Starting phenix.real_space_refine on Sat Jul 4 14:21:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ej1_31148/07_2026/7ej1_31148.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ej1_31148/07_2026/7ej1_31148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ej1_31148/07_2026/7ej1_31148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ej1_31148/07_2026/7ej1_31148.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ej1_31148/07_2026/7ej1_31148.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ej1_31148/07_2026/7ej1_31148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ej1_31148/07_2026/7ej1_31148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ej1_31148/07_2026/7ej1_31148.map" } resolution = 3.2 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 104 5.16 5 C 13696 2.51 5 N 3572 2.21 5 O 3852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21236 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "B" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2707 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 12, 'GLU:plan': 11, 'ASP:plan': 3, 'PHE:plan': 5, 'ASN:plan1': 1, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 161 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 4.63, per 1000 atoms: 0.22 Number of scatterers: 21236 At special positions: 0 Unit cell: (128.778, 128.778, 157.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 12 15.00 O 3852 8.00 N 3572 7.00 C 13696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5072 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 16 sheets defined 59.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 65 through 78 Processing helix chain 'A' and resid 96 through 107 removed outlier: 3.785A pdb=" N ILE A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.556A pdb=" N LEU A 113 " --> pdb=" O ARG A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 removed outlier: 4.006A pdb=" N ARG A 129 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 removed outlier: 3.696A pdb=" N ILE A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 179 removed outlier: 3.672A pdb=" N THR A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.878A pdb=" N ILE A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 228 removed outlier: 3.740A pdb=" N GLU A 226 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 removed outlier: 3.728A pdb=" N LEU A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.500A pdb=" N LYS A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.692A pdb=" N ALA A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 297 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.867A pdb=" N CYS A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 135 through 139 removed outlier: 4.072A pdb=" N ARG B 138 " --> pdb=" O ARG B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.556A pdb=" N TYR B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 removed outlier: 4.092A pdb=" N GLU B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.558A pdb=" N PHE B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG B 198 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 225 removed outlier: 3.977A pdb=" N LEU B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 255 removed outlier: 3.621A pdb=" N VAL B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 315 removed outlier: 3.566A pdb=" N LEU B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 304 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TRP B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 312 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 326 through 331 removed outlier: 4.222A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 335 Processing helix chain 'B' and resid 336 through 347 removed outlier: 3.774A pdb=" N THR B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 343 " --> pdb=" O TYR B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 369 removed outlier: 3.624A pdb=" N ARG B 364 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 380 removed outlier: 4.129A pdb=" N ARG B 373 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 374 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 376 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 378 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 393 removed outlier: 4.002A pdb=" N GLN B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 421 removed outlier: 3.626A pdb=" N GLY B 399 " --> pdb=" O MET B 395 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 407 " --> pdb=" O PHE B 403 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 443 Processing helix chain 'B' and resid 454 through 471 removed outlier: 4.107A pdb=" N VAL B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 492 removed outlier: 3.925A pdb=" N ARG B 489 " --> pdb=" O TYR B 485 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 490 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 491 " --> pdb=" O TYR B 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 78 Processing helix chain 'C' and resid 96 through 107 removed outlier: 3.786A pdb=" N ILE C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.554A pdb=" N LEU C 113 " --> pdb=" O ARG C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 removed outlier: 4.004A pdb=" N ARG C 129 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.696A pdb=" N ILE C 137 " --> pdb=" O ARG C 133 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 179 removed outlier: 3.671A pdb=" N THR C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 205 removed outlier: 3.878A pdb=" N ILE C 195 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET C 196 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 228 removed outlier: 3.740A pdb=" N GLU C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 removed outlier: 3.727A pdb=" N LEU C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS C 234 " --> pdb=" O PRO C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 removed outlier: 3.500A pdb=" N LYS C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 290 through 299 removed outlier: 3.691A pdb=" N ALA C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 312 removed outlier: 3.868A pdb=" N CYS C 311 " --> pdb=" O ALA C 307 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 335 Processing helix chain 'C' and resid 339 through 343 Processing helix chain 'C' and resid 344 through 356 Processing helix chain 'D' and resid 119 through 123 Processing helix chain 'D' and resid 135 through 139 removed outlier: 4.072A pdb=" N ARG D 138 " --> pdb=" O ARG D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 166 removed outlier: 3.556A pdb=" N TYR D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY D 166 " --> pdb=" O TYR D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 removed outlier: 4.093A pdb=" N GLU D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 202 removed outlier: 3.559A pdb=" N PHE D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG D 198 " --> pdb=" O MET D 194 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 225 removed outlier: 3.979A pdb=" N LEU D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE D 224 " --> pdb=" O VAL D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 255 removed outlier: 3.620A pdb=" N VAL D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 315 removed outlier: 3.565A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 304 " --> pdb=" O THR D 300 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TRP D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 310 " --> pdb=" O PHE D 306 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL D 312 " --> pdb=" O PHE D 308 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE D 315 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 326 through 331 removed outlier: 4.222A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 335 Processing helix chain 'D' and resid 336 through 347 removed outlier: 3.773A pdb=" N THR D 342 " --> pdb=" O PRO D 338 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU D 343 " --> pdb=" O TYR D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 369 removed outlier: 3.624A pdb=" N ARG D 364 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 380 removed outlier: 4.129A pdb=" N ARG D 373 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 374 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS D 376 " --> pdb=" O ARG D 373 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D 378 " --> pdb=" O PHE D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 393 removed outlier: 4.002A pdb=" N GLN D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 421 removed outlier: 3.626A pdb=" N GLY D 399 " --> pdb=" O MET D 395 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 407 " --> pdb=" O PHE D 403 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER D 413 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 443 Processing helix chain 'D' and resid 454 through 471 removed outlier: 4.107A pdb=" N VAL D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 492 removed outlier: 3.925A pdb=" N ARG D 489 " --> pdb=" O TYR D 485 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU D 490 " --> pdb=" O PHE D 486 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR D 491 " --> pdb=" O TYR D 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 78 Processing helix chain 'E' and resid 96 through 107 removed outlier: 3.786A pdb=" N ILE E 102 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 removed outlier: 3.556A pdb=" N LEU E 113 " --> pdb=" O ARG E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 129 removed outlier: 4.005A pdb=" N ARG E 129 " --> pdb=" O GLU E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 147 removed outlier: 3.697A pdb=" N ILE E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 179 removed outlier: 3.672A pdb=" N THR E 169 " --> pdb=" O PRO E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 205 removed outlier: 3.877A pdb=" N ILE E 195 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA E 202 " --> pdb=" O ALA E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 228 removed outlier: 3.740A pdb=" N GLU E 226 " --> pdb=" O ARG E 222 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL E 227 " --> pdb=" O GLU E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 236 removed outlier: 3.728A pdb=" N LEU E 232 " --> pdb=" O GLN E 228 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS E 234 " --> pdb=" O PRO E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 278 removed outlier: 3.500A pdb=" N LYS E 276 " --> pdb=" O TRP E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 287 Processing helix chain 'E' and resid 290 through 299 removed outlier: 3.691A pdb=" N ALA E 294 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA E 296 " --> pdb=" O LEU E 292 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU E 297 " --> pdb=" O GLN E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 312 removed outlier: 3.868A pdb=" N CYS E 311 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 312 " --> pdb=" O ILE E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 335 Processing helix chain 'E' and resid 339 through 343 Processing helix chain 'E' and resid 344 through 356 Processing helix chain 'F' and resid 119 through 123 Processing helix chain 'F' and resid 135 through 139 removed outlier: 4.072A pdb=" N ARG F 138 " --> pdb=" O ARG F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 166 removed outlier: 3.555A pdb=" N TYR F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR F 163 " --> pdb=" O ILE F 159 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY F 166 " --> pdb=" O TYR F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 188 removed outlier: 4.092A pdb=" N GLU F 182 " --> pdb=" O ASP F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 202 removed outlier: 3.558A pdb=" N PHE F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG F 198 " --> pdb=" O MET F 194 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 225 removed outlier: 3.979A pdb=" N LEU F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE F 224 " --> pdb=" O VAL F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 255 removed outlier: 3.622A pdb=" N VAL F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU F 242 " --> pdb=" O ILE F 238 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE F 244 " --> pdb=" O SER F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 315 removed outlier: 3.566A pdb=" N LEU F 301 " --> pdb=" O VAL F 297 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS F 302 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE F 304 " --> pdb=" O THR F 300 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TRP F 305 " --> pdb=" O LEU F 301 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 310 " --> pdb=" O PHE F 306 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL F 312 " --> pdb=" O PHE F 308 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 326 through 331 removed outlier: 4.222A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 335 Processing helix chain 'F' and resid 336 through 347 removed outlier: 3.775A pdb=" N THR F 342 " --> pdb=" O PRO F 338 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU F 343 " --> pdb=" O TYR F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 369 removed outlier: 3.624A pdb=" N ARG F 364 " --> pdb=" O LEU F 360 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL F 365 " --> pdb=" O ALA F 361 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG F 367 " --> pdb=" O LEU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 380 removed outlier: 4.129A pdb=" N ARG F 373 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE F 374 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS F 376 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER F 378 " --> pdb=" O PHE F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 393 removed outlier: 4.002A pdb=" N GLN F 385 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 421 removed outlier: 3.629A pdb=" N GLY F 399 " --> pdb=" O MET F 395 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE F 407 " --> pdb=" O PHE F 403 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER F 413 " --> pdb=" O VAL F 409 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 419 " --> pdb=" O ALA F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 443 Processing helix chain 'F' and resid 454 through 471 removed outlier: 4.107A pdb=" N VAL F 469 " --> pdb=" O ALA F 465 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU F 470 " --> pdb=" O ILE F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 492 removed outlier: 3.925A pdb=" N ARG F 489 " --> pdb=" O TYR F 485 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU F 490 " --> pdb=" O PHE F 486 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR F 491 " --> pdb=" O TYR F 487 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 78 Processing helix chain 'G' and resid 96 through 107 removed outlier: 3.785A pdb=" N ILE G 102 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.555A pdb=" N LEU G 113 " --> pdb=" O ARG G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 129 removed outlier: 4.004A pdb=" N ARG G 129 " --> pdb=" O GLU G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 147 removed outlier: 3.696A pdb=" N ILE G 137 " --> pdb=" O ARG G 133 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU G 145 " --> pdb=" O LYS G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 179 removed outlier: 3.674A pdb=" N THR G 169 " --> pdb=" O PRO G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 205 removed outlier: 3.876A pdb=" N ILE G 195 " --> pdb=" O SER G 191 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET G 196 " --> pdb=" O SER G 192 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 228 removed outlier: 3.740A pdb=" N GLU G 226 " --> pdb=" O ARG G 222 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL G 227 " --> pdb=" O GLU G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 236 removed outlier: 3.728A pdb=" N LEU G 232 " --> pdb=" O GLN G 228 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS G 234 " --> pdb=" O PRO G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 278 removed outlier: 3.500A pdb=" N LYS G 276 " --> pdb=" O TRP G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 287 Processing helix chain 'G' and resid 290 through 299 removed outlier: 3.691A pdb=" N ALA G 294 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA G 296 " --> pdb=" O LEU G 292 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU G 297 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 312 removed outlier: 3.866A pdb=" N CYS G 311 " --> pdb=" O ALA G 307 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU G 312 " --> pdb=" O ILE G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 335 Processing helix chain 'G' and resid 339 through 343 Processing helix chain 'G' and resid 344 through 356 Processing helix chain 'H' and resid 119 through 123 Processing helix chain 'H' and resid 135 through 139 removed outlier: 4.073A pdb=" N ARG H 138 " --> pdb=" O ARG H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 166 removed outlier: 3.556A pdb=" N TYR H 161 " --> pdb=" O ASP H 157 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR H 163 " --> pdb=" O ILE H 159 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY H 166 " --> pdb=" O TYR H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 188 removed outlier: 4.093A pdb=" N GLU H 182 " --> pdb=" O ASP H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 202 removed outlier: 3.561A pdb=" N PHE H 197 " --> pdb=" O ALA H 193 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG H 198 " --> pdb=" O MET H 194 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 225 removed outlier: 3.979A pdb=" N LEU H 222 " --> pdb=" O ARG H 218 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE H 224 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 255 removed outlier: 3.621A pdb=" N VAL H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU H 242 " --> pdb=" O ILE H 238 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE H 244 " --> pdb=" O SER H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 315 removed outlier: 3.566A pdb=" N LEU H 301 " --> pdb=" O VAL H 297 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS H 302 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE H 304 " --> pdb=" O THR H 300 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TRP H 305 " --> pdb=" O LEU H 301 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 310 " --> pdb=" O PHE H 306 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL H 312 " --> pdb=" O PHE H 308 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG H 313 " --> pdb=" O GLU H 309 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE H 315 " --> pdb=" O LEU H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 324 Processing helix chain 'H' and resid 326 through 331 removed outlier: 4.221A pdb=" N LEU H 330 " --> pdb=" O ASN H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 335 Processing helix chain 'H' and resid 336 through 347 removed outlier: 3.775A pdb=" N THR H 342 " --> pdb=" O PRO H 338 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU H 343 " --> pdb=" O TYR H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 360 through 369 removed outlier: 3.625A pdb=" N ARG H 364 " --> pdb=" O LEU H 360 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL H 365 " --> pdb=" O ALA H 361 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG H 367 " --> pdb=" O LEU H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 380 removed outlier: 4.129A pdb=" N ARG H 373 " --> pdb=" O ARG H 370 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE H 374 " --> pdb=" O VAL H 371 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS H 376 " --> pdb=" O ARG H 373 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER H 378 " --> pdb=" O PHE H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 393 removed outlier: 4.002A pdb=" N GLN H 385 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE H 386 " --> pdb=" O LYS H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 421 removed outlier: 3.627A pdb=" N GLY H 399 " --> pdb=" O MET H 395 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU H 401 " --> pdb=" O GLU H 397 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE H 407 " --> pdb=" O PHE H 403 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER H 413 " --> pdb=" O VAL H 409 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA H 419 " --> pdb=" O ALA H 415 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 443 Processing helix chain 'H' and resid 454 through 471 removed outlier: 4.108A pdb=" N VAL H 469 " --> pdb=" O ALA H 465 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU H 470 " --> pdb=" O ILE H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 492 removed outlier: 3.925A pdb=" N ARG H 489 " --> pdb=" O TYR H 485 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU H 490 " --> pdb=" O PHE H 486 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR H 491 " --> pdb=" O TYR H 487 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 54 removed outlier: 7.249A pdb=" N THR A 242 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.682A pdb=" N ILE A 115 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N PHE A 156 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR A 117 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP A 153 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLY A 186 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 155 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER A 188 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA A 157 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N GLN A 214 " --> pdb=" O TRP A 185 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N THR A 187 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 118 Processing sheet with id=AA5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AA6, first strand: chain 'C' and resid 52 through 54 removed outlier: 7.249A pdb=" N THR C 242 " --> pdb=" O LEU C 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 83 through 84 removed outlier: 6.680A pdb=" N ILE C 115 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N PHE C 156 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR C 117 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP C 153 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLY C 186 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL C 155 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER C 188 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA C 157 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N GLN C 214 " --> pdb=" O TRP C 185 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N THR C 187 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 113 through 118 Processing sheet with id=AA9, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AB1, first strand: chain 'E' and resid 52 through 54 removed outlier: 7.249A pdb=" N THR E 242 " --> pdb=" O LEU E 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.682A pdb=" N ILE E 115 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N PHE E 156 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR E 117 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP E 153 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLY E 186 " --> pdb=" O ASP E 153 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL E 155 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER E 188 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA E 157 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N GLN E 214 " --> pdb=" O TRP E 185 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR E 187 " --> pdb=" O GLN E 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 113 through 118 Processing sheet with id=AB4, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AB5, first strand: chain 'G' and resid 52 through 54 removed outlier: 7.248A pdb=" N THR G 242 " --> pdb=" O LEU G 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.682A pdb=" N ILE G 115 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N PHE G 156 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR G 117 " --> pdb=" O PHE G 156 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP G 153 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLY G 186 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL G 155 " --> pdb=" O GLY G 186 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER G 188 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA G 157 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N GLN G 214 " --> pdb=" O TRP G 185 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR G 187 " --> pdb=" O GLN G 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 113 through 118 889 hydrogen bonds defined for protein. 2523 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.34 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3408 1.31 - 1.43: 5850 1.43 - 1.56: 12274 1.56 - 1.68: 20 1.68 - 1.81: 172 Bond restraints: 21724 Sorted by residual: bond pdb=" C1B NAP A 401 " pdb=" C2B NAP A 401 " ideal model delta sigma weight residual 1.528 1.309 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C1B NAP G 401 " pdb=" C2B NAP G 401 " ideal model delta sigma weight residual 1.528 1.310 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C1B NAP E 401 " pdb=" C2B NAP E 401 " ideal model delta sigma weight residual 1.528 1.310 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C1B NAP C 401 " pdb=" C2B NAP C 401 " ideal model delta sigma weight residual 1.528 1.310 0.218 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C4D NAP G 401 " pdb=" O4D NAP G 401 " ideal model delta sigma weight residual 1.447 1.305 0.142 2.00e-02 2.50e+03 5.02e+01 ... (remaining 21719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 28813 2.72 - 5.44: 567 5.44 - 8.16: 92 8.16 - 10.88: 36 10.88 - 13.59: 16 Bond angle restraints: 29524 Sorted by residual: angle pdb=" N VAL B 476 " pdb=" CA VAL B 476 " pdb=" C VAL B 476 " ideal model delta sigma weight residual 108.88 119.15 -10.27 2.16e+00 2.14e-01 2.26e+01 angle pdb=" N VAL H 476 " pdb=" CA VAL H 476 " pdb=" C VAL H 476 " ideal model delta sigma weight residual 108.88 119.13 -10.25 2.16e+00 2.14e-01 2.25e+01 angle pdb=" N VAL F 476 " pdb=" CA VAL F 476 " pdb=" C VAL F 476 " ideal model delta sigma weight residual 108.88 119.13 -10.25 2.16e+00 2.14e-01 2.25e+01 angle pdb=" N VAL D 476 " pdb=" CA VAL D 476 " pdb=" C VAL D 476 " ideal model delta sigma weight residual 108.88 119.10 -10.22 2.16e+00 2.14e-01 2.24e+01 angle pdb=" N1A NAP A 401 " pdb=" C6A NAP A 401 " pdb=" N6A NAP A 401 " ideal model delta sigma weight residual 119.30 105.71 13.59 3.00e+00 1.11e-01 2.05e+01 ... (remaining 29519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 11252 16.68 - 33.36: 1163 33.36 - 50.03: 306 50.03 - 66.71: 75 66.71 - 83.39: 36 Dihedral angle restraints: 12832 sinusoidal: 4944 harmonic: 7888 Sorted by residual: dihedral pdb=" CA ILE D 366 " pdb=" C ILE D 366 " pdb=" N ARG D 367 " pdb=" CA ARG D 367 " ideal model delta harmonic sigma weight residual 180.00 164.35 15.65 0 5.00e+00 4.00e-02 9.80e+00 dihedral pdb=" CA ILE B 366 " pdb=" C ILE B 366 " pdb=" N ARG B 367 " pdb=" CA ARG B 367 " ideal model delta harmonic sigma weight residual 180.00 164.42 15.58 0 5.00e+00 4.00e-02 9.71e+00 dihedral pdb=" CA ILE H 366 " pdb=" C ILE H 366 " pdb=" N ARG H 367 " pdb=" CA ARG H 367 " ideal model delta harmonic sigma weight residual 180.00 164.43 15.57 0 5.00e+00 4.00e-02 9.69e+00 ... (remaining 12829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3027 0.090 - 0.179: 291 0.179 - 0.269: 14 0.269 - 0.359: 8 0.359 - 0.449: 4 Chirality restraints: 3344 Sorted by residual: chirality pdb=" C2B NAP A 401 " pdb=" C1B NAP A 401 " pdb=" C3B NAP A 401 " pdb=" O2B NAP A 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.31 -0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" C2B NAP G 401 " pdb=" C1B NAP G 401 " pdb=" C3B NAP G 401 " pdb=" O2B NAP G 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.31 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C2B NAP E 401 " pdb=" C1B NAP E 401 " pdb=" C3B NAP E 401 " pdb=" O2B NAP E 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.31 -0.45 2.00e-01 2.50e+01 4.99e+00 ... (remaining 3341 not shown) Planarity restraints: 3728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE H 431 " 0.059 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO H 432 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO H 432 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO H 432 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 431 " 0.059 5.00e-02 4.00e+02 8.85e-02 1.25e+01 pdb=" N PRO F 432 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO F 432 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 432 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 431 " 0.059 5.00e-02 4.00e+02 8.84e-02 1.25e+01 pdb=" N PRO B 432 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " 0.050 5.00e-02 4.00e+02 ... (remaining 3725 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5536 2.77 - 3.31: 18922 3.31 - 3.84: 34154 3.84 - 4.37: 41705 4.37 - 4.90: 70582 Nonbonded interactions: 170899 Sorted by model distance: nonbonded pdb=" O TYR F 339 " pdb=" OG1 THR F 342 " model vdw 2.243 3.040 nonbonded pdb=" O TYR H 339 " pdb=" OG1 THR H 342 " model vdw 2.243 3.040 nonbonded pdb=" O TYR D 339 " pdb=" OG1 THR D 342 " model vdw 2.243 3.040 nonbonded pdb=" O TYR B 339 " pdb=" OG1 THR B 342 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR B 417 " pdb=" O SER B 429 " model vdw 2.286 3.040 ... (remaining 170894 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.170 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 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 : 0.011 0.219 21724 Z= 0.490 Angle : 1.032 13.594 29524 Z= 0.525 Chirality : 0.059 0.449 3344 Planarity : 0.007 0.089 3728 Dihedral : 15.694 83.390 7760 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.84 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 18.17 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.79 (0.11), residues: 2708 helix: -4.44 (0.05), residues: 1428 sheet: -3.08 (0.34), residues: 180 loop : -2.84 (0.15), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 203 TYR 0.022 0.002 TYR C 270 PHE 0.012 0.001 PHE E 60 TRP 0.020 0.002 TRP A 185 HIS 0.007 0.002 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.01071 / 0.49 (21724) covalent geometry : angle 1.03168 / 0.52 (29524) hydrogen bonds : bond 0.31164 / 20.41 ( 889) hydrogen bonds : angle 9.56818 / 6.60 ( 2523) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 548 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.8472 (tpp) cc_final: 0.8198 (tpt) REVERT: B 201 GLU cc_start: 0.7855 (tp30) cc_final: 0.7593 (tp30) REVERT: B 221 TRP cc_start: 0.5856 (t-100) cc_final: 0.5300 (t60) REVERT: B 222 LEU cc_start: 0.6578 (mm) cc_final: 0.6227 (mm) REVERT: B 242 LEU cc_start: 0.8358 (mt) cc_final: 0.8136 (mt) REVERT: B 245 LEU cc_start: 0.8383 (tt) cc_final: 0.8013 (pp) REVERT: B 488 HIS cc_start: 0.8362 (m-70) cc_final: 0.7796 (m90) REVERT: C 138 GLU cc_start: 0.7227 (mt-10) cc_final: 0.7024 (mt-10) REVERT: D 194 MET cc_start: 0.8455 (tpp) cc_final: 0.8175 (tpt) REVERT: D 201 GLU cc_start: 0.7917 (tp30) cc_final: 0.7676 (tp30) REVERT: D 221 TRP cc_start: 0.5912 (t-100) cc_final: 0.5341 (t60) REVERT: D 222 LEU cc_start: 0.6514 (mm) cc_final: 0.6170 (mm) REVERT: D 242 LEU cc_start: 0.8283 (mt) cc_final: 0.8038 (mt) REVERT: D 245 LEU cc_start: 0.8392 (tt) cc_final: 0.8008 (pp) REVERT: D 435 PHE cc_start: 0.8407 (m-10) cc_final: 0.7998 (m-80) REVERT: D 488 HIS cc_start: 0.8314 (m-70) cc_final: 0.7753 (m90) REVERT: E 138 GLU cc_start: 0.7228 (mt-10) cc_final: 0.7006 (mt-10) REVERT: F 194 MET cc_start: 0.8463 (tpp) cc_final: 0.8181 (tpt) REVERT: F 201 GLU cc_start: 0.7816 (tp30) cc_final: 0.7570 (tp30) REVERT: F 221 TRP cc_start: 0.5847 (t-100) cc_final: 0.5197 (t60) REVERT: F 222 LEU cc_start: 0.6540 (mm) cc_final: 0.6180 (mm) REVERT: F 242 LEU cc_start: 0.8355 (mt) cc_final: 0.8129 (mt) REVERT: F 245 LEU cc_start: 0.8375 (tt) cc_final: 0.8006 (pp) REVERT: F 488 HIS cc_start: 0.8377 (m-70) cc_final: 0.7813 (m90) REVERT: G 138 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6989 (mt-10) REVERT: H 194 MET cc_start: 0.8464 (tpp) cc_final: 0.8106 (tpt) REVERT: H 201 GLU cc_start: 0.7834 (tp30) cc_final: 0.7563 (tp30) REVERT: H 221 TRP cc_start: 0.5847 (t-100) cc_final: 0.5183 (t60) REVERT: H 222 LEU cc_start: 0.6591 (mm) cc_final: 0.6232 (mm) REVERT: H 242 LEU cc_start: 0.8360 (mt) cc_final: 0.8135 (mt) REVERT: H 245 LEU cc_start: 0.8296 (tt) cc_final: 0.7903 (pp) REVERT: H 488 HIS cc_start: 0.8406 (m-70) cc_final: 0.7899 (m90) outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.1661 time to fit residues: 134.4815 Evaluate side-chains 486 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 HIS A 163 ASN A 204 GLN A 333 ASN B 152 ASN B 482 ASN C 63 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS C 163 ASN C 204 GLN C 333 ASN D 152 ASN D 482 ASN E 63 GLN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 HIS E 163 ASN E 204 GLN E 333 ASN F 152 ASN F 482 ASN G 63 GLN ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 HIS G 163 ASN G 204 GLN G 333 ASN H 152 ASN H 482 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.151750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105725 restraints weight = 30584.453| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.44 r_work: 0.2980 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21724 Z= 0.143 Angle : 0.642 8.915 29524 Z= 0.325 Chirality : 0.042 0.151 3344 Planarity : 0.005 0.048 3728 Dihedral : 7.019 54.539 3036 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.88 % Favored : 97.97 % Rotamer: Outliers : 1.58 % Allowed : 20.91 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.13), residues: 2708 helix: -2.53 (0.10), residues: 1436 sheet: -2.39 (0.36), residues: 176 loop : -2.19 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 284 TYR 0.017 0.001 TYR G 270 PHE 0.015 0.001 PHE B 296 TRP 0.008 0.001 TRP A 185 HIS 0.005 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (21724) covalent geometry : angle 0.64181 / 0.33 (29524) hydrogen bonds : bond 0.05458 / 3.55 ( 889) hydrogen bonds : angle 4.57850 / 3.16 ( 2523) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 544 time to evaluate : 0.712 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: B 192 GLU cc_start: 0.8070 (tp30) cc_final: 0.7713 (tp30) REVERT: B 194 MET cc_start: 0.8457 (tpp) cc_final: 0.8105 (tpt) REVERT: B 195 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8711 (pt0) REVERT: B 221 TRP cc_start: 0.5621 (t-100) cc_final: 0.5330 (t60) REVERT: B 238 ILE cc_start: 0.8049 (tt) cc_final: 0.7640 (mp) REVERT: B 242 LEU cc_start: 0.8275 (mt) cc_final: 0.8051 (mt) REVERT: B 245 LEU cc_start: 0.8369 (tt) cc_final: 0.7952 (pp) REVERT: B 488 HIS cc_start: 0.8517 (m-70) cc_final: 0.8247 (m170) REVERT: C 138 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7715 (mt-10) REVERT: D 168 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.8124 (mtp85) REVERT: D 192 GLU cc_start: 0.8049 (tp30) cc_final: 0.7694 (tp30) REVERT: D 194 MET cc_start: 0.8474 (tpp) cc_final: 0.8106 (tpt) REVERT: D 195 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8716 (pt0) REVERT: D 221 TRP cc_start: 0.5629 (t-100) cc_final: 0.5307 (t60) REVERT: D 242 LEU cc_start: 0.8227 (mt) cc_final: 0.7990 (mt) REVERT: D 245 LEU cc_start: 0.8358 (tt) cc_final: 0.7953 (pp) REVERT: D 488 HIS cc_start: 0.8552 (m-70) cc_final: 0.8233 (m-70) REVERT: E 138 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7670 (mt-10) REVERT: F 168 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.8139 (mtp85) REVERT: F 192 GLU cc_start: 0.8040 (tp30) cc_final: 0.7686 (tp30) REVERT: F 194 MET cc_start: 0.8446 (tpp) cc_final: 0.8073 (tpt) REVERT: F 195 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8719 (pt0) REVERT: F 221 TRP cc_start: 0.5628 (t-100) cc_final: 0.5310 (t60) REVERT: F 238 ILE cc_start: 0.8053 (tt) cc_final: 0.7641 (mp) REVERT: F 488 HIS cc_start: 0.8540 (m-70) cc_final: 0.8289 (m170) REVERT: G 138 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7641 (mt-10) REVERT: H 168 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.8175 (mtp85) REVERT: H 192 GLU cc_start: 0.8115 (tp30) cc_final: 0.7774 (tp30) REVERT: H 194 MET cc_start: 0.8467 (tpp) cc_final: 0.8140 (tpt) REVERT: H 195 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8580 (pt0) REVERT: H 221 TRP cc_start: 0.5593 (t-100) cc_final: 0.5306 (t60) REVERT: H 238 ILE cc_start: 0.8039 (tt) cc_final: 0.7635 (mp) REVERT: H 488 HIS cc_start: 0.8574 (m-70) cc_final: 0.8292 (m170) outliers start: 34 outliers final: 16 residues processed: 568 average time/residue: 0.1537 time to fit residues: 131.5125 Evaluate side-chains 520 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 500 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 440 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 127 optimal weight: 6.9990 chunk 181 optimal weight: 0.3980 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 266 optimal weight: 0.8980 chunk 129 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.152868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102202 restraints weight = 30689.906| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.28 r_work: 0.3032 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21724 Z= 0.125 Angle : 0.597 8.489 29524 Z= 0.295 Chirality : 0.041 0.144 3344 Planarity : 0.005 0.043 3728 Dihedral : 6.143 52.746 3036 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.36 % Favored : 97.49 % Rotamer: Outliers : 1.95 % Allowed : 21.79 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.15), residues: 2708 helix: -1.25 (0.13), residues: 1432 sheet: -2.12 (0.36), residues: 176 loop : -1.71 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 396 TYR 0.017 0.001 TYR G 270 PHE 0.012 0.001 PHE H 412 TRP 0.006 0.001 TRP D 305 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (21724) covalent geometry : angle 0.59683 / 0.30 (29524) hydrogen bonds : bond 0.04204 / 2.71 ( 889) hydrogen bonds : angle 4.11434 / 2.84 ( 2523) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 498 time to evaluate : 0.711 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: B 109 ASN cc_start: 0.9329 (t0) cc_final: 0.9091 (t0) REVERT: B 168 ARG cc_start: 0.8396 (mtm-85) cc_final: 0.8077 (mtp85) REVERT: B 192 GLU cc_start: 0.8081 (tp30) cc_final: 0.7634 (tp30) REVERT: B 194 MET cc_start: 0.8463 (tpp) cc_final: 0.8061 (tpt) REVERT: B 195 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8522 (pt0) REVERT: B 198 ARG cc_start: 0.7667 (mtp85) cc_final: 0.7429 (mtp85) REVERT: B 221 TRP cc_start: 0.5488 (t-100) cc_final: 0.5277 (t60) REVERT: B 238 ILE cc_start: 0.8074 (tt) cc_final: 0.7629 (mp) REVERT: B 251 PHE cc_start: 0.7634 (t80) cc_final: 0.7340 (t80) REVERT: B 339 TYR cc_start: 0.6568 (t80) cc_final: 0.6346 (t80) REVERT: B 370 ARG cc_start: 0.7444 (mtp180) cc_final: 0.7193 (mtp180) REVERT: B 375 PHE cc_start: 0.8250 (m-80) cc_final: 0.7885 (m-80) REVERT: B 488 HIS cc_start: 0.8500 (m-70) cc_final: 0.8179 (m170) REVERT: D 109 ASN cc_start: 0.9324 (t0) cc_final: 0.9030 (t0) REVERT: D 168 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8081 (mtp85) REVERT: D 192 GLU cc_start: 0.8035 (tp30) cc_final: 0.7657 (tp30) REVERT: D 194 MET cc_start: 0.8404 (tpp) cc_final: 0.8004 (tpt) REVERT: D 195 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8567 (pt0) REVERT: D 221 TRP cc_start: 0.5492 (t-100) cc_final: 0.5286 (t60) REVERT: D 250 ILE cc_start: 0.8911 (pp) cc_final: 0.8597 (mm) REVERT: D 339 TYR cc_start: 0.6560 (t80) cc_final: 0.6351 (t80) REVERT: D 375 PHE cc_start: 0.8253 (m-80) cc_final: 0.7911 (m-80) REVERT: D 488 HIS cc_start: 0.8484 (m-70) cc_final: 0.8152 (m170) REVERT: F 109 ASN cc_start: 0.9314 (t0) cc_final: 0.9111 (t0) REVERT: F 168 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.8049 (mtp85) REVERT: F 192 GLU cc_start: 0.8085 (tp30) cc_final: 0.7707 (tp30) REVERT: F 194 MET cc_start: 0.8430 (tpp) cc_final: 0.8031 (tpt) REVERT: F 195 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8529 (pt0) REVERT: F 221 TRP cc_start: 0.5478 (t-100) cc_final: 0.5246 (t60) REVERT: F 238 ILE cc_start: 0.8037 (tt) cc_final: 0.7618 (mp) REVERT: F 250 ILE cc_start: 0.8899 (pt) cc_final: 0.8667 (mm) REVERT: F 251 PHE cc_start: 0.7638 (t80) cc_final: 0.7281 (t80) REVERT: F 339 TYR cc_start: 0.6517 (t80) cc_final: 0.6289 (t80) REVERT: F 370 ARG cc_start: 0.7438 (mtp180) cc_final: 0.7160 (mtp180) REVERT: F 488 HIS cc_start: 0.8515 (m-70) cc_final: 0.8218 (m170) REVERT: H 109 ASN cc_start: 0.9302 (t0) cc_final: 0.9032 (t0) REVERT: H 168 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.8044 (mtp85) REVERT: H 192 GLU cc_start: 0.8072 (tp30) cc_final: 0.7680 (tp30) REVERT: H 194 MET cc_start: 0.8463 (tpp) cc_final: 0.8070 (tpt) REVERT: H 195 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8522 (pt0) REVERT: H 221 TRP cc_start: 0.5461 (t-100) cc_final: 0.5229 (t60) REVERT: H 238 ILE cc_start: 0.8020 (tt) cc_final: 0.7613 (mp) REVERT: H 250 ILE cc_start: 0.8900 (pt) cc_final: 0.8660 (mm) REVERT: H 339 TYR cc_start: 0.6558 (t80) cc_final: 0.6335 (t80) REVERT: H 488 HIS cc_start: 0.8567 (m-70) cc_final: 0.8256 (m170) outliers start: 42 outliers final: 24 residues processed: 526 average time/residue: 0.1557 time to fit residues: 123.6524 Evaluate side-chains 490 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 462 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 462 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 169 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 224 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 98 optimal weight: 0.3980 chunk 87 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.152195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105847 restraints weight = 30804.087| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.58 r_work: 0.2996 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21724 Z= 0.158 Angle : 0.596 9.250 29524 Z= 0.294 Chirality : 0.043 0.222 3344 Planarity : 0.004 0.057 3728 Dihedral : 5.745 59.476 3036 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.03 % Favored : 96.82 % Rotamer: Outliers : 3.90 % Allowed : 21.42 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.16), residues: 2708 helix: -0.56 (0.13), residues: 1432 sheet: -1.90 (0.35), residues: 176 loop : -1.43 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 396 TYR 0.017 0.001 TYR G 270 PHE 0.011 0.001 PHE F 404 TRP 0.008 0.001 TRP G 185 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (21724) covalent geometry : angle 0.59599 / 0.29 (29524) hydrogen bonds : bond 0.04072 / 2.62 ( 889) hydrogen bonds : angle 3.97070 / 2.74 ( 2523) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 480 time to evaluate : 1.011 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: B 168 ARG cc_start: 0.8438 (mtm-85) cc_final: 0.8107 (mtp85) REVERT: B 192 GLU cc_start: 0.8038 (tp30) cc_final: 0.7664 (tp30) REVERT: B 194 MET cc_start: 0.8494 (tpp) cc_final: 0.8020 (tpt) REVERT: B 195 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8497 (pt0) REVERT: B 221 TRP cc_start: 0.5514 (t-100) cc_final: 0.5217 (t60) REVERT: B 238 ILE cc_start: 0.7996 (tt) cc_final: 0.7588 (mp) REVERT: B 250 ILE cc_start: 0.8992 (pp) cc_final: 0.8699 (mm) REVERT: B 251 PHE cc_start: 0.7683 (t80) cc_final: 0.7407 (t80) REVERT: B 339 TYR cc_start: 0.6496 (t80) cc_final: 0.6285 (t80) REVERT: B 375 PHE cc_start: 0.8285 (m-80) cc_final: 0.7917 (m-80) REVERT: B 488 HIS cc_start: 0.8526 (m-70) cc_final: 0.8321 (m90) REVERT: D 168 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8098 (mtp85) REVERT: D 192 GLU cc_start: 0.8075 (tp30) cc_final: 0.7710 (tp30) REVERT: D 194 MET cc_start: 0.8466 (tpp) cc_final: 0.8012 (tpt) REVERT: D 195 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8531 (pt0) REVERT: D 221 TRP cc_start: 0.5493 (t-100) cc_final: 0.5207 (t60) REVERT: D 238 ILE cc_start: 0.7991 (tt) cc_final: 0.7563 (mp) REVERT: D 250 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8837 (mm) REVERT: D 339 TYR cc_start: 0.6529 (t80) cc_final: 0.6295 (t80) REVERT: D 341 ILE cc_start: 0.7990 (mm) cc_final: 0.7760 (mt) REVERT: D 375 PHE cc_start: 0.8258 (m-80) cc_final: 0.7894 (m-80) REVERT: D 488 HIS cc_start: 0.8475 (m-70) cc_final: 0.8254 (m90) REVERT: F 168 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.8079 (mtp85) REVERT: F 192 GLU cc_start: 0.8018 (tp30) cc_final: 0.7641 (tp30) REVERT: F 194 MET cc_start: 0.8469 (tpp) cc_final: 0.8021 (tpt) REVERT: F 195 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8500 (pt0) REVERT: F 221 TRP cc_start: 0.5489 (t-100) cc_final: 0.5260 (t60) REVERT: F 238 ILE cc_start: 0.7889 (tt) cc_final: 0.7471 (mp) REVERT: F 339 TYR cc_start: 0.6553 (t80) cc_final: 0.6338 (t80) REVERT: F 375 PHE cc_start: 0.8272 (m-80) cc_final: 0.7907 (m-80) REVERT: F 488 HIS cc_start: 0.8501 (m-70) cc_final: 0.8196 (m170) REVERT: H 192 GLU cc_start: 0.8059 (tp30) cc_final: 0.7693 (tp30) REVERT: H 194 MET cc_start: 0.8487 (tpp) cc_final: 0.8070 (tpt) REVERT: H 195 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8465 (pt0) REVERT: H 221 TRP cc_start: 0.5480 (t-100) cc_final: 0.5260 (t60) REVERT: H 238 ILE cc_start: 0.7896 (tt) cc_final: 0.7494 (mp) REVERT: H 339 TYR cc_start: 0.6510 (t80) cc_final: 0.6300 (t80) REVERT: H 488 HIS cc_start: 0.8539 (m-70) cc_final: 0.8254 (m170) outliers start: 84 outliers final: 40 residues processed: 531 average time/residue: 0.1685 time to fit residues: 133.5171 Evaluate side-chains 518 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 473 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 462 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 124 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 chunk 200 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 GLN C 305 GLN D 482 ASN E 305 GLN G 305 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.153097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.102558 restraints weight = 30599.622| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.30 r_work: 0.3009 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21724 Z= 0.139 Angle : 0.587 9.244 29524 Z= 0.291 Chirality : 0.042 0.285 3344 Planarity : 0.004 0.047 3728 Dihedral : 5.561 58.514 3036 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.21 % Allowed : 22.82 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.16), residues: 2708 helix: -0.29 (0.14), residues: 1456 sheet: -1.94 (0.35), residues: 176 loop : -1.35 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 114 TYR 0.017 0.001 TYR H 487 PHE 0.011 0.001 PHE F 203 TRP 0.007 0.001 TRP A 185 HIS 0.004 0.001 HIS G 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (21724) covalent geometry : angle 0.58745 / 0.29 (29524) hydrogen bonds : bond 0.03793 / 2.44 ( 889) hydrogen bonds : angle 3.86524 / 2.67 ( 2523) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 498 time to evaluate : 0.834 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: B 109 ASN cc_start: 0.9332 (t0) cc_final: 0.9086 (t0) REVERT: B 168 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8073 (mtp85) REVERT: B 192 GLU cc_start: 0.8061 (tp30) cc_final: 0.7703 (tp30) REVERT: B 194 MET cc_start: 0.8432 (tpp) cc_final: 0.8098 (tpt) REVERT: B 195 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8532 (pt0) REVERT: B 221 TRP cc_start: 0.5479 (t-100) cc_final: 0.5240 (t60) REVERT: B 238 ILE cc_start: 0.7864 (tt) cc_final: 0.7485 (mp) REVERT: B 250 ILE cc_start: 0.9010 (pp) cc_final: 0.8707 (mm) REVERT: B 339 TYR cc_start: 0.6497 (t80) cc_final: 0.6291 (t80) REVERT: B 375 PHE cc_start: 0.8272 (m-80) cc_final: 0.7916 (m-80) REVERT: B 396 ARG cc_start: 0.8621 (ptp-110) cc_final: 0.8366 (ptm-80) REVERT: B 488 HIS cc_start: 0.8506 (m-70) cc_final: 0.8302 (m90) REVERT: C 280 GLU cc_start: 0.8532 (pp20) cc_final: 0.8202 (mm-30) REVERT: D 168 ARG cc_start: 0.8410 (mtm-85) cc_final: 0.8084 (mtp85) REVERT: D 192 GLU cc_start: 0.8125 (tp30) cc_final: 0.7713 (tp30) REVERT: D 194 MET cc_start: 0.8424 (tpp) cc_final: 0.8078 (tpt) REVERT: D 195 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8540 (pt0) REVERT: D 221 TRP cc_start: 0.5381 (t-100) cc_final: 0.5161 (t60) REVERT: D 238 ILE cc_start: 0.7881 (tt) cc_final: 0.7488 (mp) REVERT: D 250 ILE cc_start: 0.8989 (pp) cc_final: 0.8719 (mm) REVERT: D 251 PHE cc_start: 0.7396 (t80) cc_final: 0.7160 (t80) REVERT: D 339 TYR cc_start: 0.6495 (t80) cc_final: 0.6264 (t80) REVERT: D 341 ILE cc_start: 0.8001 (mm) cc_final: 0.7754 (mt) REVERT: D 375 PHE cc_start: 0.8241 (m-80) cc_final: 0.7890 (m-80) REVERT: D 488 HIS cc_start: 0.8448 (m-70) cc_final: 0.8230 (m90) REVERT: E 284 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7650 (mtm180) REVERT: F 192 GLU cc_start: 0.8105 (tp30) cc_final: 0.7733 (tp30) REVERT: F 194 MET cc_start: 0.8426 (tpp) cc_final: 0.8094 (tpt) REVERT: F 195 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8537 (pt0) REVERT: F 221 TRP cc_start: 0.5484 (t-100) cc_final: 0.5215 (t60) REVERT: F 238 ILE cc_start: 0.7900 (tt) cc_final: 0.7518 (mp) REVERT: F 339 TYR cc_start: 0.6514 (t80) cc_final: 0.6304 (t80) REVERT: F 375 PHE cc_start: 0.8275 (m-80) cc_final: 0.7923 (m-80) REVERT: F 488 HIS cc_start: 0.8504 (m-70) cc_final: 0.8299 (m90) REVERT: G 284 ARG cc_start: 0.8064 (mtp180) cc_final: 0.7679 (mtm180) REVERT: H 109 ASN cc_start: 0.9321 (t0) cc_final: 0.9054 (t0) REVERT: H 168 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8061 (mtp85) REVERT: H 192 GLU cc_start: 0.8105 (tp30) cc_final: 0.7684 (tp30) REVERT: H 194 MET cc_start: 0.8417 (tpp) cc_final: 0.8069 (tpt) REVERT: H 195 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8466 (pt0) REVERT: H 221 TRP cc_start: 0.5509 (t-100) cc_final: 0.5238 (t60) REVERT: H 238 ILE cc_start: 0.7885 (tt) cc_final: 0.7509 (mp) REVERT: H 339 TYR cc_start: 0.6484 (t80) cc_final: 0.6270 (t80) REVERT: H 375 PHE cc_start: 0.8257 (m-80) cc_final: 0.7892 (m-80) REVERT: H 398 LEU cc_start: 0.9016 (mt) cc_final: 0.8807 (mm) REVERT: H 488 HIS cc_start: 0.8498 (m-70) cc_final: 0.8297 (m90) outliers start: 69 outliers final: 43 residues processed: 534 average time/residue: 0.1526 time to fit residues: 124.8151 Evaluate side-chains 521 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 474 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain F residue 484 ASN Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 462 SER Chi-restraints excluded: chain H residue 484 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 40 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 173 optimal weight: 0.0370 chunk 179 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 225 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.154004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.106083 restraints weight = 30450.838| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.27 r_work: 0.3038 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21724 Z= 0.119 Angle : 0.569 8.252 29524 Z= 0.282 Chirality : 0.041 0.155 3344 Planarity : 0.004 0.045 3728 Dihedral : 5.324 55.840 3036 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.81 % Allowed : 22.91 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.16), residues: 2708 helix: -0.04 (0.14), residues: 1480 sheet: -1.78 (0.35), residues: 176 loop : -1.32 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 114 TYR 0.016 0.001 TYR F 487 PHE 0.015 0.001 PHE H 412 TRP 0.007 0.001 TRP G 185 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (21724) covalent geometry : angle 0.56891 / 0.28 (29524) hydrogen bonds : bond 0.03569 / 2.30 ( 889) hydrogen bonds : angle 3.77601 / 2.60 ( 2523) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 490 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.8079 (tp30) cc_final: 0.7812 (tp30) REVERT: B 194 MET cc_start: 0.8437 (tpp) cc_final: 0.8123 (tpt) REVERT: B 195 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8537 (pt0) REVERT: B 250 ILE cc_start: 0.8980 (pp) cc_final: 0.8691 (mm) REVERT: B 339 TYR cc_start: 0.6421 (t80) cc_final: 0.6208 (t80) REVERT: B 375 PHE cc_start: 0.8348 (m-80) cc_final: 0.8005 (m-80) REVERT: B 450 MET cc_start: 0.6825 (mmp) cc_final: 0.6332 (mmm) REVERT: D 109 ASN cc_start: 0.9324 (t0) cc_final: 0.9041 (t0) REVERT: D 168 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.8057 (mtp85) REVERT: D 192 GLU cc_start: 0.8053 (tp30) cc_final: 0.7528 (tp30) REVERT: D 194 MET cc_start: 0.8438 (tpp) cc_final: 0.8130 (tpt) REVERT: D 195 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8344 (pt0) REVERT: D 238 ILE cc_start: 0.7892 (tt) cc_final: 0.7485 (mp) REVERT: D 250 ILE cc_start: 0.9038 (pp) cc_final: 0.8783 (mm) REVERT: D 339 TYR cc_start: 0.6472 (t80) cc_final: 0.6222 (t80) REVERT: D 341 ILE cc_start: 0.8048 (mm) cc_final: 0.7770 (mt) REVERT: D 375 PHE cc_start: 0.8329 (m-80) cc_final: 0.7991 (m-80) REVERT: E 292 LEU cc_start: 0.9472 (mt) cc_final: 0.9267 (mt) REVERT: F 109 ASN cc_start: 0.9320 (t0) cc_final: 0.9029 (t0) REVERT: F 168 ARG cc_start: 0.8363 (mtm-85) cc_final: 0.8050 (mtp85) REVERT: F 192 GLU cc_start: 0.8101 (tp30) cc_final: 0.7794 (tp30) REVERT: F 194 MET cc_start: 0.8437 (tpp) cc_final: 0.8103 (tpt) REVERT: F 195 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8541 (pt0) REVERT: F 339 TYR cc_start: 0.6475 (t80) cc_final: 0.6260 (t80) REVERT: F 341 ILE cc_start: 0.8008 (mm) cc_final: 0.7808 (mt) REVERT: F 375 PHE cc_start: 0.8274 (m-80) cc_final: 0.7961 (m-80) REVERT: H 109 ASN cc_start: 0.9319 (t0) cc_final: 0.9063 (t0) REVERT: H 192 GLU cc_start: 0.8035 (tp30) cc_final: 0.7590 (tp30) REVERT: H 194 MET cc_start: 0.8431 (tpp) cc_final: 0.8073 (tpt) REVERT: H 195 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8501 (pt0) REVERT: H 339 TYR cc_start: 0.6442 (t80) cc_final: 0.6224 (t80) REVERT: H 375 PHE cc_start: 0.8266 (m-80) cc_final: 0.7956 (m-80) REVERT: H 396 ARG cc_start: 0.8570 (ptp-110) cc_final: 0.8086 (ptm-80) REVERT: H 403 PHE cc_start: 0.8185 (t80) cc_final: 0.7819 (t80) REVERT: H 488 HIS cc_start: 0.8463 (m-70) cc_final: 0.8263 (m90) outliers start: 82 outliers final: 57 residues processed: 541 average time/residue: 0.1500 time to fit residues: 124.9414 Evaluate side-chains 539 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 478 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 462 SER Chi-restraints excluded: chain H residue 484 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 178 optimal weight: 0.3980 chunk 258 optimal weight: 0.6980 chunk 191 optimal weight: 0.8980 chunk 235 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 265 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 267 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.154294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104254 restraints weight = 30292.647| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.35 r_work: 0.3026 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21724 Z= 0.119 Angle : 0.583 8.464 29524 Z= 0.286 Chirality : 0.041 0.231 3344 Planarity : 0.004 0.044 3728 Dihedral : 5.234 54.316 3036 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.58 % Allowed : 23.42 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.16), residues: 2708 helix: 0.09 (0.14), residues: 1480 sheet: -1.59 (0.36), residues: 176 loop : -1.29 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 114 TYR 0.015 0.001 TYR C 270 PHE 0.019 0.001 PHE F 412 TRP 0.038 0.001 TRP H 221 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (21724) covalent geometry : angle 0.58270 / 0.29 (29524) hydrogen bonds : bond 0.03558 / 2.30 ( 889) hydrogen bonds : angle 3.70404 / 2.56 ( 2523) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 493 time to evaluate : 0.820 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 128 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8367 (mt-10) REVERT: B 192 GLU cc_start: 0.8148 (tp30) cc_final: 0.7736 (tp30) REVERT: B 194 MET cc_start: 0.8436 (tpp) cc_final: 0.8140 (tpt) REVERT: B 195 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8560 (pt0) REVERT: B 250 ILE cc_start: 0.8994 (pp) cc_final: 0.8664 (mm) REVERT: B 339 TYR cc_start: 0.6431 (t80) cc_final: 0.6230 (t80) REVERT: B 375 PHE cc_start: 0.8381 (m-80) cc_final: 0.8057 (m-80) REVERT: B 450 MET cc_start: 0.6836 (mmp) cc_final: 0.6369 (mmm) REVERT: D 109 ASN cc_start: 0.9310 (t0) cc_final: 0.9041 (t0) REVERT: D 168 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.8062 (mtp85) REVERT: D 192 GLU cc_start: 0.7970 (tp30) cc_final: 0.7732 (tp30) REVERT: D 194 MET cc_start: 0.8460 (tpp) cc_final: 0.8133 (tpt) REVERT: D 195 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8562 (pt0) REVERT: D 339 TYR cc_start: 0.6439 (t80) cc_final: 0.6233 (t80) REVERT: D 341 ILE cc_start: 0.8082 (mm) cc_final: 0.7794 (mt) REVERT: D 375 PHE cc_start: 0.8381 (m-80) cc_final: 0.8055 (m-80) REVERT: D 450 MET cc_start: 0.6831 (mmp) cc_final: 0.6372 (mmm) REVERT: D 488 HIS cc_start: 0.8433 (m90) cc_final: 0.8136 (m-70) REVERT: F 109 ASN cc_start: 0.9331 (t0) cc_final: 0.9058 (t0) REVERT: F 168 ARG cc_start: 0.8396 (mtm-85) cc_final: 0.8079 (mtp85) REVERT: F 192 GLU cc_start: 0.8121 (tp30) cc_final: 0.7902 (tp30) REVERT: F 194 MET cc_start: 0.8433 (tpp) cc_final: 0.8117 (tpt) REVERT: F 195 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8541 (pt0) REVERT: F 339 TYR cc_start: 0.6455 (t80) cc_final: 0.6248 (t80) REVERT: F 341 ILE cc_start: 0.8061 (mm) cc_final: 0.7853 (mt) REVERT: F 375 PHE cc_start: 0.8308 (m-80) cc_final: 0.8003 (m-80) REVERT: F 450 MET cc_start: 0.6878 (mmp) cc_final: 0.6389 (mmm) REVERT: H 109 ASN cc_start: 0.9330 (t0) cc_final: 0.9078 (t0) REVERT: H 192 GLU cc_start: 0.7917 (tp30) cc_final: 0.7657 (tp30) REVERT: H 194 MET cc_start: 0.8450 (tpp) cc_final: 0.8112 (tpt) REVERT: H 195 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8644 (pt0) REVERT: H 251 PHE cc_start: 0.7390 (t80) cc_final: 0.7186 (t80) REVERT: H 339 TYR cc_start: 0.6427 (t80) cc_final: 0.6208 (t80) REVERT: H 375 PHE cc_start: 0.8294 (m-80) cc_final: 0.7985 (m-80) REVERT: H 403 PHE cc_start: 0.8154 (t80) cc_final: 0.7770 (t80) outliers start: 77 outliers final: 67 residues processed: 541 average time/residue: 0.1457 time to fit residues: 121.2490 Evaluate side-chains 557 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 486 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain F residue 484 ASN Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 462 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 65 optimal weight: 0.9990 chunk 206 optimal weight: 0.7980 chunk 166 optimal weight: 0.4980 chunk 177 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 114 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 163 optimal weight: 0.4980 chunk 188 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 HIS B 488 HIS D 482 ASN E 175 HIS F 488 HIS H 482 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.155035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113749 restraints weight = 29985.416| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.38 r_work: 0.3073 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21724 Z= 0.115 Angle : 0.577 8.603 29524 Z= 0.285 Chirality : 0.041 0.161 3344 Planarity : 0.004 0.043 3728 Dihedral : 5.141 53.271 3036 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.39 % Allowed : 23.93 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.16), residues: 2708 helix: 0.24 (0.14), residues: 1480 sheet: -1.42 (0.36), residues: 176 loop : -1.24 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 114 TYR 0.014 0.001 TYR F 487 PHE 0.018 0.001 PHE B 412 TRP 0.045 0.001 TRP H 221 HIS 0.005 0.001 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (21724) covalent geometry : angle 0.57681 / 0.29 (29524) hydrogen bonds : bond 0.03470 / 2.25 ( 889) hydrogen bonds : angle 3.68080 / 2.54 ( 2523) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 506 time to evaluate : 0.727 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: A 128 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 192 GLU cc_start: 0.7926 (tp30) cc_final: 0.7693 (tp30) REVERT: B 194 MET cc_start: 0.8451 (tpp) cc_final: 0.8136 (tpt) REVERT: B 195 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8529 (pt0) REVERT: B 250 ILE cc_start: 0.8984 (pp) cc_final: 0.8574 (mm) REVERT: B 251 PHE cc_start: 0.7376 (t80) cc_final: 0.7138 (t80) REVERT: B 375 PHE cc_start: 0.8395 (m-80) cc_final: 0.8096 (m-80) REVERT: D 109 ASN cc_start: 0.9264 (t0) cc_final: 0.9004 (t0) REVERT: D 192 GLU cc_start: 0.7917 (tp30) cc_final: 0.7648 (tp30) REVERT: D 194 MET cc_start: 0.8440 (tpp) cc_final: 0.8149 (tpt) REVERT: D 195 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: D 198 ARG cc_start: 0.7462 (mtp85) cc_final: 0.7246 (ttm110) REVERT: D 339 TYR cc_start: 0.6394 (t80) cc_final: 0.6184 (t80) REVERT: D 341 ILE cc_start: 0.8086 (mm) cc_final: 0.7797 (mt) REVERT: D 375 PHE cc_start: 0.8393 (m-80) cc_final: 0.8098 (m-80) REVERT: F 109 ASN cc_start: 0.9298 (t0) cc_final: 0.9030 (t0) REVERT: F 168 ARG cc_start: 0.8357 (mtm-85) cc_final: 0.8057 (mtp85) REVERT: F 192 GLU cc_start: 0.8101 (tp30) cc_final: 0.7870 (tp30) REVERT: F 194 MET cc_start: 0.8427 (tpp) cc_final: 0.8121 (tpt) REVERT: F 195 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8501 (pt0) REVERT: F 339 TYR cc_start: 0.6416 (t80) cc_final: 0.6198 (t80) REVERT: F 341 ILE cc_start: 0.8020 (mm) cc_final: 0.7795 (mt) REVERT: F 375 PHE cc_start: 0.8270 (m-80) cc_final: 0.7978 (m-80) REVERT: H 109 ASN cc_start: 0.9296 (t0) cc_final: 0.9047 (t0) REVERT: H 168 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.8059 (mtp85) REVERT: H 192 GLU cc_start: 0.7965 (tp30) cc_final: 0.7729 (tp30) REVERT: H 194 MET cc_start: 0.8441 (tpp) cc_final: 0.8101 (tpt) REVERT: H 195 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8500 (pt0) REVERT: H 339 TYR cc_start: 0.6354 (t80) cc_final: 0.6126 (t80) REVERT: H 375 PHE cc_start: 0.8236 (m-80) cc_final: 0.7932 (m-80) outliers start: 73 outliers final: 61 residues processed: 554 average time/residue: 0.1428 time to fit residues: 121.0796 Evaluate side-chains 555 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 490 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 462 SER Chi-restraints excluded: chain H residue 484 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 93 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 223 optimal weight: 0.1980 chunk 116 optimal weight: 5.9990 chunk 258 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 482 ASN B 488 HIS D 488 HIS F 488 HIS H 488 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.154043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103578 restraints weight = 30288.739| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.17 r_work: 0.3050 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21724 Z= 0.138 Angle : 0.594 9.641 29524 Z= 0.293 Chirality : 0.042 0.164 3344 Planarity : 0.004 0.042 3728 Dihedral : 5.198 52.920 3036 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.49 % Allowed : 24.81 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2708 helix: 0.30 (0.14), residues: 1480 sheet: -1.36 (0.36), residues: 176 loop : -1.23 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 370 TYR 0.015 0.001 TYR G 270 PHE 0.015 0.001 PHE B 412 TRP 0.032 0.001 TRP H 221 HIS 0.005 0.001 HIS H 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (21724) covalent geometry : angle 0.59380 / 0.29 (29524) hydrogen bonds : bond 0.03636 / 2.36 ( 889) hydrogen bonds : angle 3.71997 / 2.56 ( 2523) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 484 time to evaluate : 0.816 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 284 ARG cc_start: 0.7980 (mtp180) cc_final: 0.7711 (mpp80) REVERT: B 168 ARG cc_start: 0.8383 (mtm-85) cc_final: 0.8057 (mtp85) REVERT: B 192 GLU cc_start: 0.7945 (tp30) cc_final: 0.7701 (tp30) REVERT: B 194 MET cc_start: 0.8467 (tpp) cc_final: 0.8159 (tpt) REVERT: B 195 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8640 (pt0) REVERT: B 375 PHE cc_start: 0.8414 (m-80) cc_final: 0.8097 (m-80) REVERT: D 109 ASN cc_start: 0.9294 (t0) cc_final: 0.9009 (t0) REVERT: D 168 ARG cc_start: 0.8389 (mtm-85) cc_final: 0.8058 (mtp85) REVERT: D 192 GLU cc_start: 0.7946 (tp30) cc_final: 0.7714 (tp30) REVERT: D 194 MET cc_start: 0.8461 (tpp) cc_final: 0.8154 (tpt) REVERT: D 195 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8593 (pt0) REVERT: D 339 TYR cc_start: 0.6373 (t80) cc_final: 0.6152 (t80) REVERT: D 341 ILE cc_start: 0.8087 (mm) cc_final: 0.7796 (mt) REVERT: D 375 PHE cc_start: 0.8414 (m-80) cc_final: 0.8103 (m-80) REVERT: F 104 GLU cc_start: 0.8404 (pm20) cc_final: 0.8187 (pm20) REVERT: F 168 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.8064 (mtp85) REVERT: F 192 GLU cc_start: 0.8144 (tp30) cc_final: 0.7901 (tp30) REVERT: F 194 MET cc_start: 0.8447 (tpp) cc_final: 0.8131 (tpt) REVERT: F 195 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8606 (pt0) REVERT: F 341 ILE cc_start: 0.8052 (mm) cc_final: 0.7818 (mt) REVERT: F 375 PHE cc_start: 0.8298 (m-80) cc_final: 0.7993 (m-80) REVERT: H 168 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.8064 (mtp85) REVERT: H 192 GLU cc_start: 0.7981 (tp30) cc_final: 0.7740 (tp30) REVERT: H 194 MET cc_start: 0.8456 (tpp) cc_final: 0.8130 (tpt) REVERT: H 195 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8613 (pt0) REVERT: H 339 TYR cc_start: 0.6327 (t80) cc_final: 0.6089 (t80) REVERT: H 375 PHE cc_start: 0.8285 (m-80) cc_final: 0.7984 (m-80) outliers start: 75 outliers final: 67 residues processed: 536 average time/residue: 0.1468 time to fit residues: 119.8085 Evaluate side-chains 554 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 483 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain F residue 484 ASN Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 462 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.3386 > 50: distance: 6 - 72: 27.908 distance: 59 - 64: 12.510 distance: 64 - 65: 9.710 distance: 65 - 66: 12.775 distance: 65 - 68: 13.344 distance: 66 - 67: 9.235 distance: 66 - 72: 3.826 distance: 68 - 69: 13.087 distance: 68 - 70: 11.288 distance: 69 - 71: 5.674 distance: 72 - 73: 6.499 distance: 73 - 74: 10.482 distance: 73 - 76: 11.671 distance: 74 - 75: 34.267 distance: 74 - 79: 7.165 distance: 76 - 77: 25.639 distance: 76 - 78: 37.637 distance: 79 - 80: 4.749 distance: 80 - 81: 46.681 distance: 80 - 83: 25.349 distance: 81 - 82: 10.161 distance: 81 - 86: 22.697 distance: 83 - 84: 11.214 distance: 83 - 85: 47.256 distance: 86 - 87: 13.997 distance: 87 - 88: 15.816 distance: 87 - 90: 19.956 distance: 88 - 89: 5.985 distance: 88 - 95: 18.013 distance: 90 - 91: 10.328 distance: 91 - 92: 21.307 distance: 92 - 93: 4.711 distance: 93 - 94: 14.969 distance: 96 - 97: 4.860 distance: 96 - 99: 8.717 distance: 97 - 98: 3.388 distance: 97 - 103: 12.676 distance: 99 - 100: 5.885 distance: 99 - 101: 21.771 distance: 100 - 102: 14.382 distance: 103 - 104: 5.517 distance: 104 - 105: 11.107 distance: 104 - 107: 7.888 distance: 105 - 106: 8.733 distance: 105 - 114: 12.668 distance: 107 - 108: 11.021 distance: 108 - 109: 6.263 distance: 108 - 110: 8.961 distance: 109 - 111: 14.152 distance: 110 - 112: 8.170 distance: 111 - 113: 15.175 distance: 112 - 113: 6.349 distance: 114 - 115: 9.408 distance: 115 - 116: 10.544 distance: 115 - 118: 9.405 distance: 116 - 117: 15.976 distance: 116 - 128: 13.007 distance: 118 - 119: 4.393 distance: 119 - 120: 16.013 distance: 119 - 121: 11.681 distance: 120 - 122: 9.773 distance: 121 - 123: 4.717 distance: 121 - 124: 12.867 distance: 122 - 123: 6.321 distance: 123 - 125: 8.490 distance: 124 - 126: 11.022 distance: 125 - 127: 7.103 distance: 126 - 127: 14.610 distance: 128 - 129: 8.554 distance: 129 - 130: 22.023 distance: 130 - 131: 8.262 distance: 130 - 132: 10.087 distance: 132 - 133: 12.383 distance: 133 - 134: 25.820 distance: 134 - 135: 29.204 distance: 134 - 136: 8.883 distance: 136 - 137: 10.715 distance: 137 - 138: 10.934 distance: 137 - 140: 9.830 distance: 138 - 139: 3.569 distance: 138 - 145: 4.903 distance: 140 - 141: 8.452 distance: 141 - 142: 11.631 distance: 142 - 143: 6.260 distance: 143 - 144: 5.616