Starting phenix.real_space_refine on Fri Mar 15 22:01:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk6_40556/03_2024/8sk6_40556.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk6_40556/03_2024/8sk6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk6_40556/03_2024/8sk6_40556.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk6_40556/03_2024/8sk6_40556.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk6_40556/03_2024/8sk6_40556.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk6_40556/03_2024/8sk6_40556.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 13.25, per 1000 atoms: 1.03 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 - 3.50 Amino acid : False - 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: 5.46 Conformation dependent library (CDL) restraints added in 4.8 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: 1.42 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: 3.90 Time building geometry restraints manager: 5.85 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: 100.54 - 107.23: 347 107.23 - 113.92: 7670 113.92 - 120.61: 4967 120.61 - 127.30: 4620 127.30 - 133.99: 114 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 2.440 nonbonded pdb=" OG SER C 57 " pdb=" OE1 GLU C 88 " model vdw 2.218 2.440 nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 88 " model vdw 2.219 2.440 nonbonded pdb=" OG SER B 57 " pdb=" OE1 GLU B 88 " model vdw 2.220 2.440 nonbonded pdb=" OG SER D 57 " pdb=" OE1 GLU D 88 " model vdw 2.224 2.440 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 48 through 53 or resid 55 through 96 or resid 98 through 3 \ 28)) selection = (chain 'B' and (resid 48 through 53 or resid 55 through 96 or resid 98 through 3 \ 28)) selection = (chain 'C' and (resid 48 through 53 or resid 55 through 96 or resid 98 through 3 \ 28)) selection = (chain 'D' and (resid 48 through 53 or resid 55 through 96 or resid 98 through 3 \ 28)) selection = (chain 'E' and (resid 48 through 53 or resid 55 through 96 or resid 98 through 3 \ 28)) selection = (chain 'F' and (resid 48 through 53 or resid 55 through 96 or resid 98 through 3 \ 28)) } 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: 1.900 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: 7.400 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 46.530 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.130 ------------------------------------------------------------------------------- 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= 0.142 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.577 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: 1.7634 time to fit residues: 283.7933 Evaluate side-chains 92 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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: 6.9990 chunk 127 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 131 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 13068 Z= 0.396 Angle : 0.575 7.040 17718 Z= 0.310 Chirality : 0.044 0.158 2082 Planarity : 0.003 0.022 2286 Dihedral : 4.230 24.867 1836 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.59 % Allowed : 7.83 % Favored : 89.58 % 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: 0.76 (0.20), residues: 1686 helix: 1.40 (0.17), residues: 942 sheet: 0.57 (0.43), residues: 186 loop : -1.04 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 86 HIS 0.003 0.001 HIS A 285 PHE 0.015 0.002 PHE D 93 TYR 0.032 0.002 TYR A 141 ARG 0.004 0.001 ARG D 78 *********************** 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 118 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 82 time to evaluate : 1.722 Fit side-chains REVERT: B 113 MET cc_start: 0.8897 (ptm) cc_final: 0.8546 (ptm) REVERT: C 183 ASP cc_start: 0.8506 (m-30) cc_final: 0.8169 (m-30) REVERT: E 113 MET cc_start: 0.8901 (ptm) cc_final: 0.8545 (ptm) REVERT: F 183 ASP cc_start: 0.8505 (m-30) cc_final: 0.8173 (m-30) outliers start: 36 outliers final: 9 residues processed: 107 average time/residue: 1.3699 time to fit residues: 159.9634 Evaluate side-chains 83 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 101 ASP Chi-restraints excluded: chain C residue 121 MET 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 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 84 optimal weight: 8.9990 chunk 47 optimal weight: 0.0010 chunk 126 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13068 Z= 0.155 Angle : 0.448 5.046 17718 Z= 0.244 Chirality : 0.040 0.137 2082 Planarity : 0.003 0.024 2286 Dihedral : 3.805 16.049 1836 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 1.58 % Allowed : 9.55 % Favored : 88.86 % 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: 0.94 (0.20), residues: 1686 helix: 1.61 (0.17), residues: 942 sheet: 0.72 (0.42), residues: 186 loop : -1.12 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 86 HIS 0.001 0.000 HIS D 66 PHE 0.012 0.001 PHE F 93 TYR 0.027 0.001 TYR A 141 ARG 0.001 0.000 ARG D 78 *********************** 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 119 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 1.656 Fit side-chains REVERT: C 183 ASP cc_start: 0.8478 (m-30) cc_final: 0.8197 (m-30) REVERT: F 183 ASP cc_start: 0.8471 (m-30) cc_final: 0.8195 (m-30) outliers start: 22 outliers final: 8 residues processed: 116 average time/residue: 1.4563 time to fit residues: 182.9472 Evaluate side-chains 102 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13068 Z= 0.169 Angle : 0.443 5.496 17718 Z= 0.240 Chirality : 0.040 0.138 2082 Planarity : 0.003 0.023 2286 Dihedral : 3.771 17.178 1836 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.65 % Allowed : 10.78 % Favored : 87.57 % 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: 1.05 (0.20), residues: 1686 helix: 1.71 (0.17), residues: 942 sheet: 0.85 (0.41), residues: 186 loop : -1.13 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 86 HIS 0.001 0.000 HIS C 285 PHE 0.013 0.001 PHE C 93 TYR 0.024 0.001 TYR D 141 ARG 0.002 0.000 ARG D 158 *********************** 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 120 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 1.649 Fit side-chains REVERT: A 151 GLU cc_start: 0.7907 (tp30) cc_final: 0.7698 (tp30) REVERT: B 233 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8046 (mpt) REVERT: B 273 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.6959 (mp10) REVERT: C 183 ASP cc_start: 0.8486 (m-30) cc_final: 0.8202 (m-30) REVERT: C 233 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7658 (mpt) REVERT: E 233 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8020 (mpt) REVERT: E 273 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.6963 (mp10) REVERT: F 183 ASP cc_start: 0.8495 (m-30) cc_final: 0.8209 (m-30) outliers start: 23 outliers final: 6 residues processed: 114 average time/residue: 1.6952 time to fit residues: 207.2614 Evaluate side-chains 98 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 0.0670 chunk 67 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 13068 Z= 0.252 Angle : 0.485 5.526 17718 Z= 0.262 Chirality : 0.042 0.154 2082 Planarity : 0.003 0.023 2286 Dihedral : 3.962 21.064 1836 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.80 % Allowed : 10.99 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.20), residues: 1686 helix: 1.65 (0.17), residues: 942 sheet: 0.88 (0.41), residues: 186 loop : -1.23 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 86 HIS 0.002 0.001 HIS F 285 PHE 0.015 0.002 PHE A 93 TYR 0.022 0.001 TYR D 141 ARG 0.003 0.000 ARG F 78 *********************** 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 116 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8017 (mpt) REVERT: C 183 ASP cc_start: 0.8499 (m-30) cc_final: 0.8218 (m-30) REVERT: E 233 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8020 (mpt) REVERT: F 183 ASP cc_start: 0.8497 (m-30) cc_final: 0.8210 (m-30) outliers start: 25 outliers final: 10 residues processed: 106 average time/residue: 1.6953 time to fit residues: 193.0780 Evaluate side-chains 101 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13068 Z= 0.200 Angle : 0.462 5.366 17718 Z= 0.250 Chirality : 0.041 0.171 2082 Planarity : 0.003 0.023 2286 Dihedral : 3.875 19.351 1836 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.08 % Allowed : 10.63 % Favored : 87.28 % 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: 0.99 (0.20), residues: 1686 helix: 1.70 (0.17), residues: 942 sheet: 0.94 (0.41), residues: 186 loop : -1.28 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.002 0.001 HIS C 285 PHE 0.014 0.001 PHE F 93 TYR 0.021 0.001 TYR A 141 ARG 0.002 0.000 ARG E 78 *********************** 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 121 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.9016 (mtt) cc_final: 0.8728 (mtp) REVERT: A 233 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8350 (mpt) REVERT: A 273 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.6987 (mp10) REVERT: B 113 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8328 (ptm) REVERT: B 233 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8008 (mpt) REVERT: B 273 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: C 113 MET cc_start: 0.8763 (ptp) cc_final: 0.8430 (ptm) REVERT: C 183 ASP cc_start: 0.8480 (m-30) cc_final: 0.8201 (m-30) REVERT: D 81 MET cc_start: 0.8957 (mtt) cc_final: 0.8701 (mtp) REVERT: D 233 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8344 (mpt) REVERT: D 273 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.6990 (mp10) REVERT: E 233 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.7994 (mpt) REVERT: E 273 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.6941 (mp10) REVERT: F 183 ASP cc_start: 0.8477 (m-30) cc_final: 0.8200 (m-30) outliers start: 29 outliers final: 8 residues processed: 113 average time/residue: 1.5461 time to fit residues: 188.4891 Evaluate side-chains 105 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 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 273 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 273 GLN Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13068 Z= 0.159 Angle : 0.443 6.259 17718 Z= 0.240 Chirality : 0.040 0.160 2082 Planarity : 0.002 0.024 2286 Dihedral : 3.760 17.361 1836 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.65 % Allowed : 10.78 % Favored : 87.57 % 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: 1.09 (0.20), residues: 1686 helix: 1.78 (0.17), residues: 942 sheet: 1.10 (0.40), residues: 186 loop : -1.29 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 86 HIS 0.001 0.000 HIS F 285 PHE 0.012 0.001 PHE F 93 TYR 0.020 0.001 TYR D 141 ARG 0.002 0.000 ARG D 158 *********************** 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 115 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 1.659 Fit side-chains REVERT: A 151 GLU cc_start: 0.7886 (tp30) cc_final: 0.7526 (tp30) REVERT: A 233 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8358 (mpt) REVERT: B 113 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8278 (ptm) REVERT: B 233 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.7998 (mpt) REVERT: B 273 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.6966 (mp10) REVERT: C 113 MET cc_start: 0.8753 (ptp) cc_final: 0.8419 (ptm) REVERT: C 183 ASP cc_start: 0.8488 (m-30) cc_final: 0.8217 (m-30) REVERT: D 151 GLU cc_start: 0.7875 (tp30) cc_final: 0.7419 (tp30) REVERT: D 233 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8393 (mpt) REVERT: E 233 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8032 (mpt) REVERT: E 273 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: F 183 ASP cc_start: 0.8479 (m-30) cc_final: 0.8208 (m-30) outliers start: 23 outliers final: 6 residues processed: 109 average time/residue: 1.6044 time to fit residues: 188.5203 Evaluate side-chains 98 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 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 323 VAL 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 323 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13068 Z= 0.388 Angle : 0.564 9.494 17718 Z= 0.299 Chirality : 0.045 0.213 2082 Planarity : 0.003 0.023 2286 Dihedral : 4.234 25.062 1836 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.65 % Allowed : 10.70 % 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: 0.76 (0.20), residues: 1686 helix: 1.50 (0.17), residues: 936 sheet: 0.90 (0.41), residues: 186 loop : -1.35 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 86 HIS 0.003 0.001 HIS D 285 PHE 0.018 0.002 PHE A 93 TYR 0.019 0.002 TYR A 141 ARG 0.003 0.000 ARG B 78 *********************** 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 109 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8999 (mtt) cc_final: 0.8708 (mtp) REVERT: A 151 GLU cc_start: 0.8038 (tp30) cc_final: 0.7809 (tp30) REVERT: A 197 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7753 (mp0) REVERT: C 113 MET cc_start: 0.8783 (ptp) cc_final: 0.8554 (ptm) REVERT: D 197 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7737 (mp0) outliers start: 23 outliers final: 12 residues processed: 101 average time/residue: 1.6142 time to fit residues: 175.5054 Evaluate side-chains 92 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 273 GLN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 136 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 13068 Z= 0.164 Angle : 0.471 10.053 17718 Z= 0.251 Chirality : 0.040 0.183 2082 Planarity : 0.003 0.024 2286 Dihedral : 3.810 16.209 1836 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.29 % Allowed : 11.28 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.01 (0.20), residues: 1686 helix: 1.71 (0.17), residues: 942 sheet: 1.05 (0.41), residues: 186 loop : -1.30 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 86 HIS 0.001 0.000 HIS A 66 PHE 0.012 0.001 PHE D 93 TYR 0.018 0.001 TYR A 141 ARG 0.002 0.000 ARG D 158 *********************** 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 111 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 1.560 Fit side-chains revert: symmetry clash REVERT: A 81 MET cc_start: 0.8930 (mtt) cc_final: 0.8562 (mtp) REVERT: A 197 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7690 (mp0) REVERT: B 273 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.7078 (mp10) REVERT: C 113 MET cc_start: 0.8782 (ptp) cc_final: 0.8458 (ptm) REVERT: C 183 ASP cc_start: 0.8455 (m-30) cc_final: 0.8180 (m-30) REVERT: D 197 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7694 (mp0) REVERT: E 273 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.7076 (mp10) REVERT: F 183 ASP cc_start: 0.8457 (m-30) cc_final: 0.8179 (m-30) outliers start: 18 outliers final: 6 residues processed: 106 average time/residue: 1.7126 time to fit residues: 194.8353 Evaluate side-chains 99 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL 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 323 VAL Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13068 Z= 0.341 Angle : 0.565 11.053 17718 Z= 0.297 Chirality : 0.043 0.209 2082 Planarity : 0.003 0.029 2286 Dihedral : 4.058 20.670 1836 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.57 % Allowed : 11.93 % 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: 0.86 (0.20), residues: 1686 helix: 1.55 (0.17), residues: 942 sheet: 0.94 (0.41), residues: 186 loop : -1.28 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 86 HIS 0.003 0.001 HIS F 285 PHE 0.015 0.002 PHE A 93 TYR 0.019 0.001 TYR D 141 ARG 0.008 0.001 ARG B 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 1.423 Fit side-chains REVERT: A 81 MET cc_start: 0.8982 (mtt) cc_final: 0.8636 (mtp) REVERT: A 151 GLU cc_start: 0.8029 (tp30) cc_final: 0.7806 (tp30) REVERT: B 131 LYS cc_start: 0.8303 (mmmt) cc_final: 0.7995 (pptt) REVERT: B 273 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.6936 (mp10) REVERT: C 113 MET cc_start: 0.8805 (ptp) cc_final: 0.8486 (ptm) REVERT: C 183 ASP cc_start: 0.8479 (m-30) cc_final: 0.8158 (m-30) REVERT: D 55 TYR cc_start: 0.8581 (m-80) cc_final: 0.8228 (m-80) REVERT: D 151 GLU cc_start: 0.8011 (tp30) cc_final: 0.7800 (tp30) REVERT: E 273 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: F 113 MET cc_start: 0.8783 (ptp) cc_final: 0.8420 (ptm) REVERT: F 183 ASP cc_start: 0.8482 (m-30) cc_final: 0.8159 (m-30) outliers start: 8 outliers final: 6 residues processed: 99 average time/residue: 1.7048 time to fit residues: 182.1439 Evaluate side-chains 94 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL 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 323 VAL Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.087125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.071815 restraints weight = 72750.637| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 4.35 r_work: 0.2765 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2202 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= 0.194 Angle : 0.527 10.239 17718 Z= 0.275 Chirality : 0.041 0.205 2082 Planarity : 0.003 0.041 2286 Dihedral : 3.891 18.543 1836 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.72 % Allowed : 11.85 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.96 (0.20), residues: 1686 helix: 1.65 (0.17), residues: 942 sheet: 1.02 (0.40), residues: 186 loop : -1.28 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 140 HIS 0.001 0.000 HIS F 285 PHE 0.014 0.001 PHE F 93 TYR 0.019 0.001 TYR D 141 ARG 0.009 0.000 ARG E 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3991.63 seconds wall clock time: 72 minutes 1.63 seconds (4321.63 seconds total)