Starting phenix.real_space_refine on Thu May 15 06:42:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sk6_40556/05_2025/8sk6_40556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sk6_40556/05_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_40556/05_2025/8sk6_40556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sk6_40556/05_2025/8sk6_40556.map" model { file = "/net/cci-nas-00/data/ceres_data/8sk6_40556/05_2025/8sk6_40556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sk6_40556/05_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-5687/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: 13.55, per 1000 atoms: 1.05 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: 2.96 Conformation dependent library (CDL) restraints added in 3.2 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: 1.47 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: 3.81 Time building geometry restraints manager: 3.47 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: 0.11 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 38.170 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.770 ------------------------------------------------------------------------------- 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 : 1.562 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: 1.7225 time to fit residues: 277.4806 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 : 1.451 ------------------------------------------------------------------------------- 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 = 0.067799 restraints weight = 81516.180| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 4.68 r_work: 0.2630 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- 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 = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 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 : 1.375 Fit side-chains REVERT: A 158 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.7795 (ttp-110) REVERT: B 158 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7663 (ttp-110) REVERT: D 158 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7767 (ttp-110) REVERT: E 113 MET cc_start: 0.9296 (ptm) cc_final: 0.8778 (ptm) REVERT: E 158 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7689 (ttp-110) outliers start: 40 outliers final: 12 residues processed: 109 average time/residue: 1.4405 time to fit residues: 170.5349 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 : 1.498 ------------------------------------------------------------------------------- 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: 2.9990 chunk 76 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.3154 r_free = 0.3154 target = 0.084068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.067284 restraints weight = 74765.212| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 4.63 r_work: 0.2669 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13068 Z= 0.188 Angle : 0.531 5.055 17718 Z= 0.285 Chirality : 0.043 0.153 2082 Planarity : 0.003 0.024 2286 Dihedral : 4.282 23.221 1836 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 2.23 % Allowed : 9.20 % 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: 1.40 (0.17), residues: 936 sheet: 0.33 (0.41), residues: 186 loop : -1.26 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 86 HIS 0.002 0.001 HIS C 285 PHE 0.016 0.002 PHE C 93 TYR 0.026 0.001 TYR D 141 ARG 0.002 0.000 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.04868 ( 676) hydrogen bonds : angle 4.69576 ( 2022) covalent geometry : bond 0.00436 (13068) covalent geometry : angle 0.53104 (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 117 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8541 (tp30) cc_final: 0.8177 (tp30) REVERT: A 158 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7710 (ttp-110) REVERT: A 233 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8492 (mpt) REVERT: B 151 GLU cc_start: 0.8512 (tp30) cc_final: 0.8144 (tp30) REVERT: B 158 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7706 (ttp-110) REVERT: B 233 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8090 (mpt) REVERT: C 233 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.7736 (mpt) REVERT: D 151 GLU cc_start: 0.8550 (tp30) cc_final: 0.8192 (tp30) REVERT: D 158 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7702 (ttp-110) REVERT: E 113 MET cc_start: 0.9234 (ptm) cc_final: 0.9021 (ptm) REVERT: E 151 GLU cc_start: 0.8505 (tp30) cc_final: 0.8137 (tp30) REVERT: E 158 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7692 (ttp-110) REVERT: E 233 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8097 (mpt) outliers start: 31 outliers final: 9 residues processed: 105 average time/residue: 1.6339 time to fit residues: 185.3837 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 : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 158 ARG 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 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=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: 3.9990 chunk 163 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 165 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 140 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 = 0.084619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.067634 restraints weight = 77680.107| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 4.71 r_work: 0.2680 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 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 = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 13068 Z= 0.162 Angle : 0.510 5.795 17718 Z= 0.275 Chirality : 0.042 0.152 2082 Planarity : 0.003 0.024 2286 Dihedral : 4.191 21.235 1836 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.23 % Allowed : 9.34 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.64 (0.20), residues: 1686 helix: 1.48 (0.17), residues: 936 sheet: 0.39 (0.41), residues: 186 loop : -1.38 (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 0.015 0.002 PHE D 93 TYR 0.024 0.001 TYR D 141 ARG 0.002 0.000 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 676) hydrogen bonds : angle 4.53642 ( 2022) covalent geometry : bond 0.00371 (13068) covalent geometry : angle 0.51029 (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 130 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8444 (tp30) cc_final: 0.8089 (tp30) REVERT: A 158 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7722 (ttp-110) REVERT: A 233 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8491 (mpt) REVERT: B 56 GLU cc_start: 0.8483 (pt0) cc_final: 0.8152 (tm-30) REVERT: B 151 GLU cc_start: 0.8451 (tp30) cc_final: 0.8141 (tp30) REVERT: B 158 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7940 (ttp-110) REVERT: B 233 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8111 (mpt) REVERT: C 233 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7722 (mpt) REVERT: D 151 GLU cc_start: 0.8468 (tp30) cc_final: 0.8124 (tp30) REVERT: D 158 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7719 (ttp-110) REVERT: E 56 GLU cc_start: 0.8482 (pt0) cc_final: 0.8158 (tm-30) REVERT: E 113 MET cc_start: 0.9212 (ptm) cc_final: 0.8650 (ptm) REVERT: E 151 GLU cc_start: 0.8429 (tp30) cc_final: 0.8079 (tp30) REVERT: E 158 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7747 (ttp-110) REVERT: E 233 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8075 (mpt) REVERT: F 233 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.7812 (mpt) outliers start: 31 outliers final: 11 residues processed: 119 average time/residue: 1.6964 time to fit residues: 216.0668 Evaluate side-chains 112 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ARG 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 158 ARG 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 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 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: 0.8980 chunk 92 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 167 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3128 r_free = 0.3128 target = 0.082573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.065908 restraints weight = 67295.691| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 4.38 r_work: 0.2650 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 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 = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2011 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= 0.246 Angle : 0.563 5.038 17718 Z= 0.300 Chirality : 0.045 0.165 2082 Planarity : 0.003 0.024 2286 Dihedral : 4.418 24.810 1836 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.44 % Allowed : 9.05 % Favored : 88.51 % 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: 0.55 (0.20), residues: 1686 helix: 1.37 (0.17), residues: 936 sheet: 0.33 (0.41), residues: 186 loop : -1.33 (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 A 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 0.05013 ( 676) hydrogen bonds : angle 4.64412 ( 2022) covalent geometry : bond 0.00575 (13068) covalent geometry : angle 0.56274 (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 128 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8519 (tp30) cc_final: 0.8173 (tp30) REVERT: A 158 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7645 (ttp-110) REVERT: A 233 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8468 (mpt) REVERT: B 56 GLU cc_start: 0.8475 (pt0) cc_final: 0.8190 (tm-30) REVERT: B 151 GLU cc_start: 0.8510 (tp30) cc_final: 0.8184 (tp30) REVERT: B 158 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7671 (ttp-110) REVERT: B 233 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8129 (mpt) REVERT: D 81 MET cc_start: 0.9458 (mtt) cc_final: 0.9253 (mtp) REVERT: D 151 GLU cc_start: 0.8520 (tp30) cc_final: 0.8179 (tp30) REVERT: D 158 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.7655 (ttp-110) REVERT: E 56 GLU cc_start: 0.8475 (pt0) cc_final: 0.8193 (tm-30) REVERT: E 113 MET cc_start: 0.9252 (ptm) cc_final: 0.8672 (ptm) REVERT: E 151 GLU cc_start: 0.8477 (tp30) cc_final: 0.8154 (tp30) REVERT: E 158 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7700 (ttp-110) REVERT: E 233 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8089 (mpt) outliers start: 34 outliers final: 10 residues processed: 114 average time/residue: 1.6781 time to fit residues: 205.1290 Evaluate side-chains 106 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 158 ARG 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 113 MET 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: 1.9990 chunk 84 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 146 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3180 r_free = 0.3180 target = 0.085472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.068446 restraints weight = 80711.125| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 4.77 r_work: 0.2699 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 13068 Z= 0.133 Angle : 0.480 4.785 17718 Z= 0.258 Chirality : 0.041 0.153 2082 Planarity : 0.003 0.024 2286 Dihedral : 4.054 18.427 1836 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: 0.72 (0.20), residues: 1686 helix: 1.58 (0.17), residues: 936 sheet: 0.41 (0.41), residues: 186 loop : -1.39 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 86 HIS 0.001 0.001 HIS D 66 PHE 0.014 0.001 PHE C 93 TYR 0.020 0.001 TYR A 141 ARG 0.002 0.000 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 676) hydrogen bonds : angle 4.37451 ( 2022) covalent geometry : bond 0.00298 (13068) covalent geometry : angle 0.48000 (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 147 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8373 (tp30) cc_final: 0.8123 (tp30) REVERT: B 56 GLU cc_start: 0.8457 (pt0) cc_final: 0.8139 (tm-30) REVERT: B 113 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8560 (ptm) REVERT: B 233 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8068 (mpt) REVERT: D 81 MET cc_start: 0.9409 (mtt) cc_final: 0.9207 (mtp) REVERT: D 151 GLU cc_start: 0.8365 (tp30) cc_final: 0.8119 (tp30) REVERT: E 56 GLU cc_start: 0.8462 (pt0) cc_final: 0.8146 (tm-30) REVERT: E 113 MET cc_start: 0.9168 (ptm) cc_final: 0.8648 (ptm) REVERT: E 151 GLU cc_start: 0.8352 (tp30) cc_final: 0.8101 (tp30) REVERT: E 233 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8080 (mpt) outliers start: 28 outliers final: 10 residues processed: 135 average time/residue: 1.6806 time to fit residues: 242.4396 Evaluate side-chains 110 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL 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 323 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 43 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3139 r_free = 0.3139 target = 0.083355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.066471 restraints weight = 73160.962| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 4.57 r_work: 0.2662 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13068 Z= 0.204 Angle : 0.544 5.441 17718 Z= 0.290 Chirality : 0.044 0.193 2082 Planarity : 0.003 0.024 2286 Dihedral : 4.254 23.168 1836 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.72 % Allowed : 10.42 % Favored : 87.86 % 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: 0.67 (0.20), residues: 1686 helix: 1.52 (0.17), residues: 936 sheet: 0.30 (0.41), residues: 186 loop : -1.35 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 86 HIS 0.002 0.001 HIS C 285 PHE 0.017 0.002 PHE A 93 TYR 0.020 0.001 TYR A 141 ARG 0.003 0.000 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.04671 ( 676) hydrogen bonds : angle 4.47717 ( 2022) covalent geometry : bond 0.00475 (13068) covalent geometry : angle 0.54376 (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 127 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8422 (tp30) cc_final: 0.8191 (tp30) REVERT: B 56 GLU cc_start: 0.8524 (pt0) cc_final: 0.8207 (tm-30) REVERT: B 233 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8108 (mpt) REVERT: C 113 MET cc_start: 0.8952 (ptp) cc_final: 0.8682 (ptm) REVERT: D 151 GLU cc_start: 0.8429 (tp30) cc_final: 0.8199 (tp30) REVERT: D 233 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8476 (mpt) REVERT: E 56 GLU cc_start: 0.8519 (pt0) cc_final: 0.8208 (tm-30) REVERT: E 113 MET cc_start: 0.9252 (ptm) cc_final: 0.8681 (ptm) REVERT: E 233 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8124 (mpt) outliers start: 24 outliers final: 14 residues processed: 117 average time/residue: 1.8233 time to fit residues: 227.8825 Evaluate side-chains 105 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 323 VAL 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 273 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 273 GLN Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 86 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3141 r_free = 0.3141 target = 0.083452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.066332 restraints weight = 74473.858| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 4.62 r_work: 0.2654 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 13068 Z= 0.219 Angle : 0.556 6.179 17718 Z= 0.295 Chirality : 0.044 0.190 2082 Planarity : 0.003 0.025 2286 Dihedral : 4.338 23.367 1836 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.65 % Allowed : 10.85 % Favored : 87.50 % 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: 1.48 (0.17), residues: 936 sheet: 0.25 (0.41), residues: 186 loop : -1.38 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 86 HIS 0.002 0.001 HIS E 285 PHE 0.016 0.002 PHE D 93 TYR 0.019 0.001 TYR A 141 ARG 0.003 0.000 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 676) hydrogen bonds : angle 4.52194 ( 2022) covalent geometry : bond 0.00512 (13068) covalent geometry : angle 0.55602 (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 119 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8433 (tp30) cc_final: 0.8176 (tp30) REVERT: B 233 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8075 (mpt) REVERT: C 113 MET cc_start: 0.8940 (ptp) cc_final: 0.8579 (ptm) REVERT: D 81 MET cc_start: 0.9398 (mtt) cc_final: 0.9182 (mtp) REVERT: D 151 GLU cc_start: 0.8427 (tp30) cc_final: 0.8190 (tp30) REVERT: D 233 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8442 (mpt) REVERT: E 56 GLU cc_start: 0.8513 (pt0) cc_final: 0.8215 (tm-30) REVERT: E 113 MET cc_start: 0.9236 (ptm) cc_final: 0.8643 (ptm) REVERT: E 233 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8082 (mpt) outliers start: 23 outliers final: 14 residues processed: 111 average time/residue: 1.7799 time to fit residues: 211.3137 Evaluate side-chains 105 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 323 VAL 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 273 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 273 GLN Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 24 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.085863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.068862 restraints weight = 74628.950| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 4.62 r_work: 0.2710 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13068 Z= 0.125 Angle : 0.495 5.614 17718 Z= 0.266 Chirality : 0.041 0.183 2082 Planarity : 0.003 0.037 2286 Dihedral : 4.019 18.050 1836 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.29 % Allowed : 11.06 % 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: 0.75 (0.20), residues: 1686 helix: 1.61 (0.17), residues: 936 sheet: 0.43 (0.40), residues: 186 loop : -1.40 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 86 HIS 0.001 0.001 HIS A 285 PHE 0.013 0.001 PHE F 93 TYR 0.019 0.001 TYR A 141 ARG 0.002 0.000 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 676) hydrogen bonds : angle 4.30984 ( 2022) covalent geometry : bond 0.00282 (13068) covalent geometry : angle 0.49547 (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 121 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8349 (tp30) cc_final: 0.8120 (tp30) REVERT: B 151 GLU cc_start: 0.8528 (tp30) cc_final: 0.8290 (tp30) REVERT: C 113 MET cc_start: 0.8958 (ptp) cc_final: 0.8559 (ptm) REVERT: D 151 GLU cc_start: 0.8334 (tp30) cc_final: 0.8073 (tp30) REVERT: D 197 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7948 (mp0) REVERT: E 56 GLU cc_start: 0.8529 (pt0) cc_final: 0.8149 (tp30) REVERT: E 113 MET cc_start: 0.9203 (ptm) cc_final: 0.8649 (ptm) REVERT: F 183 ASP cc_start: 0.8898 (m-30) cc_final: 0.8588 (m-30) outliers start: 18 outliers final: 12 residues processed: 115 average time/residue: 1.7848 time to fit residues: 219.3077 Evaluate side-chains 100 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 113 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 273 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 273 GLN Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 43 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 0.0070 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 74 optimal weight: 0.0370 chunk 55 optimal weight: 0.7980 overall best weight: 0.5276 ------------------------------------------------------------------------------- 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 = 0.3203 r_free = 0.3203 target = 0.086986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.069725 restraints weight = 76270.461| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 4.71 r_work: 0.2725 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13068 Z= 0.118 Angle : 0.556 10.851 17718 Z= 0.289 Chirality : 0.041 0.229 2082 Planarity : 0.003 0.038 2286 Dihedral : 3.961 16.921 1836 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.01 % Allowed : 12.00 % 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: 0.84 (0.20), residues: 1686 helix: 1.65 (0.17), residues: 936 sheet: 0.60 (0.40), residues: 186 loop : -1.36 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 86 HIS 0.001 0.001 HIS D 285 PHE 0.013 0.001 PHE F 93 TYR 0.019 0.001 TYR A 141 ARG 0.008 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 676) hydrogen bonds : angle 4.24321 ( 2022) covalent geometry : bond 0.00274 (13068) covalent geometry : angle 0.55569 (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 103 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.328 Fit side-chains REVERT: A 55 TYR cc_start: 0.8616 (m-80) cc_final: 0.8168 (m-80) REVERT: A 81 MET cc_start: 0.9259 (mmm) cc_final: 0.8880 (mtp) REVERT: A 151 GLU cc_start: 0.8297 (tp30) cc_final: 0.8042 (tp30) REVERT: A 273 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.6882 (mp10) REVERT: B 151 GLU cc_start: 0.8492 (tp30) cc_final: 0.8286 (tp30) REVERT: C 113 MET cc_start: 0.8928 (ptp) cc_final: 0.8503 (ptm) REVERT: C 183 ASP cc_start: 0.8917 (m-30) cc_final: 0.8630 (m-30) REVERT: D 55 TYR cc_start: 0.8598 (m-80) cc_final: 0.8142 (m-80) REVERT: D 81 MET cc_start: 0.9265 (mtt) cc_final: 0.9001 (mtp) REVERT: D 151 GLU cc_start: 0.8284 (tp30) cc_final: 0.8038 (tp30) REVERT: D 273 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.6879 (mp10) REVERT: E 113 MET cc_start: 0.9174 (ptm) cc_final: 0.8622 (ptm) REVERT: F 183 ASP cc_start: 0.8899 (m-30) cc_final: 0.8557 (m-30) REVERT: F 299 MET cc_start: 0.9358 (ptt) cc_final: 0.9115 (ptm) outliers start: 14 outliers final: 7 residues processed: 102 average time/residue: 1.6867 time to fit residues: 184.3733 Evaluate side-chains 96 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 323 VAL 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 323 VAL 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: 6.9990 chunk 118 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 90 optimal weight: 0.0570 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- 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 = 0.3191 r_free = 0.3191 target = 0.086104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.068587 restraints weight = 102569.737| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 5.18 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2408 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= 0.133 Angle : 0.549 10.141 17718 Z= 0.287 Chirality : 0.042 0.232 2082 Planarity : 0.003 0.035 2286 Dihedral : 3.949 17.240 1836 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.86 % Allowed : 12.28 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.85 (0.20), residues: 1686 helix: 1.65 (0.17), residues: 936 sheet: 0.65 (0.40), residues: 186 loop : -1.35 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 86 HIS 0.001 0.001 HIS D 285 PHE 0.014 0.002 PHE E 93 TYR 0.019 0.001 TYR A 141 ARG 0.002 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 676) hydrogen bonds : angle 4.24707 ( 2022) covalent geometry : bond 0.00311 (13068) covalent geometry : angle 0.54913 (17718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7001.13 seconds wall clock time: 122 minutes 4.89 seconds (7324.89 seconds total)