Starting phenix.real_space_refine on Mon Sep 14 02:19:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xnn_33319/09_2026/7xnn_33319_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnn_33319/09_2026/7xnn_33319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xnn_33319/09_2026/7xnn_33319_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnn_33319/09_2026/7xnn_33319_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xnn_33319/09_2026/7xnn_33319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnn_33319/09_2026/7xnn_33319.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 12 5.49 5 S 60 5.16 5 C 9268 2.51 5 N 2484 2.21 5 O 2452 1.98 5 H 13096 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27376 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1377 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 20, 'GLN:plan1': 5, 'PHE:plan': 2, 'ASP:plan': 16, 'ARG:plan': 4, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 195 Chain: "B" Number of atoms: 5387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5387 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 7, 'TRANS': 322} Chain breaks: 2 Chain: "C" Number of atoms: 5387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5387 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 7, 'TRANS': 322} Chain breaks: 2 Chain: "D" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1377 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 20, 'GLN:plan1': 5, 'PHE:plan': 2, 'ASP:plan': 16, 'ARG:plan': 4, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 195 Chain: "E" Number of atoms: 5387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5387 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 7, 'TRANS': 322} Chain breaks: 2 Chain: "F" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1377 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 20, 'GLN:plan1': 5, 'PHE:plan': 2, 'ASP:plan': 16, 'ARG:plan': 4, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 195 Chain: "G" Number of atoms: 5387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5387 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 7, 'TRANS': 322} Chain breaks: 2 Chain: "H" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1377 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 20, 'GLN:plan1': 5, 'PHE:plan': 2, 'ASP:plan': 16, 'ARG:plan': 4, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 195 Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 82 Unusual residues: {' K': 3, 'PIO': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' K': 1, 'PIO': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "E" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'PIO': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'PIO': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Time building chain proxies: 4.52, per 1000 atoms: 0.17 Number of scatterers: 27376 At special positions: 0 Unit cell: (126.75, 126.75, 114.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 60 16.00 P 12 15.00 O 2452 8.00 N 2484 7.00 C 9268 6.00 H 13096 1.00 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: 2.41 Conformation dependent library (CDL) restraints added in 773.3 milliseconds 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB I0S B 704 " pdb=" CB I0S C 702 " pdb=" CB I0S E 901 " pdb=" CB I0S G 901 " Number of C-beta restraints generated: 3512 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 0 sheets defined 76.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 11 through 18 removed outlier: 3.619A pdb=" N GLU A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 29 through 41 removed outlier: 3.782A pdb=" N GLY A 34 " --> pdb=" O THR A 30 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.922A pdb=" N ILE A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 84 through 93 removed outlier: 3.957A pdb=" N ALA A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE A 90 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.561A pdb=" N ILE A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 147 removed outlier: 3.523A pdb=" N GLN A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 115 Processing helix chain 'B' and resid 120 through 142 removed outlier: 3.582A pdb=" N LEU B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 150 through 177 removed outlier: 3.764A pdb=" N PHE B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE B 161 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 Processing helix chain 'B' and resid 185 through 195 removed outlier: 3.705A pdb=" N GLY B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 216 Processing helix chain 'B' and resid 224 through 237 removed outlier: 4.460A pdb=" N PHE B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 245 through 285 removed outlier: 5.497A pdb=" N GLN B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 311 removed outlier: 3.567A pdb=" N THR B 311 " --> pdb=" O VAL B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 336 Processing helix chain 'B' and resid 337 through 340 Processing helix chain 'B' and resid 341 through 383 removed outlier: 4.182A pdb=" N GLY B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) Proline residue: B 369 - end of helix removed outlier: 3.788A pdb=" N ILE B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 532 removed outlier: 3.769A pdb=" N LYS B 527 " --> pdb=" O PHE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 555 removed outlier: 3.549A pdb=" N VAL B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 115 Processing helix chain 'C' and resid 120 through 142 removed outlier: 3.582A pdb=" N LEU C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 150 through 177 removed outlier: 3.764A pdb=" N PHE C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE C 161 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 184 Processing helix chain 'C' and resid 185 through 195 removed outlier: 3.705A pdb=" N GLY C 189 " --> pdb=" O VAL C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 216 Processing helix chain 'C' and resid 224 through 237 removed outlier: 4.461A pdb=" N PHE C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 241 Processing helix chain 'C' and resid 245 through 285 removed outlier: 5.497A pdb=" N GLN C 260 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 311 removed outlier: 3.566A pdb=" N THR C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 336 Processing helix chain 'C' and resid 337 through 340 Processing helix chain 'C' and resid 341 through 383 removed outlier: 4.181A pdb=" N GLY C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) Proline residue: C 369 - end of helix removed outlier: 3.788A pdb=" N ILE C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG C 380 " --> pdb=" O GLN C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 532 removed outlier: 3.768A pdb=" N LYS C 527 " --> pdb=" O PHE C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 555 removed outlier: 3.548A pdb=" N VAL C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 18 removed outlier: 3.618A pdb=" N GLU D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA D 16 " --> pdb=" O GLU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 21 No H-bonds generated for 'chain 'D' and resid 19 through 21' Processing helix chain 'D' and resid 29 through 41 removed outlier: 3.782A pdb=" N GLY D 34 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 55 removed outlier: 3.923A pdb=" N ILE D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU D 55 " --> pdb=" O ASP D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 84 through 93 removed outlier: 3.958A pdb=" N ALA D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE D 90 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 118 through 128 removed outlier: 3.561A pdb=" N ILE D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 147 removed outlier: 3.523A pdb=" N GLN D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 115 Processing helix chain 'E' and resid 120 through 142 removed outlier: 3.582A pdb=" N LEU E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 150 through 177 removed outlier: 3.764A pdb=" N PHE E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP E 158 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE E 161 " --> pdb=" O PHE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 184 Processing helix chain 'E' and resid 185 through 195 removed outlier: 3.705A pdb=" N GLY E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 216 Processing helix chain 'E' and resid 224 through 237 removed outlier: 4.461A pdb=" N PHE E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 241 Processing helix chain 'E' and resid 245 through 285 removed outlier: 5.496A pdb=" N GLN E 260 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU E 261 " --> pdb=" O ILE E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 311 removed outlier: 3.566A pdb=" N THR E 311 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 336 Processing helix chain 'E' and resid 337 through 340 Processing helix chain 'E' and resid 341 through 383 removed outlier: 4.182A pdb=" N GLY E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) Proline residue: E 369 - end of helix removed outlier: 3.788A pdb=" N ILE E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG E 380 " --> pdb=" O GLN E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 532 removed outlier: 3.769A pdb=" N LYS E 527 " --> pdb=" O PHE E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 555 removed outlier: 3.549A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 18 removed outlier: 3.618A pdb=" N GLU F 15 " --> pdb=" O ALA F 11 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA F 16 " --> pdb=" O GLU F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 21 No H-bonds generated for 'chain 'F' and resid 19 through 21' Processing helix chain 'F' and resid 29 through 41 removed outlier: 3.782A pdb=" N GLY F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 removed outlier: 3.922A pdb=" N ILE F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 84 through 93 removed outlier: 3.957A pdb=" N ALA F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE F 90 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 111 Processing helix chain 'F' and resid 118 through 128 removed outlier: 3.562A pdb=" N ILE F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 147 removed outlier: 3.523A pdb=" N GLN F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET F 145 " --> pdb=" O GLU F 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 115 Processing helix chain 'G' and resid 120 through 142 removed outlier: 3.581A pdb=" N LEU G 142 " --> pdb=" O ILE G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 149 Processing helix chain 'G' and resid 150 through 177 removed outlier: 3.764A pdb=" N PHE G 157 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE G 161 " --> pdb=" O PHE G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 184 Processing helix chain 'G' and resid 185 through 195 removed outlier: 3.705A pdb=" N GLY G 189 " --> pdb=" O VAL G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 216 Processing helix chain 'G' and resid 224 through 237 removed outlier: 4.460A pdb=" N PHE G 232 " --> pdb=" O ARG G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 241 Processing helix chain 'G' and resid 245 through 285 removed outlier: 5.497A pdb=" N GLN G 260 " --> pdb=" O PHE G 256 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU G 261 " --> pdb=" O ILE G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 311 removed outlier: 3.566A pdb=" N THR G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 336 Processing helix chain 'G' and resid 337 through 340 Processing helix chain 'G' and resid 341 through 383 removed outlier: 4.182A pdb=" N GLY G 345 " --> pdb=" O ALA G 341 " (cutoff:3.500A) Proline residue: G 369 - end of helix removed outlier: 3.787A pdb=" N ILE G 375 " --> pdb=" O ALA G 371 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG G 380 " --> pdb=" O GLN G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 507 through 532 removed outlier: 3.768A pdb=" N LYS G 527 " --> pdb=" O PHE G 523 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 555 removed outlier: 3.548A pdb=" N VAL G 541 " --> pdb=" O ASP G 537 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 18 removed outlier: 3.619A pdb=" N GLU H 15 " --> pdb=" O ALA H 11 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA H 16 " --> pdb=" O GLU H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 21 No H-bonds generated for 'chain 'H' and resid 19 through 21' Processing helix chain 'H' and resid 29 through 41 removed outlier: 3.782A pdb=" N GLY H 34 " --> pdb=" O THR H 30 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR H 35 " --> pdb=" O LYS H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 55 removed outlier: 3.922A pdb=" N ILE H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 84 through 93 removed outlier: 3.957A pdb=" N ALA H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE H 90 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 111 Processing helix chain 'H' and resid 118 through 128 removed outlier: 3.561A pdb=" N ILE H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU H 128 " --> pdb=" O GLU H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 147 removed outlier: 3.523A pdb=" N GLN H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET H 145 " --> pdb=" O GLU H 141 " (cutoff:3.500A) 952 hydrogen bonds defined for protein. 2772 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: 5.63 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 13072 1.02 - 1.22: 36 1.22 - 1.42: 6534 1.42 - 1.61: 7946 1.61 - 1.81: 104 Bond restraints: 27692 Sorted by residual: bond pdb=" CAT I0S C 702 " pdb=" SBF I0S C 702 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CAT I0S B 704 " pdb=" SBF I0S B 704 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CAT I0S E 901 " pdb=" SBF I0S E 901 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CAT I0S G 901 " pdb=" SBF I0S G 901 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CBE I0S E 901 " pdb=" SBF I0S E 901 " ideal model delta sigma weight residual 1.717 1.584 0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 27687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 48655 3.17 - 6.34: 761 6.34 - 9.51: 56 9.51 - 12.68: 16 12.68 - 15.85: 12 Bond angle restraints: 49500 Sorted by residual: angle pdb=" OAQ I0S E 901 " pdb=" SAI I0S E 901 " pdb=" OAR I0S E 901 " ideal model delta sigma weight residual 119.45 103.60 15.85 3.00e+00 1.11e-01 2.79e+01 angle pdb=" OAQ I0S G 901 " pdb=" SAI I0S G 901 " pdb=" OAR I0S G 901 " ideal model delta sigma weight residual 119.45 103.61 15.84 3.00e+00 1.11e-01 2.79e+01 angle pdb=" OAQ I0S B 704 " pdb=" SAI I0S B 704 " pdb=" OAR I0S B 704 " ideal model delta sigma weight residual 119.45 103.62 15.83 3.00e+00 1.11e-01 2.79e+01 angle pdb=" OAQ I0S C 702 " pdb=" SAI I0S C 702 " pdb=" OAR I0S C 702 " ideal model delta sigma weight residual 119.45 103.62 15.83 3.00e+00 1.11e-01 2.79e+01 angle pdb=" CA I0S C 702 " pdb=" N I0S C 702 " pdb=" CAG I0S C 702 " ideal model delta sigma weight residual 121.42 107.76 13.66 3.00e+00 1.11e-01 2.07e+01 ... (remaining 49495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.18: 12856 34.18 - 68.36: 316 68.36 - 102.55: 16 102.55 - 136.73: 4 136.73 - 170.91: 8 Dihedral angle restraints: 13200 sinusoidal: 6584 harmonic: 6616 Sorted by residual: dihedral pdb=" CA TYR E 545 " pdb=" C TYR E 545 " pdb=" N SER E 546 " pdb=" CA SER E 546 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA TYR B 545 " pdb=" C TYR B 545 " pdb=" N SER B 546 " pdb=" CA SER B 546 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA TYR G 545 " pdb=" C TYR G 545 " pdb=" N SER G 546 " pdb=" CA SER G 546 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 13197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1701 0.074 - 0.147: 367 0.147 - 0.220: 93 0.220 - 0.294: 63 0.294 - 0.367: 44 Chirality restraints: 2268 Sorted by residual: chirality pdb=" CB THR B 311 " pdb=" CA THR B 311 " pdb=" OG1 THR B 311 " pdb=" CG2 THR B 311 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CB THR C 311 " pdb=" CA THR C 311 " pdb=" OG1 THR C 311 " pdb=" CG2 THR C 311 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB THR G 311 " pdb=" CA THR G 311 " pdb=" OG1 THR G 311 " pdb=" CG2 THR G 311 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 2265 not shown) Planarity restraints: 4308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 299 " 0.017 2.00e-02 2.50e+03 1.62e-02 7.88e+00 pdb=" CG TYR B 299 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR B 299 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 299 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 299 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 299 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 299 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 299 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR B 299 " -0.006 2.00e-02 2.50e+03 pdb=" HD2 TYR B 299 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 TYR B 299 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR B 299 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 299 " -0.017 2.00e-02 2.50e+03 1.60e-02 7.73e+00 pdb=" CG TYR E 299 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR E 299 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR E 299 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR E 299 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 299 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 299 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR E 299 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR E 299 " 0.006 2.00e-02 2.50e+03 pdb=" HD2 TYR E 299 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TYR E 299 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR E 299 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 299 " -0.018 2.00e-02 2.50e+03 1.60e-02 7.71e+00 pdb=" CG TYR C 299 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR C 299 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C 299 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR C 299 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 299 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 299 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 299 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR C 299 " 0.006 2.00e-02 2.50e+03 pdb=" HD2 TYR C 299 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TYR C 299 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR C 299 " -0.006 2.00e-02 2.50e+03 ... (remaining 4305 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.24: 4298 2.24 - 2.97: 72119 2.97 - 3.69: 92183 3.69 - 4.42: 140167 4.42 - 5.14: 218849 Nonbonded interactions: 527616 Sorted by model distance: nonbonded pdb=" O HIS F 108 " pdb="HD21 ASN F 112 " model vdw 1.521 2.450 nonbonded pdb=" O HIS A 108 " pdb="HD21 ASN A 112 " model vdw 1.522 2.450 nonbonded pdb=" O HIS H 108 " pdb="HD21 ASN H 112 " model vdw 1.522 2.450 nonbonded pdb=" O HIS D 108 " pdb="HD21 ASN D 112 " model vdw 1.522 2.450 nonbonded pdb=" O ILE A 101 " pdb=" H VAL A 137 " model vdw 1.526 2.450 ... (remaining 527611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'B' and resid 104 through 555) selection = (chain 'C' and resid 104 through 555) selection = (chain 'E' and resid 104 through 555) selection = (chain 'G' and resid 104 through 555) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.860 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: 0.120 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.870 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:5.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 : 0.026 0.202 14596 Z= 1.029 Angle : 1.220 15.849 19848 Z= 0.630 Chirality : 0.089 0.367 2268 Planarity : 0.006 0.069 2464 Dihedral : 13.007 170.912 4888 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.16), residues: 1864 helix: -2.90 (0.11), residues: 1372 sheet: None (None), residues: 0 loop : -2.63 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 237 TYR 0.047 0.006 TYR B 299 PHE 0.034 0.005 PHE C 351 TRP 0.026 0.003 TRP E 323 HIS 0.009 0.003 HIS G 363 Details of bonding type rmsd/Z covalent geometry : bond 0.02601 / 1.03 (14596) covalent geometry : angle 1.21978 / 0.63 (19848) hydrogen bonds : bond 0.15879 / 11.27 ( 952) hydrogen bonds : angle 7.19609 / 5.17 ( 2772) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 347 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 158 TRP cc_start: 0.5801 (m100) cc_final: 0.5537 (m-10) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 1.0834 time to fit residues: 415.7787 Evaluate side-chains 237 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.196624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.117735 restraints weight = 59891.771| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.44 r_work: 0.3293 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14596 Z= 0.182 Angle : 0.612 7.002 19848 Z= 0.333 Chirality : 0.039 0.144 2268 Planarity : 0.005 0.042 2464 Dihedral : 11.726 176.230 2232 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.21 % Allowed : 10.24 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.19), residues: 1864 helix: -0.79 (0.13), residues: 1356 sheet: None (None), residues: 0 loop : -1.34 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 237 TYR 0.016 0.002 TYR B 545 PHE 0.011 0.002 PHE A 66 TRP 0.012 0.001 TRP C 305 HIS 0.003 0.001 HIS H 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (14596) covalent geometry : angle 0.61184 / 0.33 (19848) hydrogen bonds : bond 0.05367 / 3.81 ( 952) hydrogen bonds : angle 5.13627 / 3.69 ( 2772) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 310 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 295 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 228 ARG cc_start: 0.7129 (mtt180) cc_final: 0.6759 (tpt-90) REVERT: B 235 ILE cc_start: 0.8206 (mt) cc_final: 0.7962 (mp) REVERT: B 236 LEU cc_start: 0.8278 (tp) cc_final: 0.7978 (tp) REVERT: B 361 GLN cc_start: 0.8194 (tt0) cc_final: 0.7628 (tp-100) REVERT: C 235 ILE cc_start: 0.8192 (mt) cc_final: 0.7958 (mp) REVERT: C 236 LEU cc_start: 0.8266 (tp) cc_final: 0.7950 (tp) REVERT: C 361 GLN cc_start: 0.8309 (tt0) cc_final: 0.7619 (tp-100) REVERT: E 235 ILE cc_start: 0.8191 (mt) cc_final: 0.7960 (mp) REVERT: E 236 LEU cc_start: 0.8260 (tp) cc_final: 0.7942 (tp) REVERT: E 361 GLN cc_start: 0.8328 (tt0) cc_final: 0.7644 (tp-100) REVERT: G 235 ILE cc_start: 0.8255 (mt) cc_final: 0.8005 (mp) REVERT: G 236 LEU cc_start: 0.8272 (tp) cc_final: 0.7972 (tp) REVERT: G 361 GLN cc_start: 0.8156 (tt0) cc_final: 0.7570 (tp-100) outliers start: 15 outliers final: 5 residues processed: 300 average time/residue: 0.9049 time to fit residues: 306.1123 Evaluate side-chains 255 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 250 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain G residue 180 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 181 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 176 optimal weight: 40.0000 chunk 52 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 359 GLN C 359 GLN E 359 GLN G 359 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.194224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.114771 restraints weight = 60028.625| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.43 r_work: 0.3202 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14596 Z= 0.214 Angle : 0.589 7.392 19848 Z= 0.321 Chirality : 0.039 0.159 2268 Planarity : 0.004 0.037 2464 Dihedral : 11.331 174.515 2232 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.50 % Allowed : 13.31 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.19), residues: 1864 helix: 0.21 (0.13), residues: 1396 sheet: None (None), residues: 0 loop : -1.17 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 237 TYR 0.021 0.002 TYR C 545 PHE 0.020 0.002 PHE C 166 TRP 0.009 0.001 TRP B 304 HIS 0.003 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (14596) covalent geometry : angle 0.58936 / 0.32 (19848) hydrogen bonds : bond 0.05213 / 3.68 ( 952) hydrogen bonds : angle 4.58851 / 3.29 ( 2772) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 244 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8146 (p) REVERT: B 202 ASP cc_start: 0.8234 (t70) cc_final: 0.7727 (t0) REVERT: B 228 ARG cc_start: 0.7163 (mtt180) cc_final: 0.6840 (tpt-90) REVERT: B 361 GLN cc_start: 0.8229 (tt0) cc_final: 0.7772 (tp-100) REVERT: C 143 SER cc_start: 0.8377 (OUTLIER) cc_final: 0.8117 (p) REVERT: C 202 ASP cc_start: 0.8300 (t0) cc_final: 0.7837 (t0) REVERT: C 361 GLN cc_start: 0.8370 (tt0) cc_final: 0.7825 (tp-100) REVERT: E 143 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.8095 (p) REVERT: E 202 ASP cc_start: 0.8335 (t70) cc_final: 0.7899 (t0) REVERT: E 228 ARG cc_start: 0.7161 (mtt180) cc_final: 0.6791 (tpt-90) REVERT: E 361 GLN cc_start: 0.8363 (tt0) cc_final: 0.7833 (tp-100) REVERT: F 102 SER cc_start: 0.8051 (p) cc_final: 0.7771 (m) REVERT: G 143 SER cc_start: 0.8402 (OUTLIER) cc_final: 0.8127 (p) REVERT: G 202 ASP cc_start: 0.8318 (t70) cc_final: 0.7867 (t0) REVERT: G 228 ARG cc_start: 0.7147 (mtt180) cc_final: 0.6782 (tpt-90) REVERT: G 361 GLN cc_start: 0.8201 (tt0) cc_final: 0.7741 (tp-100) outliers start: 31 outliers final: 14 residues processed: 255 average time/residue: 0.9602 time to fit residues: 275.2662 Evaluate side-chains 231 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 40.0000 chunk 112 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 187 optimal weight: 20.0000 chunk 162 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 359 GLN E 359 GLN G 359 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.195622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.117653 restraints weight = 59527.742| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.40 r_work: 0.3241 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14596 Z= 0.123 Angle : 0.518 7.207 19848 Z= 0.281 Chirality : 0.037 0.163 2268 Planarity : 0.003 0.040 2464 Dihedral : 10.920 178.291 2232 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.69 % Allowed : 15.65 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.20), residues: 1864 helix: 0.97 (0.14), residues: 1388 sheet: None (None), residues: 0 loop : -0.88 (0.32), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 237 TYR 0.018 0.001 TYR E 545 PHE 0.014 0.001 PHE G 166 TRP 0.007 0.001 TRP B 305 HIS 0.002 0.000 HIS C 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (14596) covalent geometry : angle 0.51804 / 0.28 (19848) hydrogen bonds : bond 0.04456 / 3.16 ( 952) hydrogen bonds : angle 4.23047 / 3.03 ( 2772) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 268 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 247 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8170 (p) REVERT: B 228 ARG cc_start: 0.7141 (mtt180) cc_final: 0.6817 (tpt-90) REVERT: B 361 GLN cc_start: 0.8229 (tt0) cc_final: 0.7876 (tp-100) REVERT: C 143 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.8180 (p) REVERT: C 202 ASP cc_start: 0.8354 (t0) cc_final: 0.7956 (t0) REVERT: C 228 ARG cc_start: 0.7147 (mtt180) cc_final: 0.6765 (tpt-90) REVERT: C 361 GLN cc_start: 0.8325 (tt0) cc_final: 0.7791 (tp-100) REVERT: C 543 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8306 (mt-10) REVERT: D 102 SER cc_start: 0.7794 (p) cc_final: 0.7466 (m) REVERT: E 143 SER cc_start: 0.8400 (OUTLIER) cc_final: 0.8153 (p) REVERT: E 202 ASP cc_start: 0.8214 (t70) cc_final: 0.7867 (t0) REVERT: E 228 ARG cc_start: 0.7152 (mtt180) cc_final: 0.6764 (tpt-90) REVERT: E 361 GLN cc_start: 0.8323 (tt0) cc_final: 0.7786 (tp-100) REVERT: F 102 SER cc_start: 0.8026 (p) cc_final: 0.7731 (m) REVERT: G 202 ASP cc_start: 0.8139 (t70) cc_final: 0.7704 (t0) REVERT: G 228 ARG cc_start: 0.7144 (mtt180) cc_final: 0.6761 (tpt-90) REVERT: G 361 GLN cc_start: 0.8189 (tt0) cc_final: 0.7849 (tp-100) outliers start: 21 outliers final: 12 residues processed: 256 average time/residue: 0.9029 time to fit residues: 261.1799 Evaluate side-chains 231 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 216 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 54 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 359 GLN G 359 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.195026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.116591 restraints weight = 59900.839| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.40 r_work: 0.3225 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14596 Z= 0.132 Angle : 0.509 7.031 19848 Z= 0.276 Chirality : 0.037 0.153 2268 Planarity : 0.003 0.039 2464 Dihedral : 10.751 176.789 2232 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.42 % Allowed : 17.90 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.20), residues: 1864 helix: 1.33 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.80 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 237 TYR 0.016 0.001 TYR G 545 PHE 0.019 0.001 PHE E 166 TRP 0.006 0.001 TRP B 304 HIS 0.002 0.000 HIS E 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (14596) covalent geometry : angle 0.50925 / 0.28 (19848) hydrogen bonds : bond 0.04364 / 3.09 ( 952) hydrogen bonds : angle 4.11890 / 2.95 ( 2772) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 ASP cc_start: 0.8041 (t70) cc_final: 0.7478 (t0) REVERT: B 228 ARG cc_start: 0.7131 (mtt180) cc_final: 0.6826 (tpt-90) REVERT: B 238 MET cc_start: 0.9038 (mmp) cc_final: 0.8769 (mmp) REVERT: B 361 GLN cc_start: 0.8211 (tt0) cc_final: 0.7862 (tp-100) REVERT: C 202 ASP cc_start: 0.8114 (t0) cc_final: 0.7676 (t0) REVERT: C 228 ARG cc_start: 0.7160 (mtt180) cc_final: 0.6784 (tpt-90) REVERT: C 238 MET cc_start: 0.9067 (mmp) cc_final: 0.8602 (mmp) REVERT: C 361 GLN cc_start: 0.8341 (tt0) cc_final: 0.7817 (tp-100) REVERT: D 69 PHE cc_start: 0.6892 (t80) cc_final: 0.5922 (t80) REVERT: D 102 SER cc_start: 0.7989 (p) cc_final: 0.7678 (m) REVERT: E 202 ASP cc_start: 0.8110 (t70) cc_final: 0.7637 (t0) REVERT: E 228 ARG cc_start: 0.7160 (mtt180) cc_final: 0.6782 (tpt-90) REVERT: E 238 MET cc_start: 0.9022 (mmt) cc_final: 0.8762 (mmp) REVERT: E 361 GLN cc_start: 0.8314 (tt0) cc_final: 0.7801 (tp-100) REVERT: F 102 SER cc_start: 0.8020 (p) cc_final: 0.7724 (m) REVERT: G 143 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8161 (p) REVERT: G 202 ASP cc_start: 0.8115 (t70) cc_final: 0.7714 (t0) REVERT: G 228 ARG cc_start: 0.7154 (mtt180) cc_final: 0.6772 (tpt-90) REVERT: G 361 GLN cc_start: 0.8189 (tt0) cc_final: 0.7839 (tp-100) outliers start: 30 outliers final: 17 residues processed: 232 average time/residue: 0.9054 time to fit residues: 236.2211 Evaluate side-chains 227 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 90 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 50.0000 chunk 70 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.194793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.116739 restraints weight = 60214.177| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.41 r_work: 0.3239 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14596 Z= 0.132 Angle : 0.512 6.910 19848 Z= 0.276 Chirality : 0.037 0.187 2268 Planarity : 0.003 0.039 2464 Dihedral : 10.633 176.810 2232 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.29 % Allowed : 20.08 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.21), residues: 1864 helix: 1.44 (0.14), residues: 1408 sheet: None (None), residues: 0 loop : -0.43 (0.34), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 237 TYR 0.015 0.001 TYR E 545 PHE 0.019 0.001 PHE B 166 TRP 0.006 0.001 TRP E 304 HIS 0.002 0.000 HIS E 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (14596) covalent geometry : angle 0.51173 / 0.28 (19848) hydrogen bonds : bond 0.04253 / 3.01 ( 952) hydrogen bonds : angle 4.02505 / 2.88 ( 2772) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 236 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 ASP cc_start: 0.8038 (t70) cc_final: 0.7477 (t0) REVERT: B 228 ARG cc_start: 0.7221 (mtt180) cc_final: 0.6925 (tpt-90) REVERT: C 202 ASP cc_start: 0.8129 (t0) cc_final: 0.7672 (t0) REVERT: C 228 ARG cc_start: 0.7145 (mtt180) cc_final: 0.6789 (tpt-90) REVERT: C 358 LYS cc_start: 0.8516 (tmmt) cc_final: 0.8231 (ttmm) REVERT: C 361 GLN cc_start: 0.8343 (tt0) cc_final: 0.7817 (tp-100) REVERT: D 102 SER cc_start: 0.8078 (p) cc_final: 0.7736 (m) REVERT: E 202 ASP cc_start: 0.8143 (t70) cc_final: 0.7662 (t0) REVERT: E 228 ARG cc_start: 0.7138 (mtt180) cc_final: 0.6789 (tpt-90) REVERT: E 361 GLN cc_start: 0.8324 (tt0) cc_final: 0.7830 (tp-100) REVERT: F 102 SER cc_start: 0.8008 (p) cc_final: 0.7704 (m) REVERT: G 143 SER cc_start: 0.8399 (OUTLIER) cc_final: 0.8130 (p) REVERT: G 202 ASP cc_start: 0.8172 (t70) cc_final: 0.7718 (t0) REVERT: G 228 ARG cc_start: 0.7121 (mtt180) cc_final: 0.6782 (tpt-90) REVERT: G 361 GLN cc_start: 0.8164 (tt0) cc_final: 0.7764 (tp-100) REVERT: G 543 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8333 (mt-10) outliers start: 16 outliers final: 13 residues processed: 226 average time/residue: 0.9307 time to fit residues: 238.0906 Evaluate side-chains 219 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 506 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 72 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 chunk 177 optimal weight: 0.1980 chunk 159 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 51 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.195394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.117747 restraints weight = 60187.106| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.38 r_work: 0.3259 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14596 Z= 0.122 Angle : 0.502 6.932 19848 Z= 0.271 Chirality : 0.036 0.191 2268 Planarity : 0.003 0.039 2464 Dihedral : 10.504 177.635 2232 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.61 % Allowed : 20.56 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.21), residues: 1864 helix: 1.62 (0.14), residues: 1408 sheet: None (None), residues: 0 loop : -0.33 (0.34), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 237 TYR 0.014 0.001 TYR E 545 PHE 0.020 0.001 PHE C 166 TRP 0.006 0.001 TRP E 304 HIS 0.002 0.000 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (14596) covalent geometry : angle 0.50155 / 0.27 (19848) hydrogen bonds : bond 0.04081 / 2.89 ( 952) hydrogen bonds : angle 3.94504 / 2.82 ( 2772) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 ASP cc_start: 0.8072 (t70) cc_final: 0.7498 (t0) REVERT: B 228 ARG cc_start: 0.7220 (mtt180) cc_final: 0.6940 (tpt-90) REVERT: B 543 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7997 (mt-10) REVERT: C 202 ASP cc_start: 0.8141 (t0) cc_final: 0.7671 (t0) REVERT: C 228 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6830 (tpt-90) REVERT: C 358 LYS cc_start: 0.8544 (tmmt) cc_final: 0.8336 (ttpp) REVERT: C 359 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8473 (tt0) REVERT: C 361 GLN cc_start: 0.8333 (tt0) cc_final: 0.7830 (tp-100) REVERT: C 543 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8350 (mt-10) REVERT: D 66 PHE cc_start: 0.6015 (OUTLIER) cc_final: 0.5059 (p90) REVERT: D 102 SER cc_start: 0.8067 (p) cc_final: 0.7716 (m) REVERT: E 202 ASP cc_start: 0.8142 (t70) cc_final: 0.7695 (t0) REVERT: E 228 ARG cc_start: 0.7105 (mtt180) cc_final: 0.6829 (tpt-90) REVERT: E 358 LYS cc_start: 0.8502 (tmmt) cc_final: 0.8258 (ttpp) REVERT: E 361 GLN cc_start: 0.8317 (tt0) cc_final: 0.7818 (tp-100) REVERT: F 102 SER cc_start: 0.8014 (p) cc_final: 0.7706 (m) REVERT: G 202 ASP cc_start: 0.8172 (t70) cc_final: 0.7746 (t0) REVERT: G 228 ARG cc_start: 0.7084 (mtt180) cc_final: 0.6834 (tpt-90) REVERT: G 361 GLN cc_start: 0.8185 (tt0) cc_final: 0.7782 (tp-100) outliers start: 20 outliers final: 14 residues processed: 222 average time/residue: 0.8825 time to fit residues: 221.7962 Evaluate side-chains 219 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 359 GLN Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 547 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 121 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 159 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 132 optimal weight: 0.0570 chunk 88 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.195855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.117915 restraints weight = 60403.923| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.41 r_work: 0.3262 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14596 Z= 0.114 Angle : 0.505 7.238 19848 Z= 0.270 Chirality : 0.036 0.179 2268 Planarity : 0.003 0.039 2464 Dihedral : 10.407 178.743 2232 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.29 % Allowed : 21.85 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.21), residues: 1864 helix: 1.73 (0.14), residues: 1408 sheet: None (None), residues: 0 loop : -0.18 (0.35), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 237 TYR 0.014 0.001 TYR B 545 PHE 0.019 0.001 PHE C 166 TRP 0.005 0.001 TRP E 379 HIS 0.003 0.000 HIS E 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (14596) covalent geometry : angle 0.50463 / 0.27 (19848) hydrogen bonds : bond 0.03916 / 2.77 ( 952) hydrogen bonds : angle 3.88399 / 2.78 ( 2772) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 ASP cc_start: 0.8031 (t70) cc_final: 0.7483 (t0) REVERT: B 228 ARG cc_start: 0.7202 (mtt180) cc_final: 0.6943 (tpt-90) REVERT: B 358 LYS cc_start: 0.8519 (tmmt) cc_final: 0.8232 (ttmm) REVERT: B 359 GLN cc_start: 0.8736 (pt0) cc_final: 0.8400 (tt0) REVERT: C 202 ASP cc_start: 0.8168 (t0) cc_final: 0.7755 (t0) REVERT: C 228 ARG cc_start: 0.7069 (mtt180) cc_final: 0.6814 (tpt-90) REVERT: C 359 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8489 (pt0) REVERT: C 361 GLN cc_start: 0.8319 (tt0) cc_final: 0.7821 (tp-100) REVERT: D 66 PHE cc_start: 0.5947 (OUTLIER) cc_final: 0.5101 (p90) REVERT: E 202 ASP cc_start: 0.8133 (t70) cc_final: 0.7659 (t0) REVERT: E 228 ARG cc_start: 0.7086 (mtt180) cc_final: 0.6825 (tpt-90) REVERT: E 359 GLN cc_start: 0.8716 (pt0) cc_final: 0.8445 (tt0) REVERT: E 361 GLN cc_start: 0.8310 (tt0) cc_final: 0.7825 (tp-100) REVERT: F 102 SER cc_start: 0.7996 (p) cc_final: 0.7693 (m) REVERT: G 143 SER cc_start: 0.8319 (OUTLIER) cc_final: 0.8057 (p) REVERT: G 202 ASP cc_start: 0.8143 (t70) cc_final: 0.7673 (t0) REVERT: G 228 ARG cc_start: 0.7072 (mtt180) cc_final: 0.6828 (tpt-90) REVERT: G 359 GLN cc_start: 0.8719 (pt0) cc_final: 0.8412 (tt0) REVERT: G 361 GLN cc_start: 0.8194 (tt0) cc_final: 0.7801 (tp-100) REVERT: G 543 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8284 (mt-10) outliers start: 16 outliers final: 15 residues processed: 221 average time/residue: 0.8809 time to fit residues: 220.3043 Evaluate side-chains 220 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 359 GLN Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 547 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 181 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 95 optimal weight: 0.0770 chunk 164 optimal weight: 1.9990 chunk 138 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.196945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.119191 restraints weight = 60553.604| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.41 r_work: 0.3288 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14596 Z= 0.101 Angle : 0.486 7.513 19848 Z= 0.261 Chirality : 0.035 0.164 2268 Planarity : 0.003 0.039 2464 Dihedral : 10.250 179.200 2232 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.29 % Allowed : 21.85 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.21), residues: 1864 helix: 2.09 (0.14), residues: 1356 sheet: None (None), residues: 0 loop : -0.08 (0.33), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 237 TYR 0.012 0.001 TYR B 545 PHE 0.018 0.001 PHE B 166 TRP 0.005 0.001 TRP E 379 HIS 0.004 0.000 HIS B 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (14596) covalent geometry : angle 0.48632 / 0.26 (19848) hydrogen bonds : bond 0.03697 / 2.62 ( 952) hydrogen bonds : angle 3.81659 / 2.73 ( 2772) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 ASP cc_start: 0.8054 (t70) cc_final: 0.7484 (t0) REVERT: B 228 ARG cc_start: 0.6996 (mtt180) cc_final: 0.6716 (tpt-90) REVERT: B 358 LYS cc_start: 0.8513 (tmmt) cc_final: 0.8233 (ttmm) REVERT: B 359 GLN cc_start: 0.8746 (pt0) cc_final: 0.8441 (tt0) REVERT: C 202 ASP cc_start: 0.8133 (t0) cc_final: 0.7691 (t0) REVERT: C 228 ARG cc_start: 0.7073 (mtt180) cc_final: 0.6845 (tpt-90) REVERT: C 531 GLN cc_start: 0.9116 (pt0) cc_final: 0.8907 (tm-30) REVERT: D 66 PHE cc_start: 0.6127 (OUTLIER) cc_final: 0.5325 (p90) REVERT: E 202 ASP cc_start: 0.8027 (t70) cc_final: 0.7585 (t0) REVERT: E 228 ARG cc_start: 0.7039 (mtt180) cc_final: 0.6779 (tpt-90) REVERT: E 358 LYS cc_start: 0.8680 (tppt) cc_final: 0.8384 (ttpp) REVERT: E 361 GLN cc_start: 0.8265 (tt0) cc_final: 0.7758 (tp-100) REVERT: E 531 GLN cc_start: 0.9176 (pt0) cc_final: 0.8939 (tm-30) REVERT: F 102 SER cc_start: 0.7995 (p) cc_final: 0.7685 (m) REVERT: G 143 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.8052 (p) REVERT: G 202 ASP cc_start: 0.8082 (t70) cc_final: 0.7662 (t0) REVERT: G 228 ARG cc_start: 0.6947 (mtt180) cc_final: 0.6694 (tpt-90) REVERT: G 543 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8293 (mt-10) outliers start: 16 outliers final: 15 residues processed: 218 average time/residue: 0.8924 time to fit residues: 219.8787 Evaluate side-chains 206 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 547 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 43 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 87 optimal weight: 40.0000 chunk 94 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 83 optimal weight: 0.4980 chunk 82 optimal weight: 20.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 359 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.194235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.114299 restraints weight = 60867.597| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.42 r_work: 0.3218 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14596 Z= 0.229 Angle : 0.592 7.887 19848 Z= 0.320 Chirality : 0.039 0.197 2268 Planarity : 0.003 0.038 2464 Dihedral : 10.580 172.756 2232 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.37 % Allowed : 22.42 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.20), residues: 1864 helix: 1.67 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -0.16 (0.33), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 237 TYR 0.011 0.002 TYR E 545 PHE 0.025 0.002 PHE B 296 TRP 0.007 0.001 TRP G 304 HIS 0.002 0.001 HIS G 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.23 (14596) covalent geometry : angle 0.59219 / 0.32 (19848) hydrogen bonds : bond 0.04613 / 3.25 ( 952) hydrogen bonds : angle 4.02007 / 2.88 ( 2772) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 ASP cc_start: 0.8281 (t70) cc_final: 0.7719 (t0) REVERT: B 228 ARG cc_start: 0.7226 (mtt180) cc_final: 0.6906 (tpt-90) REVERT: B 531 GLN cc_start: 0.9085 (pt0) cc_final: 0.8839 (tm-30) REVERT: C 202 ASP cc_start: 0.8278 (t0) cc_final: 0.7833 (t0) REVERT: C 228 ARG cc_start: 0.7145 (mtt180) cc_final: 0.6910 (tpt-90) REVERT: C 358 LYS cc_start: 0.8579 (tmmt) cc_final: 0.8373 (ttpp) REVERT: C 359 GLN cc_start: 0.8865 (pt0) cc_final: 0.8573 (tt0) REVERT: D 66 PHE cc_start: 0.6211 (OUTLIER) cc_final: 0.5395 (p90) REVERT: E 202 ASP cc_start: 0.8171 (t70) cc_final: 0.7676 (t0) REVERT: E 228 ARG cc_start: 0.7147 (mtt180) cc_final: 0.6919 (tpt-90) REVERT: E 358 LYS cc_start: 0.8752 (tppt) cc_final: 0.8454 (ttpp) REVERT: E 361 GLN cc_start: 0.8380 (tt0) cc_final: 0.7884 (tp-100) REVERT: E 531 GLN cc_start: 0.9104 (pt0) cc_final: 0.8844 (tm-30) REVERT: F 102 SER cc_start: 0.8007 (p) cc_final: 0.7691 (m) REVERT: G 202 ASP cc_start: 0.8194 (t70) cc_final: 0.7719 (t0) REVERT: G 228 ARG cc_start: 0.7131 (mtt180) cc_final: 0.6918 (tpt-90) REVERT: G 358 LYS cc_start: 0.8583 (tmmt) cc_final: 0.8371 (ttpp) REVERT: G 359 GLN cc_start: 0.8845 (pt0) cc_final: 0.8553 (tt0) outliers start: 17 outliers final: 13 residues processed: 202 average time/residue: 0.8554 time to fit residues: 196.6626 Evaluate side-chains 207 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 547 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 0 optimal weight: 40.0000 chunk 80 optimal weight: 40.0000 chunk 175 optimal weight: 50.0000 chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 531 GLN C 531 GLN E 359 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.194381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.114927 restraints weight = 60198.157| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.43 r_work: 0.3234 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14596 Z= 0.171 Angle : 0.540 7.682 19848 Z= 0.292 Chirality : 0.037 0.142 2268 Planarity : 0.003 0.038 2464 Dihedral : 10.469 173.880 2232 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.37 % Allowed : 22.34 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.21), residues: 1864 helix: 1.74 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -0.11 (0.34), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 237 TYR 0.012 0.001 TYR B 545 PHE 0.018 0.002 PHE E 166 TRP 0.007 0.001 TRP C 304 HIS 0.003 0.001 HIS G 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (14596) covalent geometry : angle 0.53974 / 0.29 (19848) hydrogen bonds : bond 0.04343 / 3.06 ( 952) hydrogen bonds : angle 3.97774 / 2.85 ( 2772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14560.01 seconds wall clock time: 245 minutes 40.68 seconds (14740.68 seconds total)