9255 (ptm) cc_final: 0.9038 (ptm) REVERT: E 151 GLU cc_start: 0.8477 (tp30) cc_final: 0.8241 (tp30) outliers start: 26 outliers final: 11 residues processed: 106 average time/residue: 0.7720 time to fit residues: 87.7596 Evaluate side-chains 93 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 35 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.083691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.066729 restraints weight = 78916.559| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 4.73 r_work: 0.2658 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 13068 Z= 0.208 Angle : 0.540 5.951 17718 Z= 0.290 Chirality : 0.043 0.159 2082 Planarity : 0.003 0.023 2286 Dihedral : 4.283 24.003 1836 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.72 % Allowed : 9.12 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.61 (0.20), residues: 1686 helix: 1.43 (0.17), residues: 936 sheet: 0.36 (0.41), residues: 186 loop : -1.34 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 78 TYR 0.024 0.001 TYR A 141 PHE 0.016 0.002 PHE A 93 TRP 0.007 0.001 TRP A 86 HIS 0.003 0.001 HIS F 285 Details of bonding type rmsd covalent geometry : bond 0.00482 (13068) covalent geometry : angle 0.54019 (17718) hydrogen bonds : bond 0.04819 ( 676) hydrogen bonds : angle 4.61779 ( 2022) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8480 (tp30) cc_final: 0.8213 (tp30) REVERT: B 151 GLU cc_start: 0.8447 (tp30) cc_final: 0.8212 (tp30) REVERT: B 233 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8089 (mpt) REVERT: D 151 GLU cc_start: 0.8478 (tp30) cc_final: 0.8212 (tp30) REVERT: E 113 MET cc_start: 0.9234 (ptm) cc_final: 0.8659 (ptm) REVERT: E 151 GLU cc_start: 0.8437 (tp30) cc_final: 0.8203 (tp30) REVERT: E 233 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8087 (mpt) outliers start: 24 outliers final: 10 residues processed: 100 average time/residue: 0.7538 time to fit residues: 81.1705 Evaluate side-chains 92 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 36 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 156 optimal weight: 0.0050 chunk 3 optimal weight: 4.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.085836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.068770 restraints weight = 78678.440| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 4.76 r_work: 0.2703 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 13068 Z= 0.135 Angle : 0.478 4.712 17718 Z= 0.258 Chirality : 0.041 0.149 2082 Planarity : 0.003 0.024 2286 Dihedral : 4.055 19.154 1836 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.58 % Allowed : 9.27 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.73 (0.20), residues: 1686 helix: 1.58 (0.17), residues: 936 sheet: 0.46 (0.40), residues: 186 loop : -1.40 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 78 TYR 0.022 0.001 TYR A 141 PHE 0.015 0.002 PHE C 93 TRP 0.005 0.001 TRP E 86 HIS 0.001 0.001 HIS F 285 Details of bonding type rmsd covalent geometry : bond 0.00303 (13068) covalent geometry : angle 0.47797 (17718) hydrogen bonds : bond 0.04168 ( 676) hydrogen bonds : angle 4.40152 ( 2022) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8374 (tp30) cc_final: 0.8119 (tp30) REVERT: A 233 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8452 (mpt) REVERT: B 56 GLU cc_start: 0.8467 (pt0) cc_final: 0.8135 (tm-30) REVERT: B 233 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8135 (mpt) REVERT: C 183 ASP cc_start: 0.8885 (m-30) cc_final: 0.8547 (m-30) REVERT: C 299 MET cc_start: 0.9288 (ptt) cc_final: 0.9074 (ptm) REVERT: D 81 MET cc_start: 0.9409 (mtt) cc_final: 0.9195 (mtp) REVERT: D 151 GLU cc_start: 0.8385 (tp30) cc_final: 0.8130 (tp30) REVERT: E 56 GLU cc_start: 0.8466 (pt0) cc_final: 0.8135 (tm-30) REVERT: E 113 MET cc_start: 0.9207 (ptm) cc_final: 0.8648 (ptm) REVERT: E 151 GLU cc_start: 0.8280 (tp30) cc_final: 0.8005 (tp30) REVERT: E 233 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8119 (mpt) REVERT: F 183 ASP cc_start: 0.8899 (m-30) cc_final: 0.8572 (m-30) outliers start: 22 outliers final: 10 residues processed: 138 average time/residue: 0.7967 time to fit residues: 117.0681 Evaluate side-chains 109 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.083421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.066385 restraints weight = 78772.881| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 4.73 r_work: 0.2656 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13068 Z= 0.221 Angle : 0.552 5.075 17718 Z= 0.294 Chirality : 0.044 0.189 2082 Planarity : 0.003 0.024 2286 Dihedral : 4.296 23.998 1836 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.65 % Allowed : 10.27 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.65 (0.20), residues: 1686 helix: 1.51 (0.17), residues: 936 sheet: 0.35 (0.40), residues: 186 loop : -1.40 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 78 TYR 0.020 0.001 TYR A 141 PHE 0.017 0.002 PHE A 93 TRP 0.009 0.001 TRP E 86 HIS 0.002 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00517 (13068) covalent geometry : angle 0.55196 (17718) hydrogen bonds : bond 0.04813 ( 676) hydrogen bonds : angle 4.53104 ( 2022) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8504 (tp30) cc_final: 0.8277 (tp30) REVERT: A 197 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7889 (mp0) REVERT: A 233 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8491 (mpt) REVERT: B 56 GLU cc_start: 0.8520 (pt0) cc_final: 0.8189 (tm-30) REVERT: B 233 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8157 (mpt) REVERT: C 233 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7755 (mpt) REVERT: D 151 GLU cc_start: 0.8514 (tp30) cc_final: 0.8277 (tp30) REVERT: E 56 GLU cc_start: 0.8515 (pt0) cc_final: 0.8189 (tm-30) REVERT: E 113 MET cc_start: 0.9242 (ptm) cc_final: 0.8664 (ptm) REVERT: E 151 GLU cc_start: 0.8461 (tp30) cc_final: 0.8243 (tp30) REVERT: E 233 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8139 (mpt) REVERT: F 113 MET cc_start: 0.8944 (ptp) cc_final: 0.8545 (ptm) outliers start: 23 outliers final: 8 residues processed: 123 average time/residue: 0.7860 time to fit residues: 103.0637 Evaluate side-chains 107 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 136 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.084990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.067977 restraints weight = 82358.268| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 4.83 r_work: 0.2682 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13068 Z= 0.153 Angle : 0.506 6.189 17718 Z= 0.271 Chirality : 0.042 0.166 2082 Planarity : 0.003 0.024 2286 Dihedral : 4.114 20.483 1836 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.72 % Allowed : 10.56 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.75 (0.20), residues: 1686 helix: 1.61 (0.17), residues: 936 sheet: 0.39 (0.40), residues: 186 loop : -1.40 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 78 TYR 0.019 0.001 TYR A 141 PHE 0.015 0.002 PHE C 93 TRP 0.007 0.001 TRP E 86 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00350 (13068) covalent geometry : angle 0.50586 (17718) hydrogen bonds : bond 0.04292 ( 676) hydrogen bonds : angle 4.38780 ( 2022) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7939 (mp0) REVERT: A 233 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8424 (mpt) REVERT: B 233 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8125 (mpt) REVERT: C 233 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7692 (mpt) REVERT: D 81 MET cc_start: 0.9365 (mtt) cc_final: 0.9135 (mtp) REVERT: E 56 GLU cc_start: 0.8515 (pt0) cc_final: 0.8168 (tm-30) REVERT: E 113 MET cc_start: 0.9194 (ptm) cc_final: 0.8620 (ptm) REVERT: E 151 GLU cc_start: 0.8368 (tp30) cc_final: 0.8145 (tp30) REVERT: E 233 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8124 (mpt) REVERT: F 113 MET cc_start: 0.8919 (ptp) cc_final: 0.8521 (ptm) outliers start: 24 outliers final: 11 residues processed: 118 average time/residue: 0.8096 time to fit residues: 102.3969 Evaluate side-chains 99 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 136 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 166 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.085747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.068588 restraints weight = 84458.311| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 4.87 r_work: 0.2697 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13068 Z= 0.138 Angle : 0.501 5.605 17718 Z= 0.268 Chirality : 0.041 0.167 2082 Planarity : 0.003 0.024 2286 Dihedral : 4.022 19.022 1836 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.51 % Allowed : 11.06 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.80 (0.20), residues: 1686 helix: 1.65 (0.17), residues: 936 sheet: 0.51 (0.40), residues: 186 loop : -1.41 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 158 TYR 0.019 0.001 TYR A 141 PHE 0.014 0.002 PHE C 93 TRP 0.007 0.001 TRP A 86 HIS 0.001 0.001 HIS D 66 Details of bonding type rmsd covalent geometry : bond 0.00314 (13068) covalent geometry : angle 0.50057 (17718) hydrogen bonds : bond 0.04125 ( 676) hydrogen bonds : angle 4.30853 ( 2022) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8424 (mpt) REVERT: B 233 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8100 (mpt) REVERT: C 183 ASP cc_start: 0.8915 (m-30) cc_final: 0.8605 (m-30) REVERT: C 233 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.7681 (mpt) REVERT: D 197 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7927 (mp0) REVERT: E 56 GLU cc_start: 0.8473 (pt0) cc_final: 0.8145 (tm-30) REVERT: E 151 GLU cc_start: 0.8364 (tp30) cc_final: 0.8141 (tp30) REVERT: E 233 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8140 (mpt) REVERT: F 113 MET cc_start: 0.8912 (ptp) cc_final: 0.8496 (ptm) REVERT: F 183 ASP cc_start: 0.8901 (m-30) cc_final: 0.8596 (m-30) outliers start: 21 outliers final: 13 residues processed: 117 average time/residue: 0.7912 time to fit residues: 98.8682 Evaluate side-chains 98 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 273 GLN Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 83 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.084849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.067880 restraints weight = 76410.532| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 4.65 r_work: 0.2690 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13068 Z= 0.168 Angle : 0.554 10.402 17718 Z= 0.290 Chirality : 0.042 0.211 2082 Planarity : 0.003 0.028 2286 Dihedral : 4.067 20.987 1836 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.29 % Allowed : 11.71 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.77 (0.20), residues: 1686 helix: 1.60 (0.17), residues: 936 sheet: 0.54 (0.40), residues: 186 loop : -1.38 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.019 0.001 TYR A 141 PHE 0.015 0.002 PHE D 93 TRP 0.007 0.001 TRP E 86 HIS 0.002 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00394 (13068) covalent geometry : angle 0.55419 (17718) hydrogen bonds : bond 0.04340 ( 676) hydrogen bonds : angle 4.35398 ( 2022) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8416 (mpt) REVERT: B 233 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8153 (mpt) REVERT: C 183 ASP cc_start: 0.8928 (m-30) cc_final: 0.8615 (m-30) REVERT: C 233 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.7732 (mpt) REVERT: D 55 TYR cc_start: 0.8672 (m-80) cc_final: 0.8246 (m-80) REVERT: D 81 MET cc_start: 0.9236 (mtt) cc_final: 0.8938 (mtp) REVERT: E 56 GLU cc_start: 0.8504 (pt0) cc_final: 0.8176 (tm-30) REVERT: E 151 GLU cc_start: 0.8341 (tp30) cc_final: 0.8110 (tp30) REVERT: E 233 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8181 (mpt) REVERT: F 113 MET cc_start: 0.8939 (ptp) cc_final: 0.8512 (ptm) outliers start: 18 outliers final: 13 residues processed: 95 average time/residue: 0.7044 time to fit residues: 71.6827 Evaluate side-chains 98 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 273 GLN Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 52 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.085788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.068666 restraints weight = 82983.126| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 4.81 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13068 Z= 0.146 Angle : 0.557 10.702 17718 Z= 0.290 Chirality : 0.042 0.210 2082 Planarity : 0.003 0.034 2286 Dihedral : 4.014 20.144 1836 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.22 % Allowed : 11.93 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.81 (0.20), residues: 1686 helix: 1.63 (0.17), residues: 936 sheet: 0.58 (0.40), residues: 186 loop : -1.37 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 78 TYR 0.019 0.001 TYR A 141 PHE 0.015 0.002 PHE C 93 TRP 0.007 0.001 TRP E 86 HIS 0.001 0.001 HIS D 66 Details of bonding type rmsd covalent geometry : bond 0.00342 (13068) covalent geometry : angle 0.55743 (17718) hydrogen bonds : bond 0.04176 ( 676) hydrogen bonds : angle 4.30714 ( 2022) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.9083 (mmm) cc_final: 0.8865 (mtp) REVERT: A 233 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8246 (mpt) REVERT: B 131 LYS cc_start: 0.8409 (mmmt) cc_final: 0.7957 (pptt) REVERT: B 233 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7911 (mpt) REVERT: C 183 ASP cc_start: 0.8890 (m-30) cc_final: 0.8512 (m-30) REVERT: C 233 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7522 (mpt) REVERT: D 55 TYR cc_start: 0.8504 (m-80) cc_final: 0.8074 (m-80) REVERT: D 81 MET cc_start: 0.9019 (mtt) cc_final: 0.8737 (mtp) REVERT: E 151 GLU cc_start: 0.8039 (tp30) cc_final: 0.7760 (tp30) REVERT: E 158 ARG cc_start: 0.8555 (ttp-110) cc_final: 0.8296 (ttp-110) REVERT: E 233 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7924 (mpt) REVERT: F 113 MET cc_start: 0.8757 (ptp) cc_final: 0.8315 (ptm) outliers start: 17 outliers final: 13 residues processed: 95 average time/residue: 0.7284 time to fit residues: 74.1813 Evaluate side-chains 97 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 273 GLN Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 29 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.084909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.067657 restraints weight = 90179.958| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 4.96 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13068 Z= 0.177 Angle : 0.583 10.298 17718 Z= 0.302 Chirality : 0.043 0.226 2082 Planarity : 0.003 0.037 2286 Dihedral : 4.073 21.175 1836 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.22 % Allowed : 12.07 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.77 (0.20), residues: 1686 helix: 1.58 (0.17), residues: 936 sheet: 0.54 (0.40), residues: 186 loop : -1.35 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 78 TYR 0.019 0.001 TYR A 141 PHE 0.015 0.002 PHE F 93 TRP 0.008 0.001 TRP E 86 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00420 (13068) covalent geometry : angle 0.58279 (17718) hydrogen bonds : bond 0.04350 ( 676) hydrogen bonds : angle 4.35027 ( 2022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3249.48 seconds wall clock time: 56 minutes 31.78 seconds (3391.78 seconds total)