Starting phenix.real_space_refine on Sun Oct 12 08:40:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8d_37342/10_2025/8w8d_37342.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8d_37342/10_2025/8w8d_37342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w8d_37342/10_2025/8w8d_37342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8d_37342/10_2025/8w8d_37342.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w8d_37342/10_2025/8w8d_37342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8d_37342/10_2025/8w8d_37342.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 14487 2.51 5 N 4047 2.21 5 O 4411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23063 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3261 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 Chain: "B" Number of atoms: 3245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3245 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 17, 'TRANS': 394} Chain breaks: 2 Chain: "C" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3261 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 Chain: "D" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3261 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 396} Chain breaks: 1 Chain: "E" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 398} Chain: "F" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3222 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 392} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 587 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain breaks: 1 Chain: "e" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "b" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 578 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain breaks: 1 Chain: "a" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 559 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "f" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 559 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "d" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 625 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.72, per 1000 atoms: 0.25 Number of scatterers: 23063 At special positions: 0 Unit cell: (165.41, 142.8, 145.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 118 16.00 O 4411 8.00 N 4047 7.00 C 14487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5476 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 28 sheets defined 41.9% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 10 through 21 removed outlier: 4.058A pdb=" N ILE A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 42 removed outlier: 3.647A pdb=" N ILE A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.556A pdb=" N SER A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 removed outlier: 3.706A pdb=" N ILE A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.627A pdb=" N LEU A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 255 removed outlier: 3.704A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.661A pdb=" N LEU A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.615A pdb=" N LYS A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.706A pdb=" N GLU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.824A pdb=" N SER A 363 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 391 through 404 Processing helix chain 'A' and resid 409 through 417 removed outlier: 4.312A pdb=" N PHE A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 10 through 22 Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.985A pdb=" N ALA B 127 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.765A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 165 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.678A pdb=" N LEU B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 235 through 255 removed outlier: 3.882A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.657A pdb=" N LYS B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.549A pdb=" N GLU B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.521A pdb=" N ALA B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.705A pdb=" N LEU B 370 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 391 through 404 removed outlier: 4.009A pdb=" N MET B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 30 through 42 Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.734A pdb=" N SER C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.938A pdb=" N LEU C 136 " --> pdb=" O PHE C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.130A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 removed outlier: 3.638A pdb=" N LEU C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 235 through 255 removed outlier: 3.793A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 278 removed outlier: 3.532A pdb=" N LEU C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 293 Processing helix chain 'C' and resid 294 through 302 removed outlier: 3.577A pdb=" N LYS C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.529A pdb=" N GLU C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 removed outlier: 3.596A pdb=" N ALA C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.507A pdb=" N LEU C 370 " --> pdb=" O LYS C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 388 removed outlier: 3.546A pdb=" N ILE C 386 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS C 388 " --> pdb=" O ARG C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 404 Processing helix chain 'D' and resid 2 through 9 removed outlier: 3.858A pdb=" N THR D 9 " --> pdb=" O GLU D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 20 removed outlier: 3.508A pdb=" N THR D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 42 Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 155 through 166 removed outlier: 4.092A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 removed outlier: 3.577A pdb=" N LEU D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 removed outlier: 3.536A pdb=" N VAL D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET D 219 " --> pdb=" O GLU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 255 removed outlier: 3.598A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 243 " --> pdb=" O HIS D 239 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 275 Processing helix chain 'D' and resid 285 through 289 removed outlier: 3.574A pdb=" N GLY D 288 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 293 Processing helix chain 'D' and resid 294 through 302 removed outlier: 3.531A pdb=" N LYS D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 removed outlier: 3.804A pdb=" N GLU D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 334 " --> pdb=" O VAL D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.579A pdb=" N ALA D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.581A pdb=" N LEU D 370 " --> pdb=" O LYS D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 404 removed outlier: 3.637A pdb=" N ALA D 404 " --> pdb=" O ILE D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 415 removed outlier: 3.555A pdb=" N PHE D 412 " --> pdb=" O THR D 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 30 through 42 Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 132 through 136 removed outlier: 3.706A pdb=" N ASN E 135 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU E 136 " --> pdb=" O PHE E 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 132 through 136' Processing helix chain 'E' and resid 155 through 166 removed outlier: 4.071A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.564A pdb=" N GLN E 189 " --> pdb=" O THR E 185 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN E 190 " --> pdb=" O MET E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 235 through 255 removed outlier: 3.676A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 295 through 302 Processing helix chain 'E' and resid 325 through 335 removed outlier: 3.758A pdb=" N GLU E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.580A pdb=" N ALA E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 388 removed outlier: 4.215A pdb=" N GLN E 378 " --> pdb=" O GLN E 374 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 402 Processing helix chain 'E' and resid 409 through 417 removed outlier: 3.685A pdb=" N PHE E 413 " --> pdb=" O ASP E 410 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLU E 414 " --> pdb=" O ASP E 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 Processing helix chain 'F' and resid 10 through 20 removed outlier: 3.526A pdb=" N THR F 16 " --> pdb=" O SER F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 82 through 90 removed outlier: 3.680A pdb=" N ILE F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 166 removed outlier: 4.191A pdb=" N THR F 158 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 Processing helix chain 'F' and resid 212 through 221 removed outlier: 4.061A pdb=" N ARG F 221 " --> pdb=" O THR F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 256 removed outlier: 3.836A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS F 256 " --> pdb=" O ARG F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 278 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 294 through 303 removed outlier: 3.622A pdb=" N LYS F 298 " --> pdb=" O LEU F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 336 removed outlier: 3.501A pdb=" N GLU F 329 " --> pdb=" O SER F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 352 removed outlier: 3.565A pdb=" N ALA F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 388 Processing helix chain 'F' and resid 391 through 403 removed outlier: 3.753A pdb=" N ASN F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 21 removed outlier: 3.701A pdb=" N LEU c 16 " --> pdb=" O ASP c 12 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN c 21 " --> pdb=" O GLU c 17 " (cutoff:3.500A) Processing helix chain 'e' and resid 11 through 20 Processing helix chain 'e' and resid 21 through 23 No H-bonds generated for 'chain 'e' and resid 21 through 23' Processing helix chain 'e' and resid 66 through 68 No H-bonds generated for 'chain 'e' and resid 66 through 68' Processing helix chain 'b' and resid 12 through 21 removed outlier: 3.655A pdb=" N LEU b 16 " --> pdb=" O ASP b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 22 through 24 No H-bonds generated for 'chain 'b' and resid 22 through 24' Processing helix chain 'a' and resid 9 through 19 removed outlier: 3.631A pdb=" N TYR a 13 " --> pdb=" O ASN a 9 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN a 15 " --> pdb=" O ASP a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 20 through 24 removed outlier: 3.676A pdb=" N LEU a 24 " --> pdb=" O GLN a 21 " (cutoff:3.500A) Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'f' and resid 9 through 20 removed outlier: 3.550A pdb=" N TYR f 13 " --> pdb=" O ASN f 9 " (cutoff:3.500A) Processing helix chain 'f' and resid 66 through 68 No H-bonds generated for 'chain 'f' and resid 66 through 68' Processing helix chain 'd' and resid 9 through 21 removed outlier: 3.630A pdb=" N TYR d 13 " --> pdb=" O ASN d 9 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP d 14 " --> pdb=" O CYS d 10 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN d 21 " --> pdb=" O GLU d 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 22 through 24 No H-bonds generated for 'chain 'd' and resid 22 through 24' Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 57 removed outlier: 3.603A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N TYR A 80 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N LYS A 115 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS A 100 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 116 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N SER A 98 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU A 118 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR A 96 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 4.003A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 318 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 removed outlier: 4.003A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY A 174 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA A 319 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE A 176 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 342 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 364 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 57 removed outlier: 3.585A pdb=" N ILE B 79 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS B 100 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL B 116 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N SER B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU B 118 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR B 96 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 139 removed outlier: 4.131A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE B 316 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 262 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N THR B 318 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU B 264 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N LEU B 320 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 203 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU B 263 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 204 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL B 228 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL B 206 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N SER B 230 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 208 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 removed outlier: 4.131A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY B 174 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA B 319 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE B 176 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 364 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 50 through 57 removed outlier: 3.657A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 113 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS C 100 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL C 116 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N SER C 98 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU C 118 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR C 96 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.937A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU C 204 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N VAL C 228 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL C 206 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N SER C 230 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU C 208 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.937A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY C 174 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA C 319 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE C 176 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET C 341 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 364 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 50 through 57 removed outlier: 3.555A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS D 100 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL D 116 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N SER D 98 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU D 118 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR D 96 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.974A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL D 203 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU D 263 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N MET D 205 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.974A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY D 174 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA D 319 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE D 176 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET D 341 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N HIS D 344 " --> pdb=" O ARG D 362 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ARG D 362 " --> pdb=" O HIS D 344 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 50 through 57 removed outlier: 3.514A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS E 100 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL E 116 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N SER E 98 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU E 118 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR E 96 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 226 through 231 removed outlier: 6.713A pdb=" N LEU E 204 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL E 228 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL E 206 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N SER E 230 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU E 208 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 226 through 231 removed outlier: 6.713A pdb=" N LEU E 204 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL E 228 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL E 206 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N SER E 230 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU E 208 " --> pdb=" O SER E 230 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY E 174 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ALA E 319 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE E 176 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET E 341 " --> pdb=" O ARG E 173 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 50 through 57 removed outlier: 3.653A pdb=" N ILE F 79 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU F 114 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ARG F 102 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL F 116 " --> pdb=" O LYS F 100 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LYS F 100 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU F 118 " --> pdb=" O SER F 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 226 through 231 removed outlier: 6.838A pdb=" N LEU F 204 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N VAL F 228 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL F 203 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU F 263 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET F 205 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 318 " --> pdb=" O LEU F 264 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 226 through 231 removed outlier: 6.838A pdb=" N LEU F 204 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N VAL F 228 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL F 203 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU F 263 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET F 205 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 318 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY F 174 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ALA F 319 " --> pdb=" O GLY F 174 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE F 176 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU F 342 " --> pdb=" O GLY F 364 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY F 364 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 25 through 26 Processing sheet with id=AC2, first strand: chain 'c' and resid 42 through 45 Processing sheet with id=AC3, first strand: chain 'c' and resid 71 through 72 removed outlier: 3.774A pdb=" N PHE c 71 " --> pdb=" O THR c 78 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 25 through 27 Processing sheet with id=AC5, first strand: chain 'e' and resid 42 through 46 Processing sheet with id=AC6, first strand: chain 'b' and resid 42 through 45 Processing sheet with id=AC7, first strand: chain 'a' and resid 39 through 46 removed outlier: 4.991A pdb=" N ALA a 40 " --> pdb=" O GLU a 55 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU a 55 " --> pdb=" O ALA a 40 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP a 42 " --> pdb=" O VAL a 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'f' and resid 25 through 27 Processing sheet with id=AC9, first strand: chain 'f' and resid 42 through 46 removed outlier: 3.634A pdb=" N LEU f 52 " --> pdb=" O LEU f 63 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU f 63 " --> pdb=" O LEU f 52 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL f 54 " --> pdb=" O ARG f 61 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 40 through 45 948 hydrogen bonds defined for protein. 2670 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: 4.24 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5490 1.33 - 1.45: 4211 1.45 - 1.58: 13443 1.58 - 1.70: 1 1.70 - 1.82: 218 Bond restraints: 23363 Sorted by residual: bond pdb=" N GLU D 234 " pdb=" CA GLU D 234 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.64e+01 bond pdb=" N VAL D 277 " pdb=" CA VAL D 277 " ideal model delta sigma weight residual 1.459 1.494 -0.035 9.10e-03 1.21e+04 1.50e+01 bond pdb=" C MET F 1 " pdb=" N ASN F 2 " ideal model delta sigma weight residual 1.331 1.378 -0.047 1.29e-02 6.01e+03 1.30e+01 bond pdb=" N ILE D 209 " pdb=" CA ILE D 209 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.19e-02 7.06e+03 1.26e+01 bond pdb=" N GLY F 46 " pdb=" CA GLY F 46 " ideal model delta sigma weight residual 1.444 1.477 -0.033 9.30e-03 1.16e+04 1.24e+01 ... (remaining 23358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.25: 31335 5.25 - 10.51: 105 10.51 - 15.76: 28 15.76 - 21.02: 4 21.02 - 26.27: 6 Bond angle restraints: 31478 Sorted by residual: angle pdb=" N GLY B 150 " pdb=" CA GLY B 150 " pdb=" C GLY B 150 " ideal model delta sigma weight residual 115.21 138.09 -22.88 1.30e+00 5.92e-01 3.10e+02 angle pdb=" N MET F 405 " pdb=" CA MET F 405 " pdb=" C MET F 405 " ideal model delta sigma weight residual 111.56 137.83 -26.27 1.53e+00 4.27e-01 2.95e+02 angle pdb=" N THR d 78 " pdb=" CA THR d 78 " pdb=" C THR d 78 " ideal model delta sigma weight residual 110.30 132.31 -22.01 1.50e+00 4.44e-01 2.15e+02 angle pdb=" C ARG B 149 " pdb=" CA ARG B 149 " pdb=" CB ARG B 149 " ideal model delta sigma weight residual 110.44 87.64 22.80 1.68e+00 3.54e-01 1.84e+02 angle pdb=" CA PRO B 10 " pdb=" N PRO B 10 " pdb=" CD PRO B 10 " ideal model delta sigma weight residual 112.00 94.66 17.34 1.40e+00 5.10e-01 1.53e+02 ... (remaining 31473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11847 17.97 - 35.94: 1812 35.94 - 53.91: 643 53.91 - 71.88: 149 71.88 - 89.85: 39 Dihedral angle restraints: 14490 sinusoidal: 6053 harmonic: 8437 Sorted by residual: dihedral pdb=" C LYS d 31 " pdb=" N LYS d 31 " pdb=" CA LYS d 31 " pdb=" CB LYS d 31 " ideal model delta harmonic sigma weight residual -122.60 -93.35 -29.25 0 2.50e+00 1.60e-01 1.37e+02 dihedral pdb=" C ARG B 149 " pdb=" N ARG B 149 " pdb=" CA ARG B 149 " pdb=" CB ARG B 149 " ideal model delta harmonic sigma weight residual -122.60 -100.21 -22.39 0 2.50e+00 1.60e-01 8.02e+01 dihedral pdb=" C SER F 45 " pdb=" N SER F 45 " pdb=" CA SER F 45 " pdb=" CB SER F 45 " ideal model delta harmonic sigma weight residual -122.60 -100.51 -22.09 0 2.50e+00 1.60e-01 7.80e+01 ... (remaining 14487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 3461 0.147 - 0.294: 129 0.294 - 0.440: 11 0.440 - 0.587: 10 0.587 - 0.734: 5 Chirality restraints: 3616 Sorted by residual: chirality pdb=" CA LYS d 31 " pdb=" N LYS d 31 " pdb=" C LYS d 31 " pdb=" CB LYS d 31 " both_signs ideal model delta sigma weight residual False 2.51 3.24 -0.73 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CA THR d 78 " pdb=" N THR d 78 " pdb=" C THR d 78 " pdb=" CB THR d 78 " both_signs ideal model delta sigma weight residual False 2.53 1.80 0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CA GLU D 24 " pdb=" N GLU D 24 " pdb=" C GLU D 24 " pdb=" CB GLU D 24 " both_signs ideal model delta sigma weight residual False 2.51 3.15 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 3613 not shown) Planarity restraints: 4098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 9 " -0.114 5.00e-02 4.00e+02 1.57e-01 3.96e+01 pdb=" N PRO B 10 " 0.271 5.00e-02 4.00e+02 pdb=" CA PRO B 10 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO B 10 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 150 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C GLY B 150 " -0.052 2.00e-02 2.50e+03 pdb=" O GLY B 150 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN B 151 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 404 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.24e+00 pdb=" C ALA C 404 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA C 404 " 0.018 2.00e-02 2.50e+03 pdb=" N MET C 405 " 0.017 2.00e-02 2.50e+03 ... (remaining 4095 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 8 1.99 - 2.72: 989 2.72 - 3.44: 30447 3.44 - 4.17: 48398 4.17 - 4.90: 88516 Nonbonded interactions: 168358 Sorted by model distance: nonbonded pdb=" CD2 LEU b 28 " pdb=" CA PHE b 71 " model vdw 1.262 3.890 nonbonded pdb=" CD2 LEU b 28 " pdb=" CB PHE b 71 " model vdw 1.366 3.860 nonbonded pdb=" OG1 THR b 27 " pdb=" O SER b 72 " model vdw 1.409 3.040 nonbonded pdb=" NE2 GLN E 85 " pdb=" SG CYS e 10 " model vdw 1.438 3.480 nonbonded pdb=" CD GLN E 85 " pdb=" SG CYS e 10 " model vdw 1.667 3.630 ... (remaining 168353 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 1 through 134 or resid 137 through 139 or (resid 140 throu \ gh 141 and (name N or name CA or name C or name O or name CB )) or resid 142 thr \ ough 413)) selection = (chain 'B' and (resid 1 through 139 or (resid 140 through 141 and (name N or nam \ e CA or name C or name O or name CB )) or resid 142 through 413)) selection = (chain 'C' and (resid 1 through 134 or resid 137 through 139 or (resid 140 throu \ gh 141 and (name N or name CA or name C or name O or name CB )) or resid 142 thr \ ough 413)) selection = (chain 'D' and (resid 1 through 134 or resid 137 through 139 or (resid 140 throu \ gh 141 and (name N or name CA or name C or name O or name CB )) or resid 142 thr \ ough 413)) selection = (chain 'E' and (resid 1 through 134 or resid 137 through 139 or (resid 140 throu \ gh 141 and (name N or name CA or name C or name O or name CB )) or resid 142 thr \ ough 280 or resid 284 through 413)) selection = (chain 'F' and (resid 1 through 134 or resid 137 through 413)) } ncs_group { reference = (chain 'a' and (resid 5 through 32 or resid 37 through 53 or resid 60 through 72 \ )) selection = (chain 'b' and (resid 5 through 32 or resid 37 through 72)) selection = (chain 'c' and (resid 5 through 53 or resid 60 through 72)) selection = (chain 'd' and (resid 5 through 32 or resid 37 through 53 or resid 60 through 72 \ )) selection = (chain 'e' and (resid 5 through 32 or resid 37 through 53 or resid 60 through 72 \ )) selection = (chain 'f' and (resid 5 through 32 or resid 37 through 53 or resid 60 through 72 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.890 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 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 : 0.007 0.131 23363 Z= 0.471 Angle : 1.107 26.273 31478 Z= 0.735 Chirality : 0.074 0.734 3616 Planarity : 0.005 0.157 4098 Dihedral : 19.923 89.850 9014 Min Nonbonded Distance : 1.262 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 7.73 % Allowed : 23.11 % Favored : 69.16 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: -0.87 (0.16), residues: 2881 helix: 0.68 (0.17), residues: 1066 sheet: 0.11 (0.23), residues: 492 loop : -1.96 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 109 TYR 0.011 0.001 TYR d 5 PHE 0.027 0.001 PHE D 398 TRP 0.008 0.001 TRP A 381 HIS 0.005 0.001 HIS F 295 Details of bonding type rmsd covalent geometry : bond 0.00653 (23363) covalent geometry : angle 1.10734 (31478) hydrogen bonds : bond 0.20801 ( 920) hydrogen bonds : angle 6.42710 ( 2670) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 301 time to evaluate : 0.980 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: A 130 LYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6778 (mmtm) REVERT: C 411 ASP cc_start: 0.6225 (OUTLIER) cc_final: 0.6000 (m-30) REVERT: E 186 MET cc_start: 0.4941 (ttp) cc_final: 0.4617 (ttp) outliers start: 195 outliers final: 37 residues processed: 441 average time/residue: 0.7050 time to fit residues: 351.4856 Evaluate side-chains 243 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 283 LYS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain b residue 12 ASP Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 18 LEU Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 36 LEU Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 71 PHE Chi-restraints excluded: chain b residue 78 THR Chi-restraints excluded: chain d residue 20 CYS Chi-restraints excluded: chain d residue 32 ASP Chi-restraints excluded: chain d residue 71 PHE Chi-restraints excluded: chain d residue 81 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS B 151 ASN B 409 ASN D 198 ASN D 275 ASN D 344 HIS E 25 ASN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN E 378 GLN F 25 ASN F 239 HIS ** e 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.076121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.046378 restraints weight = 85153.689| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 4.39 r_work: 0.2659 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23363 Z= 0.142 Angle : 0.661 11.289 31478 Z= 0.334 Chirality : 0.044 0.242 3616 Planarity : 0.004 0.080 4098 Dihedral : 6.622 98.696 3226 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.32 % Allowed : 27.39 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: -0.33 (0.16), residues: 2881 helix: 1.25 (0.16), residues: 1095 sheet: 0.34 (0.23), residues: 461 loop : -1.76 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG c 61 TYR 0.020 0.001 TYR B 197 PHE 0.022 0.001 PHE E 355 TRP 0.006 0.001 TRP E 381 HIS 0.011 0.001 HIS e 23 Details of bonding type rmsd covalent geometry : bond 0.00325 (23363) covalent geometry : angle 0.66072 (31478) hydrogen bonds : bond 0.04741 ( 920) hydrogen bonds : angle 4.62217 ( 2670) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 224 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.7755 (ptt) cc_final: 0.7373 (pp-130) REVERT: A 186 MET cc_start: 0.9218 (tmm) cc_final: 0.9005 (ppp) REVERT: A 205 MET cc_start: 0.8478 (mtt) cc_final: 0.8118 (mpt) REVERT: A 245 MET cc_start: 0.9496 (mmm) cc_final: 0.9244 (mmt) REVERT: A 343 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7959 (mt) REVERT: A 380 MET cc_start: 0.9550 (OUTLIER) cc_final: 0.9253 (mpt) REVERT: A 390 MET cc_start: 0.9210 (ptp) cc_final: 0.8981 (pmm) REVERT: B 348 LYS cc_start: 0.9472 (OUTLIER) cc_final: 0.9058 (mppt) REVERT: C 401 ASN cc_start: 0.9619 (OUTLIER) cc_final: 0.9344 (t0) REVERT: D 346 SER cc_start: 0.9353 (OUTLIER) cc_final: 0.9027 (p) REVERT: D 405 MET cc_start: 0.9465 (OUTLIER) cc_final: 0.9159 (mtp) REVERT: E 146 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8966 (mmp-170) REVERT: E 233 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8452 (m-30) REVERT: E 355 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.8136 (t80) REVERT: F 29 MET cc_start: 0.8618 (pmm) cc_final: 0.8300 (pmm) REVERT: c 21 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7544 (mm-40) REVERT: c 25 MET cc_start: 0.8952 (pmm) cc_final: 0.8360 (ppp) REVERT: c 66 ASP cc_start: 0.8573 (t0) cc_final: 0.8229 (m-30) REVERT: b 10 CYS cc_start: 0.8521 (t) cc_final: 0.8301 (m) REVERT: b 25 MET cc_start: 0.8296 (ppp) cc_final: 0.7104 (pp-130) REVERT: b 76 ILE cc_start: 0.7792 (mp) cc_final: 0.7307 (mp) REVERT: d 32 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8063 (p0) REVERT: d 66 ASP cc_start: 0.9212 (t0) cc_final: 0.9001 (t0) outliers start: 109 outliers final: 30 residues processed: 302 average time/residue: 0.6396 time to fit residues: 221.8614 Evaluate side-chains 233 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ARG Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain b residue 18 LEU Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 36 LEU Chi-restraints excluded: chain b residue 78 THR Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain d residue 32 ASP Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 53 VAL Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain d residue 81 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 ASN E 25 ASN E 129 ASN F 25 ASN F 239 HIS F 275 ASN ** e 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 9 ASN b 73 HIS a 9 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.073453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.043642 restraints weight = 85571.252| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 4.37 r_work: 0.2583 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 23363 Z= 0.214 Angle : 0.653 10.176 31478 Z= 0.330 Chirality : 0.044 0.163 3616 Planarity : 0.004 0.056 4098 Dihedral : 5.275 58.377 3182 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.00 % Allowed : 27.11 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: -0.15 (0.16), residues: 2881 helix: 1.52 (0.16), residues: 1098 sheet: 0.38 (0.24), residues: 453 loop : -1.74 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG d 46 TYR 0.012 0.001 TYR b 5 PHE 0.019 0.001 PHE B 355 TRP 0.007 0.001 TRP E 381 HIS 0.009 0.001 HIS e 73 Details of bonding type rmsd covalent geometry : bond 0.00510 (23363) covalent geometry : angle 0.65260 (31478) hydrogen bonds : bond 0.05397 ( 920) hydrogen bonds : angle 4.49121 ( 2670) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 214 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8151 (mpm) cc_final: 0.7749 (mpm) REVERT: A 41 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8549 (tm-30) REVERT: A 147 MET cc_start: 0.7993 (ptt) cc_final: 0.7311 (ppp) REVERT: A 343 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8029 (mt) REVERT: B 1 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6438 (ptt) REVERT: B 348 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9029 (mppt) REVERT: B 369 GLU cc_start: 0.9350 (OUTLIER) cc_final: 0.9073 (mp0) REVERT: B 396 MET cc_start: 0.9471 (mmm) cc_final: 0.9260 (mmm) REVERT: C 341 MET cc_start: 0.9378 (tmm) cc_final: 0.9038 (tmt) REVERT: D 346 SER cc_start: 0.9423 (OUTLIER) cc_final: 0.9116 (p) REVERT: D 405 MET cc_start: 0.9470 (OUTLIER) cc_final: 0.9197 (mtp) REVERT: E 146 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.8990 (mmp-170) REVERT: E 233 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8578 (m-30) REVERT: E 355 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8228 (t80) REVERT: F 29 MET cc_start: 0.8521 (pmm) cc_final: 0.8299 (pmm) REVERT: c 17 GLU cc_start: 0.9371 (tm-30) cc_final: 0.9137 (tm-30) REVERT: c 21 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7795 (mm-40) REVERT: c 25 MET cc_start: 0.9074 (pmm) cc_final: 0.8377 (ppp) REVERT: c 66 ASP cc_start: 0.8650 (t0) cc_final: 0.8228 (m-30) REVERT: e 23 HIS cc_start: 0.8687 (t-90) cc_final: 0.8381 (t-90) REVERT: e 39 LYS cc_start: 0.8472 (mmmt) cc_final: 0.8193 (mmmt) REVERT: e 66 ASP cc_start: 0.8728 (t0) cc_final: 0.8450 (t0) REVERT: b 11 ASP cc_start: 0.9158 (m-30) cc_final: 0.8652 (p0) REVERT: b 12 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8819 (OUTLIER) REVERT: b 25 MET cc_start: 0.8316 (ppp) cc_final: 0.7433 (pp-130) REVERT: b 70 SER cc_start: 0.8501 (p) cc_final: 0.8236 (m) REVERT: d 32 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.7989 (p0) REVERT: d 66 ASP cc_start: 0.9289 (t0) cc_final: 0.9070 (t0) REVERT: d 71 PHE cc_start: 0.6973 (OUTLIER) cc_final: 0.6653 (p90) REVERT: d 76 ILE cc_start: 0.6783 (mm) cc_final: 0.6562 (mp) outliers start: 101 outliers final: 48 residues processed: 290 average time/residue: 0.5933 time to fit residues: 199.9066 Evaluate side-chains 256 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 196 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ARG Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain c residue 20 CYS Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain e residue 71 PHE Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain b residue 12 ASP Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 36 LEU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 76 ILE Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 32 ASP Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 71 PHE Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain d residue 81 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 172 optimal weight: 0.9990 chunk 262 optimal weight: 0.0970 chunk 77 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 272 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN C 409 ASN D 25 ASN E 25 ASN F 239 HIS ** e 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 9 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.074315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.044573 restraints weight = 85323.839| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 4.32 r_work: 0.2622 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23363 Z= 0.118 Angle : 0.595 9.739 31478 Z= 0.295 Chirality : 0.043 0.188 3616 Planarity : 0.004 0.052 4098 Dihedral : 4.881 57.679 3177 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.33 % Allowed : 27.43 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 0.07 (0.16), residues: 2881 helix: 1.75 (0.16), residues: 1112 sheet: 0.43 (0.23), residues: 458 loop : -1.69 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 46 TYR 0.012 0.001 TYR b 5 PHE 0.022 0.001 PHE F 133 TRP 0.005 0.001 TRP E 381 HIS 0.005 0.001 HIS e 23 Details of bonding type rmsd covalent geometry : bond 0.00275 (23363) covalent geometry : angle 0.59467 (31478) hydrogen bonds : bond 0.04003 ( 920) hydrogen bonds : angle 4.18782 ( 2670) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 206 time to evaluate : 0.969 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: A 21 MET cc_start: 0.8173 (mpm) cc_final: 0.7754 (mpm) REVERT: A 41 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8518 (tm-30) REVERT: A 147 MET cc_start: 0.8166 (ptt) cc_final: 0.7548 (ppp) REVERT: A 186 MET cc_start: 0.9213 (tmm) cc_final: 0.8926 (ppp) REVERT: A 341 MET cc_start: 0.7155 (tmm) cc_final: 0.6917 (tmm) REVERT: A 343 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8000 (mt) REVERT: A 380 MET cc_start: 0.9542 (mpp) cc_final: 0.9235 (mpt) REVERT: B 29 MET cc_start: 0.8834 (mtp) cc_final: 0.8313 (ptp) REVERT: B 147 MET cc_start: 0.9462 (OUTLIER) cc_final: 0.8395 (mmm) REVERT: B 348 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.8985 (mppt) REVERT: B 369 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.9130 (mp0) REVERT: C 327 MET cc_start: 0.8725 (mtm) cc_final: 0.8404 (ttp) REVERT: D 346 SER cc_start: 0.9434 (OUTLIER) cc_final: 0.9130 (p) REVERT: D 415 MET cc_start: 0.9027 (ttp) cc_final: 0.8690 (tmm) REVERT: E 146 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.9065 (mmp-170) REVERT: E 233 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8489 (m-30) REVERT: E 355 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8174 (t80) REVERT: E 367 LYS cc_start: 0.9542 (OUTLIER) cc_final: 0.9220 (ttpp) REVERT: F 29 MET cc_start: 0.8505 (pmm) cc_final: 0.8235 (pmm) REVERT: F 390 MET cc_start: 0.8595 (mpp) cc_final: 0.8367 (mpp) REVERT: c 25 MET cc_start: 0.9084 (pmm) cc_final: 0.8412 (ppp) REVERT: c 66 ASP cc_start: 0.8689 (t0) cc_final: 0.8225 (m-30) REVERT: e 23 HIS cc_start: 0.8676 (t-90) cc_final: 0.8188 (t-90) REVERT: e 39 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8026 (mmmt) REVERT: e 66 ASP cc_start: 0.8739 (t0) cc_final: 0.8474 (t0) REVERT: b 10 CYS cc_start: 0.8713 (t) cc_final: 0.8127 (m) REVERT: b 25 MET cc_start: 0.8353 (ppp) cc_final: 0.7472 (ppp) REVERT: b 70 SER cc_start: 0.8365 (p) cc_final: 0.8044 (m) REVERT: b 71 PHE cc_start: 0.7460 (t80) cc_final: 0.7090 (t80) REVERT: d 32 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.7991 (p0) REVERT: d 71 PHE cc_start: 0.7119 (p90) cc_final: 0.6791 (p90) outliers start: 84 outliers final: 38 residues processed: 268 average time/residue: 0.6212 time to fit residues: 191.9538 Evaluate side-chains 244 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ARG Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain e residue 10 CYS Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 71 PHE Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain b residue 36 LEU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 76 ILE Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 32 ASP Chi-restraints excluded: chain d residue 43 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 188 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 239 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 chunk 202 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 145 optimal weight: 0.1980 chunk 177 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 275 ASN D 25 ASN E 25 ASN F 25 ASN F 239 HIS b 9 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.072376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.042202 restraints weight = 86748.029| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 4.36 r_work: 0.2555 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 23363 Z= 0.230 Angle : 0.638 9.692 31478 Z= 0.320 Chirality : 0.044 0.209 3616 Planarity : 0.004 0.046 4098 Dihedral : 4.800 58.842 3170 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.69 % Allowed : 27.55 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 0.03 (0.16), residues: 2881 helix: 1.75 (0.16), residues: 1110 sheet: 0.47 (0.24), residues: 441 loop : -1.73 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG e 46 TYR 0.012 0.001 TYR d 5 PHE 0.017 0.001 PHE D 133 TRP 0.007 0.001 TRP E 381 HIS 0.006 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00548 (23363) covalent geometry : angle 0.63830 (31478) hydrogen bonds : bond 0.05225 ( 920) hydrogen bonds : angle 4.37205 ( 2670) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 207 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.8313 (ptt) cc_final: 0.7708 (ppp) REVERT: A 186 MET cc_start: 0.9233 (tmm) cc_final: 0.8963 (ppp) REVERT: A 314 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.7975 (p) REVERT: A 343 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8161 (mt) REVERT: B 348 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.9026 (mppt) REVERT: B 369 GLU cc_start: 0.9376 (OUTLIER) cc_final: 0.9117 (mp0) REVERT: D 24 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8124 (tp30) REVERT: D 346 SER cc_start: 0.9448 (OUTLIER) cc_final: 0.9166 (p) REVERT: D 415 MET cc_start: 0.9153 (ttp) cc_final: 0.8630 (tmm) REVERT: E 326 LYS cc_start: 0.9053 (pptt) cc_final: 0.8827 (pptt) REVERT: E 355 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8300 (t80) REVERT: E 367 LYS cc_start: 0.9528 (OUTLIER) cc_final: 0.9243 (tppp) REVERT: F 29 MET cc_start: 0.8524 (pmm) cc_final: 0.8315 (pmm) REVERT: c 25 MET cc_start: 0.9186 (pmm) cc_final: 0.8421 (ppp) REVERT: c 59 GLU cc_start: 0.8301 (tp30) cc_final: 0.8052 (mp0) REVERT: c 66 ASP cc_start: 0.8752 (t0) cc_final: 0.8294 (m-30) REVERT: e 23 HIS cc_start: 0.8619 (t-90) cc_final: 0.8249 (t-90) REVERT: e 39 LYS cc_start: 0.8508 (mmmt) cc_final: 0.8160 (mmmt) REVERT: e 66 ASP cc_start: 0.8689 (t0) cc_final: 0.8436 (t0) REVERT: b 10 CYS cc_start: 0.8797 (t) cc_final: 0.8267 (m) REVERT: b 25 MET cc_start: 0.8502 (ppp) cc_final: 0.7582 (ppp) REVERT: b 70 SER cc_start: 0.8491 (p) cc_final: 0.7864 (m) REVERT: b 71 PHE cc_start: 0.7520 (t80) cc_final: 0.7125 (t80) REVERT: d 32 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8006 (p0) REVERT: d 37 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8833 (tm-30) REVERT: d 71 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.7115 (p90) outliers start: 93 outliers final: 51 residues processed: 279 average time/residue: 0.6218 time to fit residues: 199.8317 Evaluate side-chains 261 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 200 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain c residue 23 HIS Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain e residue 10 CYS Chi-restraints excluded: chain e residue 22 HIS Chi-restraints excluded: chain e residue 71 PHE Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain b residue 36 LEU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 76 ILE Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 32 ASP Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 71 PHE Chi-restraints excluded: chain d residue 80 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 229 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 88 optimal weight: 0.0770 chunk 126 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN E 25 ASN F 25 ASN F 239 HIS F 340 ASN b 9 ASN ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.073629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.043641 restraints weight = 86839.535| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 4.57 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23363 Z= 0.115 Angle : 0.602 9.799 31478 Z= 0.297 Chirality : 0.043 0.193 3616 Planarity : 0.004 0.046 4098 Dihedral : 4.450 52.455 3168 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.97 % Allowed : 28.42 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 0.23 (0.16), residues: 2881 helix: 1.95 (0.16), residues: 1114 sheet: 0.52 (0.24), residues: 444 loop : -1.66 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG e 46 TYR 0.030 0.001 TYR E 197 PHE 0.049 0.001 PHE B 355 TRP 0.005 0.001 TRP E 381 HIS 0.003 0.000 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00267 (23363) covalent geometry : angle 0.60182 (31478) hydrogen bonds : bond 0.03796 ( 920) hydrogen bonds : angle 4.08223 ( 2670) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 210 time to evaluate : 1.115 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: A 21 MET cc_start: 0.7921 (mpm) cc_final: 0.7439 (mpm) REVERT: A 29 MET cc_start: 0.8815 (pmm) cc_final: 0.8457 (pp-130) REVERT: A 41 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8465 (tm-30) REVERT: A 147 MET cc_start: 0.8223 (ptt) cc_final: 0.7785 (ppp) REVERT: A 343 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8071 (mt) REVERT: A 390 MET cc_start: 0.9203 (pmt) cc_final: 0.8851 (pmm) REVERT: A 415 MET cc_start: 0.9413 (mmm) cc_final: 0.9192 (mmm) REVERT: B 29 MET cc_start: 0.8637 (mtp) cc_final: 0.8210 (ptp) REVERT: B 147 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8333 (mmm) REVERT: B 348 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.9011 (mppt) REVERT: B 390 MET cc_start: 0.9278 (mtp) cc_final: 0.8306 (ttm) REVERT: C 327 MET cc_start: 0.8567 (mtm) cc_final: 0.8261 (ttp) REVERT: D 346 SER cc_start: 0.9255 (OUTLIER) cc_final: 0.8945 (p) REVERT: D 415 MET cc_start: 0.9077 (ttp) cc_final: 0.8520 (tmm) REVERT: E 367 LYS cc_start: 0.9508 (OUTLIER) cc_final: 0.9190 (tppp) REVERT: F 29 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8031 (pmm) REVERT: c 25 MET cc_start: 0.9082 (pmm) cc_final: 0.8371 (ppp) REVERT: c 66 ASP cc_start: 0.8772 (t0) cc_final: 0.8329 (m-30) REVERT: e 23 HIS cc_start: 0.8632 (t-90) cc_final: 0.8253 (t-90) REVERT: e 39 LYS cc_start: 0.8506 (mmmt) cc_final: 0.8167 (mmmt) REVERT: e 66 ASP cc_start: 0.8757 (t0) cc_final: 0.8485 (t0) REVERT: b 10 CYS cc_start: 0.8676 (t) cc_final: 0.8193 (m) REVERT: b 25 MET cc_start: 0.8743 (ppp) cc_final: 0.7993 (ppp) REVERT: b 70 SER cc_start: 0.8332 (p) cc_final: 0.7761 (m) REVERT: b 71 PHE cc_start: 0.7654 (t80) cc_final: 0.7306 (t80) REVERT: d 32 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.7941 (p0) REVERT: d 37 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8804 (tm-30) REVERT: d 71 PHE cc_start: 0.7645 (p90) cc_final: 0.7403 (p90) outliers start: 75 outliers final: 44 residues processed: 267 average time/residue: 0.5916 time to fit residues: 183.1750 Evaluate side-chains 256 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 72 SER Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain e residue 10 CYS Chi-restraints excluded: chain e residue 71 PHE Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain b residue 12 ASP Chi-restraints excluded: chain b residue 36 LEU Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 32 ASP Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 80 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 184 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 266 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 131 optimal weight: 0.4980 chunk 79 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN E 25 ASN F 25 ASN F 239 HIS b 9 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.073890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.043890 restraints weight = 86685.407| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 4.59 r_work: 0.2606 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23363 Z= 0.112 Angle : 0.606 10.581 31478 Z= 0.296 Chirality : 0.042 0.208 3616 Planarity : 0.004 0.048 4098 Dihedral : 4.301 53.185 3167 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.70 % Allowed : 28.54 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 0.35 (0.16), residues: 2881 helix: 2.01 (0.16), residues: 1119 sheet: 0.64 (0.24), residues: 461 loop : -1.61 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG e 46 TYR 0.024 0.001 TYR F 197 PHE 0.015 0.001 PHE F 133 TRP 0.005 0.001 TRP E 381 HIS 0.002 0.000 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00262 (23363) covalent geometry : angle 0.60646 (31478) hydrogen bonds : bond 0.03541 ( 920) hydrogen bonds : angle 4.02180 ( 2670) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 213 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8012 (mpm) cc_final: 0.7568 (mpm) REVERT: A 41 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8511 (tm-30) REVERT: A 147 MET cc_start: 0.8244 (ptt) cc_final: 0.7738 (ppp) REVERT: A 343 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8054 (mt) REVERT: A 380 MET cc_start: 0.9461 (mmm) cc_final: 0.8974 (mpt) REVERT: A 390 MET cc_start: 0.9113 (pmt) cc_final: 0.8821 (pmm) REVERT: B 29 MET cc_start: 0.8710 (mtp) cc_final: 0.8171 (ptp) REVERT: B 147 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.8429 (mmm) REVERT: B 348 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.9044 (mppt) REVERT: B 390 MET cc_start: 0.9342 (mtp) cc_final: 0.8445 (ttm) REVERT: C 1 MET cc_start: 0.7244 (tpp) cc_final: 0.6950 (tpp) REVERT: C 266 SER cc_start: 0.9286 (t) cc_final: 0.9062 (p) REVERT: C 327 MET cc_start: 0.8764 (mtm) cc_final: 0.8461 (ttp) REVERT: D 265 ASP cc_start: 0.8058 (p0) cc_final: 0.7771 (p0) REVERT: D 415 MET cc_start: 0.9170 (ttp) cc_final: 0.8654 (tmm) REVERT: E 367 LYS cc_start: 0.9541 (OUTLIER) cc_final: 0.9236 (tppp) REVERT: F 29 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8255 (pmt) REVERT: c 25 MET cc_start: 0.9078 (pmm) cc_final: 0.8275 (ppp) REVERT: c 59 GLU cc_start: 0.8271 (tp30) cc_final: 0.8027 (mp0) REVERT: c 66 ASP cc_start: 0.8676 (t0) cc_final: 0.8254 (m-30) REVERT: e 66 ASP cc_start: 0.8713 (t0) cc_final: 0.8434 (t0) REVERT: b 10 CYS cc_start: 0.8754 (t) cc_final: 0.8153 (m) REVERT: b 25 MET cc_start: 0.8822 (ppp) cc_final: 0.8460 (ppp) REVERT: b 70 SER cc_start: 0.8317 (p) cc_final: 0.7765 (m) REVERT: b 71 PHE cc_start: 0.7747 (t80) cc_final: 0.7329 (t80) REVERT: d 32 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.7965 (p0) REVERT: d 37 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8770 (tm-30) REVERT: d 71 PHE cc_start: 0.7562 (p90) cc_final: 0.7295 (p90) outliers start: 68 outliers final: 40 residues processed: 268 average time/residue: 0.6112 time to fit residues: 189.6139 Evaluate side-chains 250 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain e residue 10 CYS Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain b residue 12 ASP Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 32 ASP Chi-restraints excluded: chain d residue 43 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 11 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 259 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 231 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 100 optimal weight: 0.0030 chunk 94 optimal weight: 0.6980 chunk 270 optimal weight: 20.0000 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN E 25 ASN F 25 ASN F 239 HIS b 9 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.074288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.044479 restraints weight = 85921.027| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 4.46 r_work: 0.2623 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23363 Z= 0.108 Angle : 0.628 11.208 31478 Z= 0.304 Chirality : 0.043 0.195 3616 Planarity : 0.004 0.049 4098 Dihedral : 3.995 44.619 3162 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.46 % Allowed : 29.01 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 0.46 (0.16), residues: 2881 helix: 2.09 (0.16), residues: 1119 sheet: 0.68 (0.23), residues: 468 loop : -1.54 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG e 46 TYR 0.013 0.001 TYR b 5 PHE 0.021 0.001 PHE F 133 TRP 0.004 0.000 TRP E 381 HIS 0.006 0.000 HIS e 73 Details of bonding type rmsd covalent geometry : bond 0.00248 (23363) covalent geometry : angle 0.62796 (31478) hydrogen bonds : bond 0.03221 ( 920) hydrogen bonds : angle 3.96564 ( 2670) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 213 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8134 (mpm) cc_final: 0.7718 (mpm) REVERT: A 29 MET cc_start: 0.8801 (pmm) cc_final: 0.8421 (pp-130) REVERT: A 41 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8505 (tm-30) REVERT: A 147 MET cc_start: 0.8261 (ptt) cc_final: 0.7876 (pp-130) REVERT: A 205 MET cc_start: 0.8261 (mtt) cc_final: 0.8037 (mpt) REVERT: A 380 MET cc_start: 0.9422 (mmm) cc_final: 0.8940 (mpt) REVERT: A 390 MET cc_start: 0.9051 (pmt) cc_final: 0.8753 (pmm) REVERT: B 29 MET cc_start: 0.8730 (mtp) cc_final: 0.8222 (ptp) REVERT: B 147 MET cc_start: 0.9413 (OUTLIER) cc_final: 0.8423 (mmm) REVERT: B 348 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9017 (mppt) REVERT: B 390 MET cc_start: 0.9307 (mtp) cc_final: 0.8446 (ttm) REVERT: C 1 MET cc_start: 0.7191 (tpp) cc_final: 0.6957 (tpp) REVERT: C 327 MET cc_start: 0.8742 (mtm) cc_final: 0.8428 (ttp) REVERT: D 156 ASP cc_start: 0.9350 (OUTLIER) cc_final: 0.9139 (t70) REVERT: D 265 ASP cc_start: 0.8028 (p0) cc_final: 0.7710 (p0) REVERT: D 346 SER cc_start: 0.9439 (OUTLIER) cc_final: 0.9150 (p) REVERT: D 415 MET cc_start: 0.9197 (ttp) cc_final: 0.8700 (tmm) REVERT: E 367 LYS cc_start: 0.9542 (OUTLIER) cc_final: 0.9310 (tppp) REVERT: F 29 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8163 (pmm) REVERT: c 25 MET cc_start: 0.9056 (pmm) cc_final: 0.8285 (ppp) REVERT: c 66 ASP cc_start: 0.8652 (t0) cc_final: 0.8204 (m-30) REVERT: e 47 LYS cc_start: 0.9544 (mmmm) cc_final: 0.9087 (tptp) REVERT: e 66 ASP cc_start: 0.8733 (t0) cc_final: 0.8472 (t0) REVERT: b 9 ASN cc_start: 0.9238 (m-40) cc_final: 0.8929 (p0) REVERT: b 10 CYS cc_start: 0.8794 (t) cc_final: 0.8446 (m) REVERT: b 25 MET cc_start: 0.8824 (ppp) cc_final: 0.8473 (ppp) REVERT: b 70 SER cc_start: 0.8319 (p) cc_final: 0.7747 (m) REVERT: b 71 PHE cc_start: 0.7759 (t80) cc_final: 0.7234 (t80) REVERT: d 37 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8803 (tm-30) outliers start: 62 outliers final: 41 residues processed: 265 average time/residue: 0.6410 time to fit residues: 197.0040 Evaluate side-chains 249 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 201 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain e residue 10 CYS Chi-restraints excluded: chain e residue 71 PHE Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 76 ILE Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 43 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 157 optimal weight: 0.2980 chunk 83 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 212 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 199 optimal weight: 0.0980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN E 25 ASN F 25 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.073370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.043608 restraints weight = 85495.270| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 4.41 r_work: 0.2590 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23363 Z= 0.147 Angle : 0.657 12.977 31478 Z= 0.318 Chirality : 0.043 0.199 3616 Planarity : 0.004 0.049 4098 Dihedral : 4.009 44.127 3159 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.34 % Allowed : 29.13 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 0.48 (0.16), residues: 2881 helix: 2.12 (0.16), residues: 1119 sheet: 0.52 (0.23), residues: 481 loop : -1.48 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG e 46 TYR 0.022 0.001 TYR F 197 PHE 0.049 0.001 PHE B 355 TRP 0.006 0.001 TRP E 381 HIS 0.004 0.001 HIS e 23 Details of bonding type rmsd covalent geometry : bond 0.00351 (23363) covalent geometry : angle 0.65745 (31478) hydrogen bonds : bond 0.03928 ( 920) hydrogen bonds : angle 4.05937 ( 2670) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 214 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8044 (mpm) cc_final: 0.7665 (mmm) REVERT: A 29 MET cc_start: 0.8808 (pmm) cc_final: 0.8435 (pp-130) REVERT: A 41 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8519 (tm-30) REVERT: A 147 MET cc_start: 0.8210 (ptt) cc_final: 0.7793 (ppp) REVERT: A 380 MET cc_start: 0.9444 (mmm) cc_final: 0.8963 (mpt) REVERT: A 390 MET cc_start: 0.9070 (pmt) cc_final: 0.8779 (pmm) REVERT: A 415 MET cc_start: 0.9011 (mmm) cc_final: 0.8703 (mmp) REVERT: B 29 MET cc_start: 0.8742 (mtp) cc_final: 0.8236 (ptp) REVERT: B 147 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.8426 (mmm) REVERT: B 348 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9015 (mppt) REVERT: B 390 MET cc_start: 0.9345 (mtp) cc_final: 0.8474 (ttm) REVERT: C 327 MET cc_start: 0.8779 (mtm) cc_final: 0.8489 (ttp) REVERT: D 156 ASP cc_start: 0.9366 (OUTLIER) cc_final: 0.9130 (t70) REVERT: D 265 ASP cc_start: 0.8176 (p0) cc_final: 0.7888 (p0) REVERT: D 285 LEU cc_start: 0.8717 (pt) cc_final: 0.8486 (pp) REVERT: D 346 SER cc_start: 0.9440 (OUTLIER) cc_final: 0.9140 (p) REVERT: D 415 MET cc_start: 0.9190 (ttp) cc_final: 0.8672 (tmm) REVERT: E 367 LYS cc_start: 0.9536 (OUTLIER) cc_final: 0.9310 (tppp) REVERT: E 415 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8428 (pmm) REVERT: F 29 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8165 (pmm) REVERT: c 25 MET cc_start: 0.9095 (pmm) cc_final: 0.8285 (ppp) REVERT: c 59 GLU cc_start: 0.8370 (tp30) cc_final: 0.8158 (mp0) REVERT: c 66 ASP cc_start: 0.8654 (t0) cc_final: 0.8227 (m-30) REVERT: e 29 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7667 (mm-30) REVERT: e 47 LYS cc_start: 0.9547 (mmmm) cc_final: 0.9109 (tptp) REVERT: e 66 ASP cc_start: 0.8694 (t0) cc_final: 0.8450 (t0) REVERT: b 9 ASN cc_start: 0.9258 (m-40) cc_final: 0.8978 (p0) REVERT: b 10 CYS cc_start: 0.8779 (t) cc_final: 0.8524 (m) REVERT: b 25 MET cc_start: 0.8956 (ppp) cc_final: 0.8637 (ppp) REVERT: b 65 LEU cc_start: 0.9307 (mt) cc_final: 0.9063 (mm) REVERT: b 70 SER cc_start: 0.8325 (p) cc_final: 0.7822 (m) REVERT: b 71 PHE cc_start: 0.7353 (t80) cc_final: 0.6984 (t80) REVERT: d 37 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8813 (tm-30) outliers start: 59 outliers final: 37 residues processed: 263 average time/residue: 0.5825 time to fit residues: 178.4863 Evaluate side-chains 258 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 213 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain e residue 10 CYS Chi-restraints excluded: chain e residue 71 PHE Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain b residue 12 ASP Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain d residue 43 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 282 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 259 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 chunk 144 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN E 25 ASN F 25 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.074072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.044481 restraints weight = 85640.746| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 4.41 r_work: 0.2614 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23363 Z= 0.115 Angle : 0.683 12.573 31478 Z= 0.325 Chirality : 0.043 0.225 3616 Planarity : 0.004 0.049 4098 Dihedral : 3.957 43.912 3159 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.98 % Allowed : 29.41 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 0.53 (0.16), residues: 2881 helix: 2.15 (0.16), residues: 1117 sheet: 0.70 (0.23), residues: 476 loop : -1.49 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG e 46 TYR 0.013 0.001 TYR E 197 PHE 0.031 0.001 PHE F 133 TRP 0.004 0.001 TRP E 381 HIS 0.005 0.000 HIS b 22 Details of bonding type rmsd covalent geometry : bond 0.00270 (23363) covalent geometry : angle 0.68262 (31478) hydrogen bonds : bond 0.03332 ( 920) hydrogen bonds : angle 3.96919 ( 2670) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 218 time to evaluate : 1.003 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: A 21 MET cc_start: 0.8153 (mpm) cc_final: 0.7719 (mmm) REVERT: A 29 MET cc_start: 0.8808 (pmm) cc_final: 0.8433 (pp-130) REVERT: A 41 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8490 (tm-30) REVERT: A 147 MET cc_start: 0.8242 (ptt) cc_final: 0.7906 (pp-130) REVERT: A 205 MET cc_start: 0.8275 (mtt) cc_final: 0.8067 (mpt) REVERT: A 380 MET cc_start: 0.9393 (mmm) cc_final: 0.8933 (mpt) REVERT: A 390 MET cc_start: 0.9003 (pmt) cc_final: 0.8727 (pmm) REVERT: B 29 MET cc_start: 0.8737 (mtp) cc_final: 0.8201 (ptp) REVERT: B 147 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.8539 (mmm) REVERT: B 348 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9040 (mppt) REVERT: B 390 MET cc_start: 0.9292 (mtp) cc_final: 0.8453 (ttm) REVERT: C 1 MET cc_start: 0.6665 (tpp) cc_final: 0.6379 (tpp) REVERT: C 327 MET cc_start: 0.8757 (mtm) cc_final: 0.8468 (ttp) REVERT: D 156 ASP cc_start: 0.9352 (OUTLIER) cc_final: 0.9144 (t70) REVERT: D 265 ASP cc_start: 0.8041 (p0) cc_final: 0.7758 (p0) REVERT: D 285 LEU cc_start: 0.8751 (pt) cc_final: 0.8524 (pp) REVERT: D 346 SER cc_start: 0.9436 (OUTLIER) cc_final: 0.9135 (p) REVERT: D 415 MET cc_start: 0.9190 (ttp) cc_final: 0.8651 (tmm) REVERT: E 367 LYS cc_start: 0.9538 (OUTLIER) cc_final: 0.9308 (tppp) REVERT: E 415 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8502 (pmm) REVERT: c 25 MET cc_start: 0.9063 (pmm) cc_final: 0.8294 (ppp) REVERT: c 66 ASP cc_start: 0.8621 (t0) cc_final: 0.8059 (m-30) REVERT: c 67 LYS cc_start: 0.8433 (mmtm) cc_final: 0.8155 (mppt) REVERT: e 29 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7700 (mm-30) REVERT: e 47 LYS cc_start: 0.9546 (mmmm) cc_final: 0.9109 (tptp) REVERT: e 66 ASP cc_start: 0.8713 (t0) cc_final: 0.8465 (t0) REVERT: b 9 ASN cc_start: 0.9277 (m-40) cc_final: 0.8993 (p0) REVERT: b 10 CYS cc_start: 0.8776 (t) cc_final: 0.8514 (m) REVERT: b 12 ASP cc_start: 0.9299 (p0) cc_final: 0.8611 (OUTLIER) REVERT: b 25 MET cc_start: 0.9044 (ppp) cc_final: 0.8822 (ppp) REVERT: b 65 LEU cc_start: 0.9308 (mt) cc_final: 0.9080 (mm) REVERT: b 70 SER cc_start: 0.8404 (p) cc_final: 0.7925 (m) REVERT: b 71 PHE cc_start: 0.7437 (t80) cc_final: 0.6952 (t80) REVERT: d 37 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8772 (tm130) outliers start: 50 outliers final: 33 residues processed: 257 average time/residue: 0.5994 time to fit residues: 178.9691 Evaluate side-chains 244 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain e residue 10 CYS Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 43 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 50 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 0 optimal weight: 10.9990 chunk 119 optimal weight: 0.0570 chunk 216 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS D 25 ASN E 25 ASN F 25 ASN F 239 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.073095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.043484 restraints weight = 85627.720| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 4.29 r_work: 0.2586 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23363 Z= 0.153 Angle : 0.675 13.486 31478 Z= 0.324 Chirality : 0.043 0.183 3616 Planarity : 0.004 0.049 4098 Dihedral : 4.000 43.444 3157 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.10 % Allowed : 29.53 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 0.53 (0.16), residues: 2881 helix: 2.14 (0.16), residues: 1119 sheet: 0.69 (0.23), residues: 476 loop : -1.49 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG e 46 TYR 0.040 0.001 TYR E 197 PHE 0.053 0.001 PHE B 355 TRP 0.006 0.001 TRP E 381 HIS 0.005 0.001 HIS b 22 Details of bonding type rmsd covalent geometry : bond 0.00367 (23363) covalent geometry : angle 0.67522 (31478) hydrogen bonds : bond 0.04002 ( 920) hydrogen bonds : angle 4.06419 ( 2670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10337.80 seconds wall clock time: 175 minutes 58.40 seconds (10558.40 seconds total)