Starting phenix.real_space_refine on Wed Jul 30 22:32:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sk6_40556/07_2025/8sk6_40556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sk6_40556/07_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_40556/07_2025/8sk6_40556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sk6_40556/07_2025/8sk6_40556.map" model { file = "/net/cci-nas-00/data/ceres_data/8sk6_40556/07_2025/8sk6_40556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sk6_40556/07_2025/8sk6_40556.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 14.85, per 1000 atoms: 1.15 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: 3.07 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 1.26 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: 3.92 Time building geometry restraints manager: 3.76 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 4.500 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: 0.040 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 42.170 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.100 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:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.550 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.002 0.001 TRP E 86 HIS 0.001 0.000 HIS A 66 PHE 0.008 0.001 PHE E 114 TYR 0.005 0.001 TYR D 186 ARG 0.002 0.000 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.22192 ( 676) hydrogen bonds : angle 7.09867 ( 2022) covalent geometry : bond 0.00214 (13068) covalent geometry : angle 0.44049 (17718) *********************** 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 : 1.463 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: 1.7061 time to fit residues: 274.9757 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 : 1.352 ------------------------------------------------------------------------------- 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 141 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 71 GLN F 129 GLN F 303 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.084538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.067801 restraints weight = 81516.181| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 4.68 r_work: 0.2629 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 13068 Z= 0.302 Angle : 0.630 7.111 17718 Z= 0.337 Chirality : 0.046 0.159 2082 Planarity : 0.004 0.023 2286 Dihedral : 4.419 26.651 1836 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.87 % Allowed : 7.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1686 helix: 1.41 (0.17), residues: 936 sheet: 0.53 (0.41), residues: 192 loop : -1.07 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 86 HIS 0.003 0.001 HIS A 285 PHE 0.017 0.003 PHE B 93 TYR 0.031 0.002 TYR D 141 ARG 0.005 0.001 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.05810 ( 676) hydrogen bonds : angle 4.98110 ( 2022) covalent geometry : bond 0.00708 (13068) covalent geometry : angle 0.62975 (17718) *********************** 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 124 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 84 time to evaluate : 1.374 Fit side-chains REVERT: A 158 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7791 (ttp-110) REVERT: B 158 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7657 (ttp-110) REVERT: D 158 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7762 (ttp-110) REVERT: E 113 MET cc_start: 0.9296 (ptm) cc_final: 0.8777 (ptm) REVERT: E 158 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7684 (ttp-110) outliers start: 40 outliers final: 12 residues processed: 109 average time/residue: 1.4453 time to fit residues: 170.9915 Evaluate side-chains 93 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 158 ARG Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 158 ARG Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 121 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 92 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.084860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.068068 restraints weight = 74495.038| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 4.64 r_work: 0.2685 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 13068 Z= 0.162 Angle : 0.511 5.001 17718 Z= 0.275 Chirality : 0.042 0.149 2082 Planarity : 0.003 0.024 2286 Dihedral : 4.192 21.491 1836 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 2.30 % Allowed : 9.12 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 1686 helix: 1.45 (0.17), residues: 936 sheet: 0.34 (0.41), residues: 186 loop : -1.25 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 86 HIS 0.002 0.001 HIS D 66 PHE 0.015 0.002 PHE C 93 TYR 0.027 0.001 TYR D 141 ARG 0.002 0.000 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.04647 ( 676) hydrogen bonds : angle 4.63820 ( 2022) covalent geometry : bond 0.00370 (13068) covalent geometry : angle 0.51149 (17718) *********************** 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 120 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8486 (tp30) cc_final: 0.8110 (tp30) REVERT: A 158 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7706 (ttp-110) REVERT: B 151 GLU cc_start: 0.8493 (tp30) cc_final: 0.8278 (tp30) REVERT: B 233 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8142 (mpt) REVERT: C 183 ASP cc_start: 0.8958 (m-30) cc_final: 0.8614 (m-30) REVERT: C 233 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.7757 (mpt) REVERT: D 151 GLU cc_start: 0.8508 (tp30) cc_final: 0.8139 (tp30) REVERT: D 158 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7707 (ttp-110) REVERT: D 233 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8514 (mpt) REVERT: E 113 MET cc_start: 0.9222 (ptm) cc_final: 0.9012 (ptm) REVERT: E 151 GLU cc_start: 0.8482 (tp30) cc_final: 0.8125 (tp30) REVERT: E 158 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7716 (ttp-110) REVERT: E 233 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8089 (mpt) REVERT: F 183 ASP cc_start: 0.8963 (m-30) cc_final: 0.8623 (m-30) REVERT: F 233 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.7821 (mpt) outliers start: 32 outliers final: 9 residues processed: 107 average time/residue: 1.6051 time to fit residues: 185.2233 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 : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ARG 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 323 VAL Chi-restraints excluded: chain D residue 158 ARG Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 158 ARG 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 233 MET 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 63 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3157 r_free = 0.3157 target = 0.084067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.067157 restraints weight = 77990.919| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 4.69 r_work: 0.2667 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 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 = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1941 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= 0.185 Angle : 0.525 5.861 17718 Z= 0.282 Chirality : 0.043 0.155 2082 Planarity : 0.003 0.024 2286 Dihedral : 4.228 22.449 1836 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.01 % Allowed : 9.41 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.20), residues: 1686 helix: 1.45 (0.17), residues: 936 sheet: 0.38 (0.41), residues: 186 loop : -1.37 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.002 0.001 HIS F 285 PHE 0.016 0.002 PHE D 93 TYR 0.024 0.001 TYR A 141 ARG 0.002 0.000 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 676) hydrogen bonds : angle 4.57309 ( 2022) covalent geometry : bond 0.00429 (13068) covalent geometry : angle 0.52541 (17718) *********************** 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 118 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8479 (tp30) cc_final: 0.8132 (tp30) REVERT: A 158 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.7726 (ttp-110) REVERT: B 151 GLU cc_start: 0.8459 (tp30) cc_final: 0.8236 (tp30) REVERT: B 233 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8088 (mpt) REVERT: C 233 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.7757 (mpt) REVERT: D 151 GLU cc_start: 0.8514 (tp30) cc_final: 0.8177 (tp30) REVERT: D 158 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.7725 (ttp-110) REVERT: E 56 GLU cc_start: 0.8495 (pt0) cc_final: 0.8170 (tm-30) REVERT: E 113 MET cc_start: 0.9223 (ptm) cc_final: 0.8650 (ptm) REVERT: E 151 GLU cc_start: 0.8454 (tp30) cc_final: 0.8145 (tp30) REVERT: E 158 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7917 (ttp-110) REVERT: E 233 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8076 (mpt) REVERT: F 233 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.7801 (mpt) outliers start: 28 outliers final: 13 residues processed: 108 average time/residue: 1.6871 time to fit residues: 195.4870 Evaluate side-chains 106 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ARG 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 273 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 158 ARG Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 158 ARG 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 233 MET Chi-restraints excluded: chain F residue 273 GLN 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 57 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3134 r_free = 0.3134 target = 0.082870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.066037 restraints weight = 67632.927| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 4.46 r_work: 0.2652 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 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 = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 13068 Z= 0.248 Angle : 0.561 5.041 17718 Z= 0.299 Chirality : 0.045 0.166 2082 Planarity : 0.003 0.024 2286 Dihedral : 4.424 25.013 1836 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.30 % Allowed : 9.12 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1686 helix: 1.36 (0.17), residues: 936 sheet: 0.31 (0.41), residues: 186 loop : -1.37 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 86 HIS 0.003 0.001 HIS D 285 PHE 0.017 0.002 PHE D 93 TYR 0.021 0.002 TYR D 141 ARG 0.004 0.000 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 676) hydrogen bonds : angle 4.64306 ( 2022) covalent geometry : bond 0.00578 (13068) covalent geometry : angle 0.56095 (17718) *********************** 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 121 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8508 (tp30) cc_final: 0.8157 (tp30) REVERT: A 158 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7640 (ttp-110) REVERT: B 151 GLU cc_start: 0.8439 (tp30) cc_final: 0.8219 (tp30) REVERT: B 233 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8089 (mpt) REVERT: D 151 GLU cc_start: 0.8512 (tp30) cc_final: 0.8180 (tp30) REVERT: D 158 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.7674 (ttp-110) REVERT: E 56 GLU cc_start: 0.8481 (pt0) cc_final: 0.8193 (tm-30) REVERT: E 113 MET cc_start: 0.9249 (ptm) cc_final: 0.8656 (ptm) REVERT: E 151 GLU cc_start: 0.8446 (tp30) cc_final: 0.8119 (tp30) REVERT: E 158 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7711 (ttp-110) REVERT: E 233 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8073 (mpt) outliers start: 32 outliers final: 8 residues processed: 109 average time/residue: 2.0027 time to fit residues: 235.9928 Evaluate side-chains 98 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ARG 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 323 VAL Chi-restraints excluded: chain D residue 158 ARG Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 158 ARG 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 64 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3173 r_free = 0.3173 target = 0.084933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.067886 restraints weight = 80972.860| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 4.82 r_work: 0.2683 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 13068 Z= 0.143 Angle : 0.490 4.803 17718 Z= 0.262 Chirality : 0.042 0.156 2082 Planarity : 0.003 0.024 2286 Dihedral : 4.133 19.966 1836 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 2.01 % Allowed : 9.20 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1686 helix: 1.51 (0.17), residues: 936 sheet: 0.36 (0.41), residues: 186 loop : -1.41 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 86 HIS 0.002 0.001 HIS F 285 PHE 0.015 0.002 PHE C 93 TYR 0.021 0.001 TYR A 141 ARG 0.002 0.000 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 676) hydrogen bonds : angle 4.42006 ( 2022) covalent geometry : bond 0.00325 (13068) covalent geometry : angle 0.48967 (17718) *********************** 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 146 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8427 (tp30) cc_final: 0.8086 (tp30) REVERT: A 158 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7758 (ttp-110) REVERT: B 56 GLU cc_start: 0.8480 (pt0) cc_final: 0.8161 (tm-30) REVERT: B 113 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8582 (ptm) REVERT: B 151 GLU cc_start: 0.8360 (tp30) cc_final: 0.8138 (tp30) REVERT: B 158 ARG cc_start: 0.8800 (ttp-110) cc_final: 0.8599 (ttp-110) REVERT: B 233 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8133 (mpt) REVERT: D 151 GLU cc_start: 0.8423 (tp30) cc_final: 0.8079 (tp30) REVERT: D 158 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7757 (ttp-110) REVERT: E 56 GLU cc_start: 0.8468 (pt0) cc_final: 0.8161 (tm-30) REVERT: E 151 GLU cc_start: 0.8412 (tp30) cc_final: 0.8185 (tp30) REVERT: E 233 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8139 (mpt) outliers start: 28 outliers final: 12 residues processed: 136 average time/residue: 1.7154 time to fit residues: 249.5865 Evaluate side-chains 119 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 113 MET 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 128 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 158 ARG 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 128 LEU 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 43 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.084776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.067736 restraints weight = 73282.682| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 4.63 r_work: 0.2685 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13068 Z= 0.163 Angle : 0.516 5.461 17718 Z= 0.276 Chirality : 0.042 0.190 2082 Planarity : 0.003 0.024 2286 Dihedral : 4.143 20.657 1836 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.72 % Allowed : 9.99 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1686 helix: 1.56 (0.17), residues: 936 sheet: 0.36 (0.41), residues: 186 loop : -1.37 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 86 HIS 0.002 0.001 HIS B 285 PHE 0.015 0.002 PHE C 93 TYR 0.020 0.001 TYR A 141 ARG 0.002 0.000 ARG C 78 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 676) hydrogen bonds : angle 4.40497 ( 2022) covalent geometry : bond 0.00377 (13068) covalent geometry : angle 0.51591 (17718) *********************** 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 128 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLU cc_start: 0.8485 (pt0) cc_final: 0.8167 (tm-30) REVERT: B 233 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8116 (mpt) REVERT: C 183 ASP cc_start: 0.8887 (m-30) cc_final: 0.8565 (m-30) REVERT: D 151 GLU cc_start: 0.8416 (tp30) cc_final: 0.8206 (tp30) REVERT: D 197 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7922 (mp0) REVERT: E 56 GLU cc_start: 0.8462 (pt0) cc_final: 0.8157 (tm-30) REVERT: E 233 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8084 (mpt) outliers start: 24 outliers final: 14 residues processed: 121 average time/residue: 1.7939 time to fit residues: 231.9200 Evaluate side-chains 99 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 101 ASP Chi-restraints excluded: chain C residue 128 LEU 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 128 LEU 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 86 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 140 optimal weight: 7.9990 chunk 144 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 147 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3183 r_free = 0.3183 target = 0.085468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.068567 restraints weight = 73910.871| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 4.58 r_work: 0.2708 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13068 Z= 0.141 Angle : 0.505 6.426 17718 Z= 0.270 Chirality : 0.042 0.179 2082 Planarity : 0.003 0.024 2286 Dihedral : 4.084 19.656 1836 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.08 % Allowed : 10.27 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1686 helix: 1.65 (0.17), residues: 930 sheet: 0.45 (0.40), residues: 186 loop : -1.30 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.002 0.001 HIS C 285 PHE 0.014 0.002 PHE B 93 TYR 0.019 0.001 TYR D 141 ARG 0.002 0.000 ARG D 74 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 676) hydrogen bonds : angle 4.33206 ( 2022) covalent geometry : bond 0.00324 (13068) covalent geometry : angle 0.50541 (17718) *********************** 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 137 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.349 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: 0.8632 (OUTLIER) cc_final: 0.8401 (mpt) REVERT: B 56 GLU cc_start: 0.8466 (pt0) cc_final: 0.8167 (tm-30) REVERT: B 233 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8085 (mpt) REVERT: C 183 ASP cc_start: 0.8910 (m-30) cc_final: 0.8582 (m-30) REVERT: C 233 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.7684 (mpt) REVERT: D 151 GLU cc_start: 0.8359 (tp30) cc_final: 0.8135 (tp30) REVERT: E 56 GLU cc_start: 0.8462 (pt0) cc_final: 0.8163 (tm-30) REVERT: E 233 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8071 (mpt) REVERT: F 233 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.7698 (mpt) REVERT: F 299 MET cc_start: 0.9409 (ptt) cc_final: 0.9183 (ptm) outliers start: 29 outliers final: 15 residues processed: 126 average time/residue: 1.7926 time to fit residues: 240.9627 Evaluate side-chains 100 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 128 LEU 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 128 LEU Chi-restraints excluded: chain F residue 233 MET 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 24 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3161 r_free = 0.3161 target = 0.084464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.067467 restraints weight = 75262.147| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 4.61 r_work: 0.2682 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 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 : 0.004 0.046 13068 Z= 0.175 Angle : 0.568 10.498 17718 Z= 0.296 Chirality : 0.043 0.223 2082 Planarity : 0.003 0.030 2286 Dihedral : 4.141 21.522 1836 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.58 % Allowed : 11.21 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1686 helix: 1.60 (0.17), residues: 930 sheet: 0.43 (0.40), residues: 186 loop : -1.25 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 86 HIS 0.002 0.001 HIS F 285 PHE 0.015 0.002 PHE A 93 TYR 0.019 0.001 TYR A 141 ARG 0.003 0.000 ARG D 158 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 676) hydrogen bonds : angle 4.38345 ( 2022) covalent geometry : bond 0.00413 (13068) covalent geometry : angle 0.56839 (17718) *********************** 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 106 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.8633 (m-80) cc_final: 0.8257 (m-80) REVERT: A 233 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8390 (mpt) REVERT: B 233 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8089 (mpt) REVERT: C 113 MET cc_start: 0.8932 (ptp) cc_final: 0.8491 (ptm) REVERT: C 233 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.7707 (mpt) REVERT: D 151 GLU cc_start: 0.8458 (tp30) cc_final: 0.8252 (tp30) REVERT: E 131 LYS cc_start: 0.8482 (mmmt) cc_final: 0.8049 (pptt) REVERT: E 233 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8039 (mpt) REVERT: F 113 MET cc_start: 0.8904 (ptp) cc_final: 0.8437 (ptm) REVERT: F 233 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.7721 (mpt) outliers start: 22 outliers final: 12 residues processed: 100 average time/residue: 1.6431 time to fit residues: 176.5616 Evaluate side-chains 100 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 233 MET 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 43 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 76 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.085354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.068431 restraints weight = 76726.800| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 4.63 r_work: 0.2697 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13068 Z= 0.138 Angle : 0.559 10.268 17718 Z= 0.290 Chirality : 0.042 0.212 2082 Planarity : 0.003 0.035 2286 Dihedral : 4.078 20.417 1836 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.15 % Allowed : 11.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1686 helix: 1.63 (0.17), residues: 930 sheet: 0.50 (0.40), residues: 186 loop : -1.25 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 86 HIS 0.001 0.001 HIS B 285 PHE 0.014 0.002 PHE C 93 TYR 0.019 0.001 TYR A 141 ARG 0.003 0.000 ARG D 158 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 676) hydrogen bonds : angle 4.33193 ( 2022) covalent geometry : bond 0.00322 (13068) covalent geometry : angle 0.55875 (17718) ********************** 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 100 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.9255 (mmm) cc_final: 0.8769 (mtp) REVERT: A 233 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8399 (mpt) REVERT: B 131 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8028 (pptt) REVERT: B 233 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8080 (mpt) REVERT: C 113 MET cc_start: 0.8943 (ptp) cc_final: 0.8503 (ptm) REVERT: C 233 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7691 (mpt) REVERT: D 55 TYR cc_start: 0.8618 (m-80) cc_final: 0.8172 (m-80) REVERT: D 81 MET cc_start: 0.9279 (mmm) cc_final: 0.8914 (mtp) REVERT: D 151 GLU cc_start: 0.8411 (tp30) cc_final: 0.8199 (tp30) REVERT: E 131 LYS cc_start: 0.8546 (mmmt) cc_final: 0.8039 (pptt) REVERT: E 233 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8027 (mpt) REVERT: F 113 MET cc_start: 0.8905 (ptp) cc_final: 0.8441 (ptm) REVERT: F 233 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.7714 (mpt) REVERT: F 299 MET cc_start: 0.9378 (ptt) cc_final: 0.9154 (ptm) outliers start: 16 outliers final: 11 residues processed: 95 average time/residue: 1.8450 time to fit residues: 188.5922 Evaluate side-chains 97 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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 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 233 MET 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 57 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.081726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.064313 restraints weight = 104556.232| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 5.15 r_work: 0.2600 rms_B_bonded: 5.07 restraints_weight: 2.0000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 13068 Z= 0.318 Angle : 0.671 9.925 17718 Z= 0.348 Chirality : 0.047 0.244 2082 Planarity : 0.003 0.029 2286 Dihedral : 4.506 26.315 1836 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.29 % Allowed : 11.78 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.20), residues: 1686 helix: 1.35 (0.17), residues: 930 sheet: 0.13 (0.41), residues: 186 loop : -1.21 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 86 HIS 0.004 0.001 HIS B 285 PHE 0.018 0.003 PHE B 93 TYR 0.018 0.002 TYR A 141 ARG 0.004 0.001 ARG D 78 Details of bonding type rmsd hydrogen bonds : bond 0.05275 ( 676) hydrogen bonds : angle 4.65019 ( 2022) covalent geometry : bond 0.00744 (13068) covalent geometry : angle 0.67097 (17718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7336.65 seconds wall clock time: 127 minutes 26.99 seconds (7646.99 seconds total)