Starting phenix.real_space_refine on Thu Mar 5 20:11:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6shn_10201/03_2026/6shn_10201_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6shn_10201/03_2026/6shn_10201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6shn_10201/03_2026/6shn_10201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6shn_10201/03_2026/6shn_10201.map" model { file = "/net/cci-nas-00/data/ceres_data/6shn_10201/03_2026/6shn_10201_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6shn_10201/03_2026/6shn_10201_trim.cif" } resolution = 3.3 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= 0.001 sd= 0.114 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 80 5.16 5 C 8088 2.51 5 N 2251 2.21 5 O 2403 1.98 5 H 12513 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25339 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 6331 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 411, 6312 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 411, 6312 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 6357 Chain: "A" Number of atoms: 6327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6327 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 6341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6341 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6300 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 2, 'TYR:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FBP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FBP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.75, per 1000 atoms: 0.23 Number of scatterers: 25339 At special positions: 0 Unit cell: (106.794, 105.747, 102.606, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 4 15.00 O 2403 8.00 N 2251 7.00 C 8088 6.00 H 12513 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: 1.89 Conformation dependent library (CDL) restraints added in 792.2 milliseconds 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3082 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 24 sheets defined 31.5% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'D' and resid 11 through 19 removed outlier: 3.858A pdb=" N GLN D 15 " --> pdb=" O MET D 11 " (cutoff:3.500A) Proline residue: D 17 - end of helix Processing helix chain 'D' and resid 41 through 44 Processing helix chain 'D' and resid 54 through 64 Processing helix chain 'D' and resid 78 through 88 Processing helix chain 'D' and resid 117 through 124 removed outlier: 3.710A pdb=" N VAL D 121 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 130 removed outlier: 3.783A pdb=" N ARG D 130 " --> pdb=" O ASP D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 160 removed outlier: 3.724A pdb=" N MET D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 177 removed outlier: 5.644A pdb=" N SER D 176 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 232 removed outlier: 3.593A pdb=" N ARG D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 252 removed outlier: 4.671A pdb=" N ILE D 245 " --> pdb=" O GLY D 241 " (cutoff:3.500A) Proline residue: D 246 - end of helix Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.756A pdb=" N LEU D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA D 291 " --> pdb=" O ASN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 407 Processing helix chain 'D' and resid 418 through 425 Processing helix chain 'A' and resid 11 through 16 removed outlier: 3.714A pdb=" N GLN A 15 " --> pdb=" O MET A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 54 through 64 removed outlier: 3.528A pdb=" N ASN A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 88 Processing helix chain 'A' and resid 117 through 124 removed outlier: 4.320A pdb=" N ASN A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 130 removed outlier: 3.860A pdb=" N ARG A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.610A pdb=" N MET A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 removed outlier: 5.618A pdb=" N SER A 176 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 232 removed outlier: 3.661A pdb=" N GLU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 252 removed outlier: 4.770A pdb=" N ILE A 245 " --> pdb=" O GLY A 241 " (cutoff:3.500A) Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 279 through 292 removed outlier: 3.824A pdb=" N LEU A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 407 Processing helix chain 'A' and resid 418 through 426 Processing helix chain 'C' and resid 11 through 19 removed outlier: 4.076A pdb=" N GLN C 15 " --> pdb=" O MET C 11 " (cutoff:3.500A) Proline residue: C 17 - end of helix Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 53 through 65 removed outlier: 4.075A pdb=" N ALA C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 88 Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 117 through 124 removed outlier: 4.126A pdb=" N ASN C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 130 removed outlier: 3.612A pdb=" N ARG C 130 " --> pdb=" O ASP C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 159 removed outlier: 3.782A pdb=" N ASP C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 5.551A pdb=" N SER C 176 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 removed outlier: 3.525A pdb=" N GLU C 228 " --> pdb=" O TYR C 224 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 252 removed outlier: 3.629A pdb=" N LYS C 247 " --> pdb=" O ASP C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 279 through 292 removed outlier: 3.740A pdb=" N LEU C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA C 291 " --> pdb=" O ASN C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 407 Processing helix chain 'C' and resid 418 through 426 removed outlier: 3.622A pdb=" N LEU C 422 " --> pdb=" O THR C 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 19 removed outlier: 4.045A pdb=" N LEU B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 14 through 19' Processing helix chain 'B' and resid 41 through 44 Processing helix chain 'B' and resid 53 through 64 removed outlier: 4.075A pdb=" N ALA B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.910A pdb=" N VAL B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 117 through 124 removed outlier: 3.599A pdb=" N VAL B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 148 through 159 removed outlier: 3.506A pdb=" N ASP B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 removed outlier: 5.575A pdb=" N SER B 176 " --> pdb=" O GLU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 232 removed outlier: 3.639A pdb=" N GLU B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 252 removed outlier: 3.687A pdb=" N LYS B 247 " --> pdb=" O ASP B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 279 through 292 removed outlier: 3.866A pdb=" N LEU B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 418 through 426 Processing sheet with id=AA1, first strand: chain 'D' and resid 98 through 101 removed outlier: 7.421A pdb=" N SER D 20 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLY D 70 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA D 22 " --> pdb=" O GLY D 70 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ALA D 166 " --> pdb=" O MET D 213 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE D 215 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR D 164 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N CYS D 163 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N HIS D 257 " --> pdb=" O CYS D 163 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL D 165 " --> pdb=" O HIS D 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 47 Processing sheet with id=AA3, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AA4, first strand: chain 'D' and resid 179 through 183 removed outlier: 6.891A pdb=" N VAL D 180 " --> pdb=" O PHE D 192 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE D 192 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA D 182 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.352A pdb=" N MET C 328 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL C 344 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N SER C 364 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N VAL C 346 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL C 366 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 349 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU C 333 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS D 317 " --> pdb=" O ILE D 340 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL D 339 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG D 355 " --> pdb=" O VAL D 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.352A pdb=" N MET C 328 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL C 344 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N SER C 364 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N VAL C 346 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL C 366 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN C 361 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ARG C 381 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N ASP C 363 " --> pdb=" O ARG C 381 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N VAL C 383 " --> pdb=" O ASP C 363 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N ALA C 365 " --> pdb=" O VAL C 383 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N VAL C 415 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ARG C 381 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N VAL C 417 " --> pdb=" O ARG C 381 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C 383 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR C 408 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 344 through 346 removed outlier: 6.586A pdb=" N VAL D 344 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N SER D 364 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N VAL D 346 " --> pdb=" O SER D 364 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL D 366 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN D 361 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ARG D 381 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ASP D 363 " --> pdb=" O ARG D 381 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N VAL D 383 " --> pdb=" O ASP D 363 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N ALA D 365 " --> pdb=" O VAL D 383 " (cutoff:3.500A) removed outlier: 10.504A pdb=" N VAL D 415 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG D 381 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL D 417 " --> pdb=" O ARG D 381 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL D 383 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR D 408 " --> pdb=" O LEU D 416 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 395 through 396 removed outlier: 6.203A pdb=" N ARG D 378 " --> pdb=" O ILE D 396 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN D 361 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ARG D 381 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ASP D 363 " --> pdb=" O ARG D 381 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N VAL D 383 " --> pdb=" O ASP D 363 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N ALA D 365 " --> pdb=" O VAL D 383 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL D 349 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU D 333 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 339 " --> pdb=" O VAL C 356 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG C 355 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TRP C 372 " --> pdb=" O ILE C 390 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 98 through 101 removed outlier: 7.351A pdb=" N SER A 20 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLY A 70 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA A 22 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 21 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA A 166 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE A 215 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR A 164 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N CYS A 163 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N HIS A 257 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A 165 " --> pdb=" O HIS A 257 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 143 through 145 Processing sheet with id=AB2, first strand: chain 'A' and resid 179 through 183 removed outlier: 6.883A pdb=" N VAL A 180 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE A 192 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA A 182 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.306A pdb=" N MET B 328 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B 344 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N SER B 364 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VAL B 346 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL B 366 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN B 361 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ARG B 381 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ASP B 363 " --> pdb=" O ARG B 381 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL B 383 " --> pdb=" O ASP B 363 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N ALA B 365 " --> pdb=" O VAL B 383 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG B 378 " --> pdb=" O ILE B 396 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 372 through 373 removed outlier: 6.547A pdb=" N ARG A 355 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A 339 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS A 317 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 333 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 349 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN B 361 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ARG B 381 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ASP B 363 " --> pdb=" O ARG B 381 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL B 383 " --> pdb=" O ASP B 363 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N ALA B 365 " --> pdb=" O VAL B 383 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL B 415 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ARG B 381 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N VAL B 417 " --> pdb=" O ARG B 381 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 383 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 408 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 333 through 334 removed outlier: 6.507A pdb=" N LEU A 333 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A 349 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASN A 361 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ARG A 381 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N ASP A 363 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N VAL A 383 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N ALA A 365 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG A 378 " --> pdb=" O ILE A 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 344 through 346 removed outlier: 6.603A pdb=" N VAL A 344 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N SER A 364 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N VAL A 346 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL A 366 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASN A 361 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ARG A 381 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N ASP A 363 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N VAL A 383 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N ALA A 365 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 10.441A pdb=" N VAL A 415 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG A 381 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N VAL A 417 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 383 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR A 408 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 98 through 101 removed outlier: 6.500A pdb=" N MET C 69 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N SER C 20 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY C 70 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA C 22 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ALA C 166 " --> pdb=" O MET C 213 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE C 215 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR C 164 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N CYS C 163 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N HIS C 257 " --> pdb=" O CYS C 163 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL C 165 " --> pdb=" O HIS C 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB9, first strand: chain 'C' and resid 179 through 183 removed outlier: 6.945A pdb=" N VAL C 180 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE C 192 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA C 182 " --> pdb=" O ILE C 190 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 20 through 24 removed outlier: 3.572A pdb=" N VAL B 21 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ALA B 166 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 215 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR B 164 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N CYS B 163 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N HIS B 257 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL B 165 " --> pdb=" O HIS B 257 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.532A pdb=" N PHE B 51 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 68 through 71 removed outlier: 6.555A pdb=" N MET B 69 " --> pdb=" O ASP B 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 143 through 145 Processing sheet with id=AC5, first strand: chain 'B' and resid 179 through 183 removed outlier: 6.930A pdb=" N VAL B 180 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE B 192 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA B 182 " --> pdb=" O ILE B 190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 317 through 319 removed outlier: 6.434A pdb=" N LYS B 317 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B 339 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG B 355 " --> pdb=" O VAL B 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 335 hydrogen bonds defined for protein. 918 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: 5.91 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 12478 1.01 - 1.21: 37 1.21 - 1.41: 5506 1.41 - 1.62: 7461 1.62 - 1.82: 124 Bond restraints: 25606 Sorted by residual: bond pdb=" C5 FBP D 501 " pdb=" O5 FBP D 501 " ideal model delta sigma weight residual 1.608 1.405 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C5 FBP C 501 " pdb=" O5 FBP C 501 " ideal model delta sigma weight residual 1.608 1.426 0.182 2.00e-02 2.50e+03 8.30e+01 bond pdb=" C4 FBP D 501 " pdb=" C5 FBP D 501 " ideal model delta sigma weight residual 1.346 1.523 -0.177 2.00e-02 2.50e+03 7.83e+01 bond pdb=" C4 FBP C 501 " pdb=" C5 FBP C 501 " ideal model delta sigma weight residual 1.346 1.510 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" C2 FBP C 501 " pdb=" O5 FBP C 501 " ideal model delta sigma weight residual 1.294 1.422 -0.128 2.00e-02 2.50e+03 4.11e+01 ... (remaining 25601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.81: 46084 5.81 - 11.62: 128 11.62 - 17.44: 2 17.44 - 23.25: 4 23.25 - 29.06: 11 Bond angle restraints: 46229 Sorted by residual: angle pdb=" CG1 VAL B 217 " pdb=" CB VAL B 217 " pdb=" HB VAL B 217 " ideal model delta sigma weight residual 108.00 78.94 29.06 3.00e+00 1.11e-01 9.38e+01 angle pdb=" CG2 VAL B 217 " pdb=" CB VAL B 217 " pdb=" HB VAL B 217 " ideal model delta sigma weight residual 108.00 80.67 27.33 3.00e+00 1.11e-01 8.30e+01 angle pdb=" CA VAL B 217 " pdb=" CB VAL B 217 " pdb=" HB VAL B 217 " ideal model delta sigma weight residual 109.00 82.02 26.98 3.00e+00 1.11e-01 8.09e+01 angle pdb=" CD1 LEU D 18 " pdb=" CG LEU D 18 " pdb=" HG LEU D 18 " ideal model delta sigma weight residual 108.00 81.28 26.72 3.00e+00 1.11e-01 7.93e+01 angle pdb=" CD2 LEU D 18 " pdb=" CG LEU D 18 " pdb=" HG LEU D 18 " ideal model delta sigma weight residual 108.00 83.02 24.98 3.00e+00 1.11e-01 6.93e+01 ... (remaining 46224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 10782 17.81 - 35.63: 945 35.63 - 53.44: 309 53.44 - 71.26: 75 71.26 - 89.07: 19 Dihedral angle restraints: 12130 sinusoidal: 6621 harmonic: 5509 Sorted by residual: dihedral pdb=" CA GLY A 342 " pdb=" C GLY A 342 " pdb=" N SER A 343 " pdb=" CA SER A 343 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA GLY B 342 " pdb=" C GLY B 342 " pdb=" N SER B 343 " pdb=" CA SER B 343 " ideal model delta harmonic sigma weight residual 180.00 156.71 23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA GLY C 342 " pdb=" C GLY C 342 " pdb=" N SER C 343 " pdb=" CA SER C 343 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 12127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.385: 1976 0.385 - 0.770: 0 0.770 - 1.154: 0 1.154 - 1.539: 2 1.539 - 1.924: 3 Chirality restraints: 1981 Sorted by residual: chirality pdb=" CG LEU A 18 " pdb=" CB LEU A 18 " pdb=" CD1 LEU A 18 " pdb=" CD2 LEU A 18 " both_signs ideal model delta sigma weight residual False -2.59 -0.67 -1.92 2.00e-01 2.50e+01 9.26e+01 chirality pdb=" CG LEU C 18 " pdb=" CB LEU C 18 " pdb=" CD1 LEU C 18 " pdb=" CD2 LEU C 18 " both_signs ideal model delta sigma weight residual False -2.59 -0.75 -1.84 2.00e-01 2.50e+01 8.50e+01 chirality pdb=" CG LEU B 18 " pdb=" CB LEU B 18 " pdb=" CD1 LEU B 18 " pdb=" CD2 LEU B 18 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.23e+01 ... (remaining 1978 not shown) Planarity restraints: 3872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 178 " 0.042 2.00e-02 2.50e+03 7.35e-02 1.62e+02 pdb=" CG PHE C 178 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE C 178 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE C 178 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 PHE C 178 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 PHE C 178 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHE C 178 " 0.016 2.00e-02 2.50e+03 pdb=" HD1 PHE C 178 " -0.166 2.00e-02 2.50e+03 pdb=" HD2 PHE C 178 " -0.101 2.00e-02 2.50e+03 pdb=" HE1 PHE C 178 " 0.058 2.00e-02 2.50e+03 pdb=" HE2 PHE C 178 " 0.026 2.00e-02 2.50e+03 pdb=" HZ PHE C 178 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 56 " -0.038 2.00e-02 2.50e+03 7.30e-02 1.60e+02 pdb=" CG PHE C 56 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE C 56 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 56 " 0.088 2.00e-02 2.50e+03 pdb=" CE1 PHE C 56 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE C 56 " 0.067 2.00e-02 2.50e+03 pdb=" CZ PHE C 56 " 0.064 2.00e-02 2.50e+03 pdb=" HD1 PHE C 56 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 PHE C 56 " 0.051 2.00e-02 2.50e+03 pdb=" HE1 PHE C 56 " -0.034 2.00e-02 2.50e+03 pdb=" HE2 PHE C 56 " -0.198 2.00e-02 2.50e+03 pdb=" HZ PHE C 56 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 284 " 0.008 2.00e-02 2.50e+03 6.18e-02 1.53e+02 pdb=" CG TRP C 284 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 284 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP C 284 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP C 284 " 0.081 2.00e-02 2.50e+03 pdb=" CE2 TRP C 284 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP C 284 " -0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 284 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 284 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 284 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP C 284 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP C 284 " -0.102 2.00e-02 2.50e+03 pdb=" HE3 TRP C 284 " -0.069 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 284 " -0.101 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 284 " -0.034 2.00e-02 2.50e+03 pdb=" HH2 TRP C 284 " 0.154 2.00e-02 2.50e+03 ... (remaining 3869 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2340 2.20 - 2.80: 54225 2.80 - 3.40: 65578 3.40 - 4.00: 93263 4.00 - 4.60: 145866 Nonbonded interactions: 361272 Sorted by model distance: nonbonded pdb=" O ASN D 60 " pdb=" HG SER D 64 " model vdw 1.596 2.450 nonbonded pdb=" H ALA D 118 " pdb=" O HIS D 238 " model vdw 1.610 2.450 nonbonded pdb=" HE2 HIS D 156 " pdb=" OD1 ASP D 219 " model vdw 1.623 2.450 nonbonded pdb="HH21 ARG A 423 " pdb=" OE2 GLU A 430 " model vdw 1.624 2.450 nonbonded pdb=" HB VAL B 217 " pdb="HG22 VAL B 217 " model vdw 1.648 1.952 ... (remaining 361267 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' and (resid 10 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 30 through 73 or (resid \ 74 through 77 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 78 through 92 or (resid 93 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H or \ name HA )) or (resid 94 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 95 through 129 or resid 131 through 431)) selection = (chain 'B' and (resid 10 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 40 through 92 or (resid \ 93 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name OE1 or name OE2 or name H or name HA )) or (resid 94 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 95 through 12 \ 9 or resid 131 through 431)) selection = (chain 'C' and (resid 10 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 30 through 31 or (resid \ 32 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 33 through 38 or (resid 39 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 40 through 73 or (resid 74 through 7 \ 7 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 78 through 92 or (resid 93 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name OE1 or name OE2 or name H or name HA )) \ or (resid 94 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 95 through 129 or resid 131 through 431)) selection = (chain 'D' and (resid 10 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 33 through 38 or (resid \ 39 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 40 through 75 or (resid 76 through 77 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 78 through 129 or resid 1 \ 31 through 431)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.140 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.220 Find NCS groups from input model: 0.400 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: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 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 : 0.021 0.203 13092 Z= 0.802 Angle : 1.170 12.163 17767 Z= 0.626 Chirality : 0.124 1.924 1981 Planarity : 0.009 0.060 2319 Dihedral : 13.950 87.436 4893 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.41 % Favored : 94.47 % Rotamer: Outliers : 4.81 % Allowed : 7.00 % Favored : 88.19 % 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: -3.18 (0.17), residues: 1629 helix: -2.13 (0.19), residues: 400 sheet: -3.00 (0.29), residues: 208 loop : -1.95 (0.17), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.005 ARG C 162 TYR 0.036 0.008 TYR B 145 PHE 0.046 0.009 PHE B 178 TRP 0.073 0.013 TRP B 304 HIS 0.030 0.009 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.02091 (13092) covalent geometry : angle 1.16970 (17767) hydrogen bonds : bond 0.22549 ( 331) hydrogen bonds : angle 9.31507 ( 918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 370 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 305 time to evaluate : 0.628 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: D 85 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: D 126 ASP cc_start: 0.7537 (t0) cc_final: 0.7328 (t0) REVERT: D 222 TYR cc_start: 0.8290 (t80) cc_final: 0.7689 (t80) REVERT: D 289 ASP cc_start: 0.7333 (t70) cc_final: 0.7110 (t0) REVERT: D 302 ARG cc_start: 0.8357 (mmt90) cc_final: 0.8111 (mmt-90) REVERT: D 375 ARG cc_start: 0.7170 (mtt180) cc_final: 0.6968 (mtm-85) REVERT: D 424 LYS cc_start: 0.8663 (mtmt) cc_final: 0.8387 (mtpt) REVERT: A 93 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7245 (mm-30) REVERT: A 285 LYS cc_start: 0.8490 (tttt) cc_final: 0.8259 (ttpp) REVERT: A 353 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8301 (mtp-110) REVERT: A 424 LYS cc_start: 0.8602 (mtmt) cc_final: 0.8402 (mtpt) REVERT: C 50 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7797 (ptmt) REVERT: C 74 GLN cc_start: 0.8502 (tt0) cc_final: 0.8098 (tm-30) REVERT: C 76 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7302 (mp10) REVERT: C 95 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.5669 (mmt) REVERT: C 162 ARG cc_start: 0.7885 (mmm160) cc_final: 0.7405 (mmm160) REVERT: C 219 ASP cc_start: 0.5726 (p0) cc_final: 0.5303 (p0) REVERT: C 285 LYS cc_start: 0.8280 (tttt) cc_final: 0.7856 (ttpp) REVERT: C 301 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8133 (t0) REVERT: C 319 VAL cc_start: 0.8842 (m) cc_final: 0.8562 (m) REVERT: C 408 TYR cc_start: 0.8137 (t80) cc_final: 0.6811 (t80) REVERT: C 418 THR cc_start: 0.8829 (m) cc_final: 0.8532 (p) REVERT: B 154 ILE cc_start: 0.8401 (mm) cc_final: 0.8152 (mt) REVERT: B 164 THR cc_start: 0.9110 (t) cc_final: 0.8861 (m) REVERT: B 188 LYS cc_start: 0.7667 (tttt) cc_final: 0.7214 (tttm) REVERT: B 213 MET cc_start: 0.8067 (mtp) cc_final: 0.7744 (mtp) REVERT: B 328 MET cc_start: 0.6610 (mtt) cc_final: 0.5880 (ttt) REVERT: B 399 ASN cc_start: 0.6225 (t0) cc_final: 0.5563 (m-40) outliers start: 65 outliers final: 35 residues processed: 359 average time/residue: 0.2940 time to fit residues: 145.5931 Evaluate side-chains 237 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 423 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN A 310 ASN C 46 HIS C 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.161586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.127089 restraints weight = 42117.419| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.94 r_work: 0.3535 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13092 Z= 0.132 Angle : 0.613 10.800 17767 Z= 0.313 Chirality : 0.094 1.701 1981 Planarity : 0.005 0.046 2319 Dihedral : 9.047 72.863 1969 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.84 % Allowed : 12.10 % Favored : 85.06 % 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: -2.09 (0.19), residues: 1629 helix: -0.40 (0.23), residues: 416 sheet: -2.68 (0.29), residues: 208 loop : -1.56 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 380 TYR 0.021 0.001 TYR D 224 PHE 0.010 0.001 PHE A 51 TRP 0.012 0.001 TRP D 284 HIS 0.007 0.001 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00303 (13092) covalent geometry : angle 0.61301 (17767) hydrogen bonds : bond 0.04927 ( 331) hydrogen bonds : angle 6.14603 ( 918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 0.620 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: D 122 THR cc_start: 0.8136 (m) cc_final: 0.7859 (p) REVERT: D 126 ASP cc_start: 0.7725 (t0) cc_final: 0.7488 (t0) REVERT: D 134 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8025 (mt-10) REVERT: D 213 MET cc_start: 0.8360 (mtp) cc_final: 0.7838 (mtp) REVERT: D 289 ASP cc_start: 0.7805 (t70) cc_final: 0.7437 (t0) REVERT: D 375 ARG cc_start: 0.7307 (mtt180) cc_final: 0.6921 (mtm-85) REVERT: D 403 ASP cc_start: 0.6539 (m-30) cc_final: 0.6333 (m-30) REVERT: A 82 GLN cc_start: 0.8665 (tt0) cc_final: 0.8458 (tt0) REVERT: A 191 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6835 (pt0) REVERT: A 213 MET cc_start: 0.8772 (mtm) cc_final: 0.8311 (mtp) REVERT: A 285 LYS cc_start: 0.8466 (tttt) cc_final: 0.8224 (ttpp) REVERT: A 310 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.7482 (p0) REVERT: A 353 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8417 (mtp-110) REVERT: C 74 GLN cc_start: 0.8879 (tt0) cc_final: 0.8674 (tm-30) REVERT: C 162 ARG cc_start: 0.7843 (mmm160) cc_final: 0.7529 (mmm160) REVERT: C 163 CYS cc_start: 0.8396 (t) cc_final: 0.8143 (t) REVERT: C 232 ARG cc_start: 0.8614 (mtt90) cc_final: 0.8188 (mtt90) REVERT: C 285 LYS cc_start: 0.8128 (tttt) cc_final: 0.7906 (ttmm) REVERT: C 301 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8154 (t0) REVERT: C 418 THR cc_start: 0.8873 (m) cc_final: 0.8212 (m) REVERT: C 421 MET cc_start: 0.8472 (mpt) cc_final: 0.7639 (mpt) REVERT: B 154 ILE cc_start: 0.8301 (mm) cc_final: 0.8094 (mt) REVERT: B 209 SER cc_start: 0.8462 (t) cc_final: 0.7967 (p) REVERT: B 213 MET cc_start: 0.8141 (mtp) cc_final: 0.7809 (mtp) REVERT: B 399 ASN cc_start: 0.6130 (t0) cc_final: 0.5691 (t0) outliers start: 39 outliers final: 27 residues processed: 253 average time/residue: 0.2831 time to fit residues: 100.1230 Evaluate side-chains 219 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 423 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 100 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.160279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.125635 restraints weight = 42319.999| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.98 r_work: 0.3516 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13092 Z= 0.120 Angle : 0.567 10.446 17767 Z= 0.286 Chirality : 0.093 1.711 1981 Planarity : 0.004 0.042 2319 Dihedral : 7.786 75.137 1931 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.55 % Allowed : 13.41 % Favored : 84.04 % 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: -1.42 (0.20), residues: 1629 helix: 0.41 (0.25), residues: 416 sheet: -2.27 (0.29), residues: 208 loop : -1.25 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 162 TYR 0.015 0.001 TYR D 224 PHE 0.008 0.001 PHE A 359 TRP 0.008 0.001 TRP C 284 HIS 0.005 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00283 (13092) covalent geometry : angle 0.56665 (17767) hydrogen bonds : bond 0.03895 ( 331) hydrogen bonds : angle 5.48058 ( 918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.475 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: D 122 THR cc_start: 0.7839 (m) cc_final: 0.7546 (p) REVERT: D 126 ASP cc_start: 0.7709 (t0) cc_final: 0.7429 (t0) REVERT: D 134 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7967 (mt-10) REVERT: D 213 MET cc_start: 0.8533 (mtp) cc_final: 0.8135 (mtp) REVERT: D 222 TYR cc_start: 0.8334 (t80) cc_final: 0.7678 (t80) REVERT: D 363 ASP cc_start: 0.8350 (t0) cc_final: 0.8084 (t0) REVERT: D 375 ARG cc_start: 0.7454 (mtt180) cc_final: 0.7073 (mtm-85) REVERT: D 403 ASP cc_start: 0.6713 (m-30) cc_final: 0.6468 (m-30) REVERT: D 424 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8482 (mtpt) REVERT: D 425 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8887 (mp) REVERT: A 123 GLN cc_start: 0.7967 (mm110) cc_final: 0.7715 (mm-40) REVERT: A 191 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7041 (pt0) REVERT: A 213 MET cc_start: 0.8768 (mtm) cc_final: 0.8426 (mtp) REVERT: A 285 LYS cc_start: 0.8465 (tttt) cc_final: 0.8264 (ttpp) REVERT: A 353 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8479 (mtp-110) REVERT: A 363 ASP cc_start: 0.8832 (t0) cc_final: 0.8541 (t0) REVERT: A 423 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8156 (mtp180) REVERT: C 29 ARG cc_start: 0.7140 (mtt-85) cc_final: 0.6222 (tpm170) REVERT: C 162 ARG cc_start: 0.7965 (mmm160) cc_final: 0.7468 (mmm160) REVERT: C 301 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8136 (t0) REVERT: C 363 ASP cc_start: 0.8338 (t0) cc_final: 0.8108 (t0) REVERT: C 408 TYR cc_start: 0.8171 (t80) cc_final: 0.6929 (t80) REVERT: C 418 THR cc_start: 0.8854 (m) cc_final: 0.8242 (m) REVERT: C 421 MET cc_start: 0.8553 (mpt) cc_final: 0.7909 (mpt) REVERT: B 154 ILE cc_start: 0.8264 (mm) cc_final: 0.8030 (mt) REVERT: B 213 MET cc_start: 0.8199 (mtp) cc_final: 0.7950 (mtp) outliers start: 35 outliers final: 26 residues processed: 224 average time/residue: 0.2857 time to fit residues: 88.7028 Evaluate side-chains 209 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 423 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 119 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN B 92 ASN B 310 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.153077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.118358 restraints weight = 43904.860| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.98 r_work: 0.3427 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13092 Z= 0.185 Angle : 0.576 10.405 17767 Z= 0.295 Chirality : 0.094 1.703 1981 Planarity : 0.004 0.042 2319 Dihedral : 7.378 73.072 1919 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.92 % Allowed : 13.27 % Favored : 83.82 % 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: -1.21 (0.20), residues: 1629 helix: 0.52 (0.26), residues: 412 sheet: -2.01 (0.32), residues: 208 loop : -1.11 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 406 TYR 0.011 0.001 TYR D 224 PHE 0.013 0.001 PHE B 56 TRP 0.009 0.001 TRP C 284 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00431 (13092) covalent geometry : angle 0.57599 (17767) hydrogen bonds : bond 0.03691 ( 331) hydrogen bonds : angle 5.33796 ( 918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.617 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: D 122 THR cc_start: 0.7761 (m) cc_final: 0.7461 (p) REVERT: D 126 ASP cc_start: 0.7777 (t0) cc_final: 0.7485 (t0) REVERT: D 134 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7951 (mt-10) REVERT: D 213 MET cc_start: 0.8733 (mtp) cc_final: 0.8376 (mtp) REVERT: D 222 TYR cc_start: 0.8439 (t80) cc_final: 0.7719 (t80) REVERT: D 363 ASP cc_start: 0.8443 (t0) cc_final: 0.8146 (t0) REVERT: D 425 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8838 (mp) REVERT: A 69 MET cc_start: 0.8469 (mtm) cc_final: 0.8024 (mtm) REVERT: A 191 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7163 (pt0) REVERT: A 213 MET cc_start: 0.8902 (mtm) cc_final: 0.8426 (mtp) REVERT: A 285 LYS cc_start: 0.8461 (tttt) cc_final: 0.8241 (ttpp) REVERT: A 296 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7118 (mt-10) REVERT: A 353 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8554 (mtp-110) REVERT: A 423 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8056 (mtp180) REVERT: A 429 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7509 (mm-40) REVERT: C 232 ARG cc_start: 0.8648 (mtt90) cc_final: 0.8401 (mtt90) REVERT: C 301 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8112 (t0) REVERT: C 408 TYR cc_start: 0.8141 (t80) cc_final: 0.6894 (t80) REVERT: B 92 ASN cc_start: 0.7764 (OUTLIER) cc_final: 0.7233 (p0) REVERT: B 126 ASP cc_start: 0.8380 (p0) cc_final: 0.8083 (m-30) REVERT: B 302 ARG cc_start: 0.8301 (mmm160) cc_final: 0.7751 (mmm160) REVERT: B 344 VAL cc_start: 0.8190 (t) cc_final: 0.7972 (p) outliers start: 40 outliers final: 27 residues processed: 225 average time/residue: 0.2636 time to fit residues: 84.4346 Evaluate side-chains 213 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 91 PHE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 407 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 18 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN B 310 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.157640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.122462 restraints weight = 48917.454| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.18 r_work: 0.3403 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13092 Z= 0.168 Angle : 0.559 10.578 17767 Z= 0.282 Chirality : 0.094 1.716 1981 Planarity : 0.004 0.041 2319 Dihedral : 6.888 72.641 1906 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.41 % Allowed : 14.29 % Favored : 83.31 % 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: -1.29 (0.21), residues: 1629 helix: 0.29 (0.25), residues: 436 sheet: -2.00 (0.33), residues: 212 loop : -1.11 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 14 TYR 0.010 0.001 TYR D 224 PHE 0.010 0.001 PHE D 218 TRP 0.008 0.001 TRP D 284 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00394 (13092) covalent geometry : angle 0.55871 (17767) hydrogen bonds : bond 0.03475 ( 331) hydrogen bonds : angle 5.30253 ( 918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.615 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: D 122 THR cc_start: 0.7780 (m) cc_final: 0.7478 (p) REVERT: D 126 ASP cc_start: 0.7782 (t0) cc_final: 0.7483 (t0) REVERT: D 134 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7941 (mt-10) REVERT: D 213 MET cc_start: 0.8793 (mtp) cc_final: 0.8488 (mtp) REVERT: D 222 TYR cc_start: 0.8463 (t80) cc_final: 0.7738 (t80) REVERT: D 363 ASP cc_start: 0.8531 (t0) cc_final: 0.8220 (t0) REVERT: D 425 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8865 (mp) REVERT: A 69 MET cc_start: 0.8505 (mtm) cc_final: 0.8082 (mtm) REVERT: A 191 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7268 (pt0) REVERT: A 213 MET cc_start: 0.8917 (mtm) cc_final: 0.8507 (mtp) REVERT: A 285 LYS cc_start: 0.8515 (tttt) cc_final: 0.8299 (ttpp) REVERT: A 296 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7206 (mt-10) REVERT: A 353 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8622 (mtp-110) REVERT: A 423 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8003 (mtp180) REVERT: A 429 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7528 (mm-40) REVERT: C 162 ARG cc_start: 0.8143 (mmm160) cc_final: 0.7906 (mmm-85) REVERT: C 232 ARG cc_start: 0.8645 (mtt90) cc_final: 0.8420 (mtt90) REVERT: C 301 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8178 (t0) REVERT: C 421 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8037 (mpt) REVERT: B 126 ASP cc_start: 0.8343 (p0) cc_final: 0.7997 (m-30) outliers start: 33 outliers final: 26 residues processed: 204 average time/residue: 0.2636 time to fit residues: 76.6968 Evaluate side-chains 206 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 407 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 2 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN C 303 ASN B 310 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.159145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.124991 restraints weight = 44268.771| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.00 r_work: 0.3443 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13092 Z= 0.116 Angle : 0.534 10.725 17767 Z= 0.266 Chirality : 0.094 1.718 1981 Planarity : 0.004 0.040 2319 Dihedral : 6.742 76.232 1906 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.26 % Allowed : 14.72 % Favored : 83.02 % 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: -1.14 (0.21), residues: 1629 helix: 0.42 (0.26), residues: 436 sheet: -1.91 (0.33), residues: 212 loop : -1.03 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 14 TYR 0.010 0.001 TYR D 224 PHE 0.012 0.001 PHE A 91 TRP 0.008 0.001 TRP D 284 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00271 (13092) covalent geometry : angle 0.53407 (17767) hydrogen bonds : bond 0.03166 ( 331) hydrogen bonds : angle 5.10377 ( 918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.587 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: D 122 THR cc_start: 0.7669 (m) cc_final: 0.7367 (p) REVERT: D 126 ASP cc_start: 0.7745 (t0) cc_final: 0.7434 (t0) REVERT: D 134 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7902 (mt-10) REVERT: D 222 TYR cc_start: 0.8408 (t80) cc_final: 0.7678 (t80) REVERT: D 363 ASP cc_start: 0.8481 (t0) cc_final: 0.8078 (t0) REVERT: D 425 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8804 (mp) REVERT: A 191 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7636 (pt0) REVERT: A 213 MET cc_start: 0.8938 (mtm) cc_final: 0.8541 (mtp) REVERT: A 285 LYS cc_start: 0.8454 (tttt) cc_final: 0.8229 (ttpp) REVERT: A 296 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7165 (mt-10) REVERT: A 423 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7984 (mtp180) REVERT: A 429 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7525 (mm-40) REVERT: C 29 ARG cc_start: 0.7183 (mtt-85) cc_final: 0.6203 (tpm170) REVERT: C 162 ARG cc_start: 0.8115 (mmm160) cc_final: 0.7877 (mmm-85) REVERT: C 301 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8114 (t0) REVERT: C 363 ASP cc_start: 0.8356 (t0) cc_final: 0.8045 (t0) REVERT: C 421 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8008 (mpt) REVERT: B 126 ASP cc_start: 0.8331 (p0) cc_final: 0.8077 (m-30) REVERT: B 302 ARG cc_start: 0.8347 (mmm160) cc_final: 0.7792 (mmm160) outliers start: 31 outliers final: 22 residues processed: 205 average time/residue: 0.2605 time to fit residues: 76.2630 Evaluate side-chains 201 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 407 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 105 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN B 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.154964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.120566 restraints weight = 42860.062| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.96 r_work: 0.3455 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13092 Z= 0.110 Angle : 0.527 10.790 17767 Z= 0.260 Chirality : 0.094 1.716 1981 Planarity : 0.004 0.040 2319 Dihedral : 6.235 70.955 1897 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.26 % Allowed : 14.80 % Favored : 82.94 % 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: -0.95 (0.21), residues: 1629 helix: 0.59 (0.26), residues: 436 sheet: -1.76 (0.34), residues: 212 loop : -0.91 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 232 TYR 0.010 0.001 TYR D 224 PHE 0.007 0.001 PHE D 218 TRP 0.008 0.001 TRP D 284 HIS 0.003 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00260 (13092) covalent geometry : angle 0.52694 (17767) hydrogen bonds : bond 0.03000 ( 331) hydrogen bonds : angle 4.92823 ( 918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 1.101 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: D 122 THR cc_start: 0.7631 (m) cc_final: 0.7326 (p) REVERT: D 126 ASP cc_start: 0.7716 (t0) cc_final: 0.7400 (t0) REVERT: D 134 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7858 (mt-10) REVERT: D 222 TYR cc_start: 0.8396 (t80) cc_final: 0.7672 (t80) REVERT: D 363 ASP cc_start: 0.8560 (t0) cc_final: 0.8137 (t0) REVERT: D 425 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8752 (mp) REVERT: A 191 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7656 (pt0) REVERT: A 213 MET cc_start: 0.8913 (mtm) cc_final: 0.8492 (mtp) REVERT: A 249 THR cc_start: 0.8785 (m) cc_final: 0.8535 (p) REVERT: A 285 LYS cc_start: 0.8446 (tttt) cc_final: 0.8221 (ttpp) REVERT: A 296 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7173 (mt-10) REVERT: A 302 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7790 (mtp-110) REVERT: A 423 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7976 (mtp180) REVERT: A 429 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7604 (mm-40) REVERT: C 29 ARG cc_start: 0.7183 (mtt-85) cc_final: 0.6207 (tpm170) REVERT: C 162 ARG cc_start: 0.8123 (mmm160) cc_final: 0.7914 (mmm-85) REVERT: C 301 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8162 (t0) REVERT: C 363 ASP cc_start: 0.8330 (t0) cc_final: 0.8009 (t0) REVERT: C 408 TYR cc_start: 0.8080 (t80) cc_final: 0.6901 (t80) REVERT: C 421 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8029 (mpt) REVERT: B 126 ASP cc_start: 0.8352 (p0) cc_final: 0.8123 (m-30) outliers start: 31 outliers final: 24 residues processed: 205 average time/residue: 0.2512 time to fit residues: 75.1409 Evaluate side-chains 204 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 407 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 58 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 120 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 96 ASN A 156 HIS C 303 ASN B 310 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.151887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.117596 restraints weight = 43264.359| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.94 r_work: 0.3419 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13092 Z= 0.157 Angle : 0.545 10.715 17767 Z= 0.273 Chirality : 0.094 1.698 1981 Planarity : 0.004 0.039 2319 Dihedral : 6.223 71.842 1895 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.62 % Allowed : 15.09 % Favored : 82.29 % 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: -0.96 (0.21), residues: 1629 helix: 0.57 (0.26), residues: 436 sheet: -1.74 (0.34), residues: 212 loop : -0.93 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 14 TYR 0.008 0.001 TYR B 273 PHE 0.010 0.001 PHE B 56 TRP 0.008 0.001 TRP D 284 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00373 (13092) covalent geometry : angle 0.54539 (17767) hydrogen bonds : bond 0.03159 ( 331) hydrogen bonds : angle 4.99695 ( 918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.669 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: D 122 THR cc_start: 0.7709 (m) cc_final: 0.7395 (p) REVERT: D 126 ASP cc_start: 0.7867 (t0) cc_final: 0.7545 (t0) REVERT: D 363 ASP cc_start: 0.8745 (t0) cc_final: 0.8311 (t0) REVERT: D 425 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8781 (mp) REVERT: A 69 MET cc_start: 0.8540 (mtm) cc_final: 0.8157 (mtm) REVERT: A 249 THR cc_start: 0.8824 (m) cc_final: 0.8560 (p) REVERT: A 265 GLN cc_start: 0.6512 (OUTLIER) cc_final: 0.6184 (pm20) REVERT: A 296 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7407 (mt-10) REVERT: A 302 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7875 (mtp-110) REVERT: A 353 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8420 (mtp180) REVERT: A 423 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7979 (mtp180) REVERT: A 429 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7769 (mm-40) REVERT: C 29 ARG cc_start: 0.7316 (mtt-85) cc_final: 0.6234 (tpm170) REVERT: C 162 ARG cc_start: 0.8250 (mmm160) cc_final: 0.8039 (mmm-85) REVERT: C 301 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8284 (t0) REVERT: C 408 TYR cc_start: 0.8227 (t80) cc_final: 0.7041 (t80) REVERT: C 421 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8154 (mpt) REVERT: B 126 ASP cc_start: 0.8458 (p0) cc_final: 0.8194 (m-30) REVERT: B 289 ASP cc_start: 0.8201 (t70) cc_final: 0.7971 (t0) REVERT: B 348 SER cc_start: 0.8382 (m) cc_final: 0.8130 (p) outliers start: 36 outliers final: 23 residues processed: 200 average time/residue: 0.2785 time to fit residues: 78.5868 Evaluate side-chains 200 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 407 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 58 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.162074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.121690 restraints weight = 46496.240| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.28 r_work: 0.3387 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13092 Z= 0.145 Angle : 0.541 10.731 17767 Z= 0.270 Chirality : 0.094 1.694 1981 Planarity : 0.004 0.041 2319 Dihedral : 6.153 70.653 1893 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.26 % Allowed : 15.31 % Favored : 82.43 % 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: -1.00 (0.21), residues: 1629 helix: 0.53 (0.26), residues: 440 sheet: -1.68 (0.35), residues: 212 loop : -0.97 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 14 TYR 0.008 0.001 TYR D 224 PHE 0.008 0.001 PHE B 56 TRP 0.008 0.001 TRP D 284 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00343 (13092) covalent geometry : angle 0.54142 (17767) hydrogen bonds : bond 0.03089 ( 331) hydrogen bonds : angle 4.94890 ( 918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.540 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: D 122 THR cc_start: 0.7577 (m) cc_final: 0.7267 (p) REVERT: D 126 ASP cc_start: 0.7706 (t0) cc_final: 0.7395 (t0) REVERT: D 134 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7836 (mt-10) REVERT: D 363 ASP cc_start: 0.8587 (t0) cc_final: 0.8153 (t0) REVERT: D 425 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8760 (mp) REVERT: A 69 MET cc_start: 0.8460 (mtm) cc_final: 0.8031 (mtm) REVERT: A 191 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7660 (pt0) REVERT: A 249 THR cc_start: 0.8834 (m) cc_final: 0.8558 (p) REVERT: A 265 GLN cc_start: 0.6349 (OUTLIER) cc_final: 0.6051 (pm20) REVERT: A 296 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7213 (mt-10) REVERT: A 302 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7684 (mtp-110) REVERT: A 353 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8279 (mtp180) REVERT: A 423 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7943 (mtp180) REVERT: A 429 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7686 (mm-40) REVERT: C 29 ARG cc_start: 0.7235 (mtt-85) cc_final: 0.6231 (tpm170) REVERT: C 162 ARG cc_start: 0.8179 (mmm160) cc_final: 0.7975 (mmm-85) REVERT: C 301 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8198 (t0) REVERT: C 302 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.7839 (mmt90) REVERT: C 408 TYR cc_start: 0.8104 (t80) cc_final: 0.6895 (t80) REVERT: C 421 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8084 (mpt) REVERT: B 100 ASP cc_start: 0.7648 (t0) cc_final: 0.7151 (t0) REVERT: B 126 ASP cc_start: 0.8398 (p0) cc_final: 0.8170 (m-30) REVERT: B 289 ASP cc_start: 0.8043 (t70) cc_final: 0.7840 (t0) REVERT: B 302 ARG cc_start: 0.8350 (mmm160) cc_final: 0.7754 (mmm160) REVERT: B 348 SER cc_start: 0.8409 (m) cc_final: 0.8134 (p) outliers start: 31 outliers final: 22 residues processed: 197 average time/residue: 0.2730 time to fit residues: 76.0330 Evaluate side-chains 201 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 407 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 112 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 303 ASN B 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.152261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.117251 restraints weight = 46288.817| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.06 r_work: 0.3411 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13092 Z= 0.138 Angle : 0.539 10.720 17767 Z= 0.268 Chirality : 0.093 1.694 1981 Planarity : 0.004 0.041 2319 Dihedral : 6.098 72.946 1893 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.33 % Allowed : 15.23 % Favored : 82.43 % 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: -0.95 (0.21), residues: 1629 helix: 0.57 (0.26), residues: 440 sheet: -1.64 (0.35), residues: 212 loop : -0.95 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 14 TYR 0.008 0.001 TYR D 224 PHE 0.008 0.001 PHE D 218 TRP 0.008 0.001 TRP D 284 HIS 0.003 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00328 (13092) covalent geometry : angle 0.53876 (17767) hydrogen bonds : bond 0.03013 ( 331) hydrogen bonds : angle 4.88484 ( 918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.676 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: D 126 ASP cc_start: 0.7713 (t0) cc_final: 0.7408 (t0) REVERT: D 134 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7740 (mt-10) REVERT: D 363 ASP cc_start: 0.8591 (t0) cc_final: 0.8147 (t0) REVERT: D 425 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8762 (mp) REVERT: A 69 MET cc_start: 0.8473 (mtm) cc_final: 0.8046 (mtm) REVERT: A 249 THR cc_start: 0.8848 (m) cc_final: 0.8570 (p) REVERT: A 296 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7195 (mt-10) REVERT: A 302 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7653 (mtp-110) REVERT: A 328 MET cc_start: 0.6634 (mtt) cc_final: 0.6369 (mtt) REVERT: A 353 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8264 (mtp180) REVERT: A 423 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7918 (mtp180) REVERT: A 429 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7717 (mm-40) REVERT: C 29 ARG cc_start: 0.7283 (mtt-85) cc_final: 0.6268 (tpm170) REVERT: C 162 ARG cc_start: 0.8168 (mmm160) cc_final: 0.7961 (mmm-85) REVERT: C 301 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8319 (t0) REVERT: C 408 TYR cc_start: 0.8081 (t80) cc_final: 0.6869 (t80) REVERT: C 421 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8072 (mpt) REVERT: B 100 ASP cc_start: 0.7662 (t0) cc_final: 0.7157 (t0) REVERT: B 302 ARG cc_start: 0.8369 (mmm160) cc_final: 0.7790 (mmm160) outliers start: 32 outliers final: 25 residues processed: 202 average time/residue: 0.2898 time to fit residues: 81.7542 Evaluate side-chains 202 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 407 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 62 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 303 ASN B 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.157017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.123115 restraints weight = 43460.047| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.94 r_work: 0.3419 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.322 13092 Z= 0.276 Angle : 0.911 59.181 17767 Z= 0.582 Chirality : 0.094 1.694 1981 Planarity : 0.005 0.126 2319 Dihedral : 6.116 72.970 1893 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.33 % Allowed : 15.31 % Favored : 82.36 % Cbeta Deviations : 0.06 % 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: -0.93 (0.21), residues: 1629 helix: 0.58 (0.26), residues: 440 sheet: -1.64 (0.35), residues: 212 loop : -0.92 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 14 TYR 0.009 0.001 TYR D 224 PHE 0.014 0.001 PHE B 91 TRP 0.008 0.001 TRP D 284 HIS 0.003 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00565 (13092) covalent geometry : angle 0.91128 (17767) hydrogen bonds : bond 0.03015 ( 331) hydrogen bonds : angle 4.88790 ( 918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5808.74 seconds wall clock time: 99 minutes 0.91 seconds (5940.91 seconds total)