Starting phenix.real_space_refine on Tue Jan 14 02:45:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xav_38204/01_2025/8xav_38204.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xav_38204/01_2025/8xav_38204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xav_38204/01_2025/8xav_38204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xav_38204/01_2025/8xav_38204.map" model { file = "/net/cci-nas-00/data/ceres_data/8xav_38204/01_2025/8xav_38204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xav_38204/01_2025/8xav_38204.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 30870 2.51 5 N 8038 2.21 5 O 9272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 48264 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4539 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 545} Chain: "B" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4539 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 545} Chain: "C" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4539 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 545} Chain: "D" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4539 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 545} Chain: "E" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4518 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 542} Chain: "F" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4518 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 542} Chain: "G" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "H" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "I" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "J" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "K" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "L" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "M" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "N" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "O" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "P" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "Q" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "R" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Time building chain proxies: 20.24, per 1000 atoms: 0.42 Number of scatterers: 48264 At special positions: 0 Unit cell: (174.8, 187.15, 191.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 9272 8.00 N 8038 7.00 C 30870 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: 8.56 Conformation dependent library (CDL) restraints added in 4.4 seconds 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11316 Finding SS restraints... Secondary structure from input PDB file: 261 helices and 32 sheets defined 43.6% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.50 Creating SS restraints... Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.879A pdb=" N TYR A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.621A pdb=" N PHE A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.553A pdb=" N LEU A 214 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 removed outlier: 3.501A pdb=" N PHE A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 249 Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.884A pdb=" N LYS A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 258' Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 306 through 311 removed outlier: 3.557A pdb=" N ARG A 309 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 311 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.742A pdb=" N SER A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 387 through 412 removed outlier: 3.556A pdb=" N SER A 406 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A 409 " --> pdb=" O HIS A 405 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 431 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.598A pdb=" N GLU A 470 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 507 through 511 removed outlier: 3.508A pdb=" N LEU A 510 " --> pdb=" O ILE A 507 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 511 " --> pdb=" O THR A 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 507 through 511' Processing helix chain 'A' and resid 547 through 553 Processing helix chain 'A' and resid 561 through 569 removed outlier: 3.552A pdb=" N GLN A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 36 removed outlier: 4.116A pdb=" N GLU B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 removed outlier: 3.889A pdb=" N TYR B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 139 through 145 removed outlier: 3.607A pdb=" N PHE B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 170 Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 216 through 225 Processing helix chain 'B' and resid 231 through 250 removed outlier: 3.549A pdb=" N PHE B 238 " --> pdb=" O GLN B 234 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.681A pdb=" N THR B 256 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 282 Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.866A pdb=" N LEU B 310 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE B 311 " --> pdb=" O HIS B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 307 through 311' Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.517A pdb=" N SER B 338 " --> pdb=" O ASP B 334 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 344 No H-bonds generated for 'chain 'B' and resid 342 through 344' Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.542A pdb=" N SER B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 384 through 412 removed outlier: 4.463A pdb=" N SER B 389 " --> pdb=" O PHE B 385 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE B 390 " --> pdb=" O GLU B 386 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 409 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 412 " --> pdb=" O LYS B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 removed outlier: 4.052A pdb=" N TYR B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 440 through 454 Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 467 through 471 removed outlier: 4.169A pdb=" N GLU B 470 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 507 through 511 removed outlier: 3.567A pdb=" N LEU B 510 " --> pdb=" O ILE B 507 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 511 " --> pdb=" O THR B 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 507 through 511' Processing helix chain 'B' and resid 547 through 553 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.911A pdb=" N TYR C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 145 removed outlier: 3.840A pdb=" N PHE C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 171 Processing helix chain 'C' and resid 191 through 195 removed outlier: 3.945A pdb=" N GLU C 194 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN C 195 " --> pdb=" O GLU C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 195' Processing helix chain 'C' and resid 211 through 215 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 231 through 249 removed outlier: 3.869A pdb=" N VAL C 237 " --> pdb=" O ASN C 233 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE C 238 " --> pdb=" O GLN C 234 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.564A pdb=" N ASN C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 341 removed outlier: 3.699A pdb=" N ASP C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG C 335 " --> pdb=" O ASN C 331 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE C 341 " --> pdb=" O GLN C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 344 No H-bonds generated for 'chain 'C' and resid 342 through 344' Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.804A pdb=" N LYS C 354 " --> pdb=" O GLY C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 366 Processing helix chain 'C' and resid 384 through 407 removed outlier: 4.528A pdb=" N SER C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 432 removed outlier: 3.932A pdb=" N TYR C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 458 removed outlier: 4.528A pdb=" N GLU C 445 " --> pdb=" O ARG C 441 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA C 446 " --> pdb=" O THR C 442 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ARG C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LYS C 456 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 471 removed outlier: 3.747A pdb=" N GLU C 470 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 477 Processing helix chain 'C' and resid 489 through 500 Processing helix chain 'C' and resid 506 through 514 Proline residue: C 512 - end of helix Processing helix chain 'C' and resid 547 through 553 Processing helix chain 'C' and resid 558 through 569 removed outlier: 4.319A pdb=" N ASP C 562 " --> pdb=" O ASP C 558 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS C 563 " --> pdb=" O SER C 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 35 Processing helix chain 'D' and resid 104 through 113 removed outlier: 3.518A pdb=" N ILE D 108 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.721A pdb=" N PHE D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 171 Processing helix chain 'D' and resid 191 through 195 removed outlier: 3.977A pdb=" N GLU D 194 " --> pdb=" O SER D 191 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN D 195 " --> pdb=" O GLU D 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 191 through 195' Processing helix chain 'D' and resid 211 through 215 removed outlier: 3.520A pdb=" N LEU D 214 " --> pdb=" O PRO D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 231 through 249 removed outlier: 3.913A pdb=" N VAL D 237 " --> pdb=" O ASN D 233 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE D 238 " --> pdb=" O GLN D 234 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS D 247 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 Processing helix chain 'D' and resid 269 through 282 removed outlier: 3.527A pdb=" N ASN D 282 " --> pdb=" O ASN D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 311 removed outlier: 4.056A pdb=" N HIS D 308 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 310 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE D 311 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 341 removed outlier: 3.635A pdb=" N ASP D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D 341 " --> pdb=" O GLN D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 344 No H-bonds generated for 'chain 'D' and resid 342 through 344' Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 350 through 356 removed outlier: 3.800A pdb=" N LYS D 354 " --> pdb=" O GLY D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 366 Processing helix chain 'D' and resid 384 through 407 removed outlier: 4.492A pdb=" N SER D 389 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ILE D 390 " --> pdb=" O GLU D 386 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 432 removed outlier: 3.895A pdb=" N TYR D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 454 removed outlier: 4.532A pdb=" N GLU D 445 " --> pdb=" O ARG D 441 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA D 446 " --> pdb=" O THR D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 471 removed outlier: 3.760A pdb=" N GLU D 470 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 477 Processing helix chain 'D' and resid 489 through 500 Processing helix chain 'D' and resid 510 through 514 removed outlier: 3.743A pdb=" N LEU D 514 " --> pdb=" O LEU D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 554 removed outlier: 3.816A pdb=" N LYS D 554 " --> pdb=" O ASP D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 569 removed outlier: 4.393A pdb=" N ASP D 562 " --> pdb=" O ASP D 558 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS D 563 " --> pdb=" O SER D 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 35 removed outlier: 4.398A pdb=" N ALA E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 removed outlier: 3.809A pdb=" N TYR E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 139 through 144 removed outlier: 4.033A pdb=" N PHE E 143 " --> pdb=" O GLY E 139 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 139 through 144' Processing helix chain 'E' and resid 156 through 170 Processing helix chain 'E' and resid 192 through 197 removed outlier: 4.183A pdb=" N ALA E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 215 Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.529A pdb=" N GLU E 222 " --> pdb=" O ASP E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 249 removed outlier: 3.819A pdb=" N ILE E 242 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 259 removed outlier: 3.964A pdb=" N ILE E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 281 Processing helix chain 'E' and resid 306 through 312 removed outlier: 4.020A pdb=" N PHE E 311 " --> pdb=" O HIS E 308 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS E 312 " --> pdb=" O ARG E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 341 Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 350 through 356 removed outlier: 3.742A pdb=" N LYS E 354 " --> pdb=" O GLY E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 366 removed outlier: 3.751A pdb=" N LEU E 362 " --> pdb=" O PHE E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 407 removed outlier: 4.473A pdb=" N SER E 389 " --> pdb=" O PHE E 385 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE E 390 " --> pdb=" O GLU E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 414 Processing helix chain 'E' and resid 427 through 432 removed outlier: 3.972A pdb=" N TYR E 431 " --> pdb=" O GLU E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 439 No H-bonds generated for 'chain 'E' and resid 437 through 439' Processing helix chain 'E' and resid 440 through 458 removed outlier: 5.200A pdb=" N ARG E 455 " --> pdb=" O ALA E 451 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LYS E 456 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR E 457 " --> pdb=" O GLU E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 471 Processing helix chain 'E' and resid 472 through 477 Processing helix chain 'E' and resid 489 through 500 Processing helix chain 'E' and resid 506 through 514 Proline residue: E 512 - end of helix Processing helix chain 'E' and resid 547 through 553 Processing helix chain 'E' and resid 561 through 568 removed outlier: 3.512A pdb=" N ILE E 565 " --> pdb=" O PHE E 561 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP E 568 " --> pdb=" O ILE E 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 35 removed outlier: 4.352A pdb=" N ALA F 32 " --> pdb=" O GLU F 28 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU F 33 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU F 34 " --> pdb=" O LYS F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 114 removed outlier: 3.829A pdb=" N TYR F 112 " --> pdb=" O ILE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 119 No H-bonds generated for 'chain 'F' and resid 117 through 119' Processing helix chain 'F' and resid 139 through 144 removed outlier: 3.633A pdb=" N PHE F 143 " --> pdb=" O GLY F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 171 Processing helix chain 'F' and resid 192 through 197 removed outlier: 4.220A pdb=" N ALA F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 215 Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.502A pdb=" N PHE F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 249 removed outlier: 3.621A pdb=" N ILE F 242 " --> pdb=" O PHE F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 281 Processing helix chain 'F' and resid 306 through 312 removed outlier: 4.050A pdb=" N PHE F 311 " --> pdb=" O HIS F 308 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS F 312 " --> pdb=" O ARG F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 341 removed outlier: 3.548A pdb=" N SER F 338 " --> pdb=" O ASP F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 350 through 356 removed outlier: 3.780A pdb=" N LYS F 354 " --> pdb=" O GLY F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 366 removed outlier: 3.763A pdb=" N LEU F 362 " --> pdb=" O PHE F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 405 removed outlier: 4.437A pdb=" N SER F 389 " --> pdb=" O PHE F 385 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ILE F 390 " --> pdb=" O GLU F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 414 Processing helix chain 'F' and resid 427 through 432 removed outlier: 3.909A pdb=" N TYR F 431 " --> pdb=" O GLU F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 439 No H-bonds generated for 'chain 'F' and resid 437 through 439' Processing helix chain 'F' and resid 440 through 454 Processing helix chain 'F' and resid 467 through 471 removed outlier: 3.515A pdb=" N GLU F 470 " --> pdb=" O ARG F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 477 Processing helix chain 'F' and resid 489 through 500 Processing helix chain 'F' and resid 506 through 511 Processing helix chain 'F' and resid 547 through 553 removed outlier: 3.556A pdb=" N ARG F 553 " --> pdb=" O LEU F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 568 removed outlier: 3.503A pdb=" N GLU F 566 " --> pdb=" O ASP F 562 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN F 567 " --> pdb=" O LYS F 563 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP F 568 " --> pdb=" O ILE F 564 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 169 removed outlier: 3.761A pdb=" N LYS G 158 " --> pdb=" O ASP G 154 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR G 160 " --> pdb=" O GLN G 156 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE G 164 " --> pdb=" O THR G 160 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN G 166 " --> pdb=" O GLN G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 178 removed outlier: 4.135A pdb=" N ALA G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU G 176 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS G 177 " --> pdb=" O TYR G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 192 removed outlier: 3.660A pdb=" N ARG G 185 " --> pdb=" O SER G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 209 removed outlier: 4.047A pdb=" N PHE G 204 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU G 206 " --> pdb=" O SER G 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER G 207 " --> pdb=" O ASP G 203 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE G 208 " --> pdb=" O PHE G 204 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN G 209 " --> pdb=" O VAL G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 237 removed outlier: 6.856A pdb=" N ARG G 225 " --> pdb=" O GLN G 221 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N LYS G 226 " --> pdb=" O TYR G 222 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU G 227 " --> pdb=" O GLU G 223 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU G 229 " --> pdb=" O ARG G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 274 removed outlier: 3.576A pdb=" N VAL G 263 " --> pdb=" O ASP G 259 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS G 266 " --> pdb=" O THR G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 309 Processing helix chain 'G' and resid 325 through 332 removed outlier: 4.082A pdb=" N LEU G 329 " --> pdb=" O THR G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 355 removed outlier: 3.621A pdb=" N ASN G 354 " --> pdb=" O ASN G 350 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER G 355 " --> pdb=" O GLU G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 394 removed outlier: 4.089A pdb=" N LYS G 391 " --> pdb=" O PHE G 387 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU G 392 " --> pdb=" O ALA G 388 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 169 removed outlier: 3.914A pdb=" N ILE H 161 " --> pdb=" O LYS H 157 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN H 162 " --> pdb=" O LYS H 158 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE H 163 " --> pdb=" O GLU H 159 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE H 164 " --> pdb=" O THR H 160 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS H 167 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE H 168 " --> pdb=" O ILE H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 192 removed outlier: 3.905A pdb=" N ARG H 185 " --> pdb=" O SER H 181 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS H 186 " --> pdb=" O ASN H 182 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE H 190 " --> pdb=" O LYS H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 222 Processing helix chain 'H' and resid 223 through 237 removed outlier: 4.161A pdb=" N GLU H 227 " --> pdb=" O GLU H 223 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER H 235 " --> pdb=" O LYS H 231 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE H 236 " --> pdb=" O LEU H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 274 removed outlier: 3.683A pdb=" N VAL H 263 " --> pdb=" O ASP H 259 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS H 264 " --> pdb=" O ILE H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 309 Processing helix chain 'H' and resid 326 through 334 removed outlier: 3.703A pdb=" N ILE H 330 " --> pdb=" O PRO H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 354 removed outlier: 3.802A pdb=" N GLU H 351 " --> pdb=" O ASP H 347 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR H 352 " --> pdb=" O ASP H 348 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN H 354 " --> pdb=" O ASN H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 386 through 393 removed outlier: 3.549A pdb=" N LYS H 391 " --> pdb=" O ALA H 388 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 169 removed outlier: 3.601A pdb=" N LYS I 157 " --> pdb=" O PHE I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 177 Processing helix chain 'I' and resid 178 through 190 removed outlier: 3.700A pdb=" N ASN I 182 " --> pdb=" O TYR I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 209 Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'I' and resid 224 through 236 removed outlier: 3.576A pdb=" N SER I 235 " --> pdb=" O LYS I 231 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE I 236 " --> pdb=" O LEU I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 274 Processing helix chain 'I' and resid 295 through 309 removed outlier: 3.546A pdb=" N GLU I 309 " --> pdb=" O GLN I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 334 removed outlier: 4.091A pdb=" N LEU I 329 " --> pdb=" O THR I 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 removed outlier: 3.843A pdb=" N ASN I 354 " --> pdb=" O ASN I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 392 removed outlier: 4.083A pdb=" N LYS I 391 " --> pdb=" O PHE I 387 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU I 392 " --> pdb=" O ALA I 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 387 through 392' Processing helix chain 'J' and resid 155 through 159 removed outlier: 4.297A pdb=" N LYS J 158 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 169 Processing helix chain 'J' and resid 171 through 177 removed outlier: 3.519A pdb=" N GLU J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS J 177 " --> pdb=" O TYR J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 193 removed outlier: 3.660A pdb=" N ASN J 182 " --> pdb=" O TYR J 178 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN J 193 " --> pdb=" O ASP J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 208 removed outlier: 3.973A pdb=" N ILE J 208 " --> pdb=" O PHE J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 222 Processing helix chain 'J' and resid 224 through 232 removed outlier: 3.520A pdb=" N ARG J 230 " --> pdb=" O LYS J 226 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU J 232 " --> pdb=" O TYR J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 274 Processing helix chain 'J' and resid 295 through 309 removed outlier: 3.554A pdb=" N LEU J 302 " --> pdb=" O ASN J 298 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU J 309 " --> pdb=" O GLN J 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 334 removed outlier: 4.039A pdb=" N LEU J 329 " --> pdb=" O THR J 325 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER J 334 " --> pdb=" O ILE J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 345 through 354 removed outlier: 3.556A pdb=" N LEU J 353 " --> pdb=" O PHE J 349 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN J 354 " --> pdb=" O ASN J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 392 removed outlier: 4.024A pdb=" N LYS J 391 " --> pdb=" O PHE J 387 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU J 392 " --> pdb=" O ALA J 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 387 through 392' Processing helix chain 'K' and resid 152 through 168 removed outlier: 3.632A pdb=" N ILE K 163 " --> pdb=" O GLU K 159 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE K 164 " --> pdb=" O THR K 160 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN K 166 " --> pdb=" O GLN K 162 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS K 167 " --> pdb=" O ILE K 163 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE K 168 " --> pdb=" O ILE K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 177 removed outlier: 4.431A pdb=" N GLU K 176 " --> pdb=" O ASP K 172 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS K 177 " --> pdb=" O TYR K 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 172 through 177' Processing helix chain 'K' and resid 179 through 192 removed outlier: 3.886A pdb=" N ARG K 185 " --> pdb=" O SER K 181 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR K 187 " --> pdb=" O ALA K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 207 removed outlier: 3.644A pdb=" N PHE K 204 " --> pdb=" O LYS K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 224 Processing helix chain 'K' and resid 224 through 237 removed outlier: 3.682A pdb=" N LEU K 229 " --> pdb=" O ARG K 225 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG K 230 " --> pdb=" O LYS K 226 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER K 235 " --> pdb=" O LYS K 231 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 274 removed outlier: 3.608A pdb=" N VAL K 263 " --> pdb=" O ASP K 259 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N CYS K 266 " --> pdb=" O THR K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 309 removed outlier: 3.689A pdb=" N GLU K 309 " --> pdb=" O GLN K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 332 removed outlier: 4.244A pdb=" N LEU K 329 " --> pdb=" O THR K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 355 removed outlier: 3.631A pdb=" N SER K 355 " --> pdb=" O GLU K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 394 removed outlier: 4.225A pdb=" N LYS K 391 " --> pdb=" O PHE K 387 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU K 392 " --> pdb=" O ALA K 388 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 169 removed outlier: 5.150A pdb=" N LYS L 158 " --> pdb=" O ASP L 154 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE L 161 " --> pdb=" O LYS L 157 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N HIS L 167 " --> pdb=" O ILE L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 177 Processing helix chain 'L' and resid 179 through 193 removed outlier: 3.530A pdb=" N ARG L 185 " --> pdb=" O SER L 181 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR L 188 " --> pdb=" O PHE L 184 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE L 190 " --> pdb=" O LYS L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 209 removed outlier: 3.596A pdb=" N ILE L 208 " --> pdb=" O PHE L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 216 through 224 removed outlier: 3.765A pdb=" N GLU L 223 " --> pdb=" O PHE L 219 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 237 removed outlier: 3.675A pdb=" N PHE L 236 " --> pdb=" O LEU L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 274 removed outlier: 3.686A pdb=" N VAL L 263 " --> pdb=" O ASP L 259 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS L 264 " --> pdb=" O ILE L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 309 removed outlier: 3.544A pdb=" N ASN L 308 " --> pdb=" O ASN L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 326 through 334 removed outlier: 3.923A pdb=" N ILE L 330 " --> pdb=" O PRO L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 354 removed outlier: 3.825A pdb=" N GLU L 351 " --> pdb=" O ASP L 347 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR L 352 " --> pdb=" O ASP L 348 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU L 353 " --> pdb=" O PHE L 349 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN L 354 " --> pdb=" O ASN L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 392 removed outlier: 4.109A pdb=" N LYS L 391 " --> pdb=" O PHE L 387 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU L 392 " --> pdb=" O ALA L 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 387 through 392' Processing helix chain 'M' and resid 225 through 234 removed outlier: 4.191A pdb=" N LEU M 229 " --> pdb=" O ARG M 225 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU M 234 " --> pdb=" O ARG M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 274 removed outlier: 3.773A pdb=" N VAL M 263 " --> pdb=" O ASP M 259 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS M 264 " --> pdb=" O ILE M 260 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS M 266 " --> pdb=" O THR M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 309 removed outlier: 3.589A pdb=" N LEU M 299 " --> pdb=" O SER M 295 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE M 307 " --> pdb=" O LYS M 303 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN M 308 " --> pdb=" O ASN M 304 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 334 removed outlier: 3.999A pdb=" N LEU M 329 " --> pdb=" O THR M 325 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER M 334 " --> pdb=" O ILE M 330 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 354 removed outlier: 3.628A pdb=" N ASN M 354 " --> pdb=" O ASN M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 386 through 388 No H-bonds generated for 'chain 'M' and resid 386 through 388' Processing helix chain 'M' and resid 389 through 394 Processing helix chain 'N' and resid 225 through 236 removed outlier: 4.352A pdb=" N LEU N 229 " --> pdb=" O ARG N 225 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU N 232 " --> pdb=" O TYR N 228 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS N 233 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU N 234 " --> pdb=" O ARG N 230 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE N 236 " --> pdb=" O LEU N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 260 through 274 removed outlier: 3.732A pdb=" N LYS N 264 " --> pdb=" O ILE N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 295 through 309 Processing helix chain 'N' and resid 325 through 335 removed outlier: 4.157A pdb=" N LEU N 329 " --> pdb=" O THR N 325 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER N 334 " --> pdb=" O ILE N 330 " (cutoff:3.500A) Processing helix chain 'N' and resid 345 through 356 Processing helix chain 'N' and resid 386 through 388 No H-bonds generated for 'chain 'N' and resid 386 through 388' Processing helix chain 'N' and resid 389 through 394 removed outlier: 3.974A pdb=" N ILE N 393 " --> pdb=" O ASP N 389 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 234 removed outlier: 3.862A pdb=" N LEU O 232 " --> pdb=" O TYR O 228 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU O 234 " --> pdb=" O ARG O 230 " (cutoff:3.500A) Processing helix chain 'O' and resid 259 through 274 removed outlier: 3.883A pdb=" N VAL O 263 " --> pdb=" O ASP O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 295 through 309 removed outlier: 3.573A pdb=" N PHE O 307 " --> pdb=" O LYS O 303 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 334 Processing helix chain 'O' and resid 345 through 354 removed outlier: 3.524A pdb=" N ASN O 354 " --> pdb=" O ASN O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 386 through 388 No H-bonds generated for 'chain 'O' and resid 386 through 388' Processing helix chain 'O' and resid 389 through 394 removed outlier: 3.519A pdb=" N ILE O 393 " --> pdb=" O ASP O 389 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 234 removed outlier: 3.544A pdb=" N LYS P 231 " --> pdb=" O GLU P 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 259 through 275 removed outlier: 3.506A pdb=" N VAL P 263 " --> pdb=" O ASP P 259 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 309 removed outlier: 3.507A pdb=" N PHE P 307 " --> pdb=" O LYS P 303 " (cutoff:3.500A) Processing helix chain 'P' and resid 327 through 332 removed outlier: 3.659A pdb=" N GLY P 332 " --> pdb=" O MET P 328 " (cutoff:3.500A) Processing helix chain 'P' and resid 345 through 353 Processing helix chain 'P' and resid 386 through 388 No H-bonds generated for 'chain 'P' and resid 386 through 388' Processing helix chain 'P' and resid 389 through 394 removed outlier: 3.603A pdb=" N ILE P 393 " --> pdb=" O ASP P 389 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 234 removed outlier: 3.860A pdb=" N LEU Q 229 " --> pdb=" O ARG Q 225 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU Q 232 " --> pdb=" O TYR Q 228 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU Q 234 " --> pdb=" O ARG Q 230 " (cutoff:3.500A) Processing helix chain 'Q' and resid 259 through 275 removed outlier: 3.583A pdb=" N VAL Q 263 " --> pdb=" O ASP Q 259 " (cutoff:3.500A) Processing helix chain 'Q' and resid 295 through 309 Processing helix chain 'Q' and resid 327 through 335 removed outlier: 3.577A pdb=" N PHE Q 333 " --> pdb=" O LEU Q 329 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER Q 334 " --> pdb=" O ILE Q 330 " (cutoff:3.500A) Processing helix chain 'Q' and resid 345 through 354 removed outlier: 3.510A pdb=" N ASN Q 354 " --> pdb=" O ASN Q 350 " (cutoff:3.500A) Processing helix chain 'Q' and resid 386 through 388 No H-bonds generated for 'chain 'Q' and resid 386 through 388' Processing helix chain 'Q' and resid 389 through 394 removed outlier: 3.788A pdb=" N ILE Q 393 " --> pdb=" O ASP Q 389 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 234 removed outlier: 4.164A pdb=" N GLU R 234 " --> pdb=" O ARG R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 274 removed outlier: 3.757A pdb=" N VAL R 263 " --> pdb=" O ASP R 259 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS R 264 " --> pdb=" O ILE R 260 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP R 265 " --> pdb=" O LYS R 261 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS R 266 " --> pdb=" O THR R 262 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 309 removed outlier: 3.568A pdb=" N PHE R 307 " --> pdb=" O LYS R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 334 removed outlier: 3.950A pdb=" N LEU R 329 " --> pdb=" O THR R 325 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER R 334 " --> pdb=" O ILE R 330 " (cutoff:3.500A) Processing helix chain 'R' and resid 345 through 354 removed outlier: 3.731A pdb=" N ASN R 354 " --> pdb=" O ASN R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 386 through 388 No H-bonds generated for 'chain 'R' and resid 386 through 388' Processing helix chain 'R' and resid 389 through 394 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 15 removed outlier: 6.411A pdb=" N ASN A 8 " --> pdb=" O ASP A 24 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS A 20 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL A 14 " --> pdb=" O LYS A 18 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 18 through 26 current: chain 'A' and resid 50 through 58 removed outlier: 5.477A pdb=" N ILE A 56 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER A 76 " --> pdb=" O ILE A 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 73 through 77 current: chain 'A' and resid 85 through 88 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 85 through 88 current: chain 'D' and resid 9 through 14 removed outlier: 6.593A pdb=" N LYS D 20 " --> pdb=" O VAL D 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 19 through 23 current: chain 'D' and resid 50 through 62 removed outlier: 6.892A pdb=" N VAL D 50 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS D 82 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU D 52 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU D 80 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA D 54 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE D 78 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE D 56 " --> pdb=" O SER D 76 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER D 76 " --> pdb=" O ILE D 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 85 through 88 current: chain 'F' and resid 19 through 23 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 19 through 23 current: chain 'F' and resid 50 through 62 removed outlier: 6.879A pdb=" N VAL F 50 " --> pdb=" O LYS F 82 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS F 82 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU F 52 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU F 80 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA F 54 " --> pdb=" O ILE F 78 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE F 78 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ILE F 56 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER F 76 " --> pdb=" O ILE F 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 61 through 62 current: chain 'B' and resid 18 through 26 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 18 through 26 current: chain 'B' and resid 50 through 58 removed outlier: 5.388A pdb=" N ILE B 56 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER B 76 " --> pdb=" O ILE B 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 73 through 77 current: chain 'B' and resid 85 through 88 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 85 through 88 current: chain 'C' and resid 19 through 23 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 19 through 23 current: chain 'C' and resid 50 through 62 removed outlier: 6.895A pdb=" N VAL C 50 " --> pdb=" O LYS C 82 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS C 82 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU C 52 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU C 80 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA C 54 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 78 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE C 56 " --> pdb=" O SER C 76 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER C 76 " --> pdb=" O ILE C 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 85 through 88 current: chain 'E' and resid 18 through 23 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 23 current: chain 'E' and resid 50 through 62 removed outlier: 6.869A pdb=" N VAL E 50 " --> pdb=" O LYS E 82 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LYS E 82 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU E 52 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU E 80 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA E 54 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE E 78 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE E 56 " --> pdb=" O SER E 76 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER E 76 " --> pdb=" O ILE E 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 138 removed outlier: 4.573A pdb=" N SER A 125 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL A 137 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR A 123 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 521 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ALA A 148 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 147 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER A 465 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 149 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS A 183 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VAL A 424 " --> pdb=" O HIS A 183 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE A 185 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU A 426 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N PHE A 187 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 184 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU A 378 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 186 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN A 201 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASP A 379 " --> pdb=" O ASN A 201 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 203 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 301 Processing sheet with id=AA6, first strand: chain 'B' and resid 134 through 138 removed outlier: 4.568A pdb=" N SER B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL B 137 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N THR B 123 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ALA B 148 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 147 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N SER B 465 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 149 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE B 185 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU B 426 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE B 187 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE B 184 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU B 378 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE B 186 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AA8, first strand: chain 'B' and resid 299 through 301 removed outlier: 3.898A pdb=" N ILE B 292 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 134 through 138 removed outlier: 4.557A pdb=" N SER C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL C 137 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N THR C 123 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N HIS C 146 " --> pdb=" O CYS C 479 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE C 147 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N SER C 465 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE C 149 " --> pdb=" O SER C 465 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE C 185 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU C 426 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE C 187 " --> pdb=" O GLU C 426 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 184 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU C 378 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE C 186 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 201 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 298 through 301 removed outlier: 3.532A pdb=" N GLY C 298 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE C 292 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 134 through 138 removed outlier: 4.493A pdb=" N SER D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL D 137 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR D 123 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE D 147 " --> pdb=" O LEU D 463 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N SER D 465 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE D 149 " --> pdb=" O SER D 465 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE D 421 " --> pdb=" O THR D 460 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU D 462 " --> pdb=" O ILE D 421 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE D 423 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA D 464 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR D 425 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE D 185 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLU D 426 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE D 187 " --> pdb=" O GLU D 426 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 184 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU D 378 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE D 186 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN D 201 " --> pdb=" O ILE D 375 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 298 through 301 removed outlier: 3.509A pdb=" N GLY D 298 " --> pdb=" O ASP D 295 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 121 through 122 removed outlier: 3.528A pdb=" N VAL E 137 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 125 through 127 removed outlier: 3.509A pdb=" N SER E 530 " --> pdb=" O ILE E 521 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N HIS E 146 " --> pdb=" O THR E 481 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE E 483 " --> pdb=" O HIS E 146 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA E 148 " --> pdb=" O ILE E 483 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE E 147 " --> pdb=" O LEU E 463 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N SER E 465 " --> pdb=" O ILE E 147 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE E 149 " --> pdb=" O SER E 465 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE E 185 " --> pdb=" O VAL E 424 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU E 426 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE E 187 " --> pdb=" O GLU E 426 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE E 184 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU E 378 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE E 186 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 284 through 285 Processing sheet with id=AB7, first strand: chain 'E' and resid 298 through 301 Processing sheet with id=AB8, first strand: chain 'F' and resid 121 through 122 Processing sheet with id=AB9, first strand: chain 'F' and resid 125 through 127 removed outlier: 6.299A pdb=" N HIS F 146 " --> pdb=" O THR F 481 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE F 483 " --> pdb=" O HIS F 146 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA F 148 " --> pdb=" O ILE F 483 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE F 147 " --> pdb=" O LEU F 463 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N SER F 465 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE F 149 " --> pdb=" O SER F 465 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE F 421 " --> pdb=" O THR F 460 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU F 462 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE F 423 " --> pdb=" O LEU F 462 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA F 464 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TYR F 425 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 185 " --> pdb=" O VAL F 424 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU F 426 " --> pdb=" O ILE F 185 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N PHE F 187 " --> pdb=" O GLU F 426 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE F 184 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU F 378 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE F 186 " --> pdb=" O LEU F 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 284 through 285 Processing sheet with id=AC2, first strand: chain 'F' and resid 298 through 301 Processing sheet with id=AC3, first strand: chain 'G' and resid 313 through 314 removed outlier: 6.167A pdb=" N THR G 314 " --> pdb=" O PHE G 342 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE G 291 " --> pdb=" O ILE G 343 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS G 292 " --> pdb=" O LEU G 252 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 212 through 213 removed outlier: 6.201A pdb=" N ALA H 247 " --> pdb=" O GLU H 361 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N TYR H 363 " --> pdb=" O ALA H 247 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE H 249 " --> pdb=" O TYR H 363 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N PHE H 365 " --> pdb=" O PHE H 249 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE H 251 " --> pdb=" O PHE H 365 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS H 292 " --> pdb=" O LEU H 252 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE H 291 " --> pdb=" O ILE H 343 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR H 314 " --> pdb=" O PHE H 342 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 313 through 314 removed outlier: 6.002A pdb=" N THR I 314 " --> pdb=" O PHE I 342 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE I 291 " --> pdb=" O ILE I 343 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ALA I 247 " --> pdb=" O GLU I 361 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N TYR I 363 " --> pdb=" O ALA I 247 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE I 249 " --> pdb=" O TYR I 363 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE I 365 " --> pdb=" O PHE I 249 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE I 251 " --> pdb=" O PHE I 365 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 313 through 314 removed outlier: 6.111A pdb=" N THR J 314 " --> pdb=" O PHE J 342 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE J 291 " --> pdb=" O ILE J 343 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG J 248 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU J 290 " --> pdb=" O ARG J 248 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE J 250 " --> pdb=" O LEU J 290 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N HIS J 292 " --> pdb=" O PHE J 250 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU J 252 " --> pdb=" O HIS J 292 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ALA J 247 " --> pdb=" O GLU J 361 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N TYR J 363 " --> pdb=" O ALA J 247 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE J 249 " --> pdb=" O TYR J 363 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N PHE J 365 " --> pdb=" O PHE J 249 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE J 251 " --> pdb=" O PHE J 365 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 313 through 314 removed outlier: 6.155A pdb=" N THR K 314 " --> pdb=" O PHE K 342 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE K 291 " --> pdb=" O ILE K 343 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA K 247 " --> pdb=" O GLU K 361 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N TYR K 363 " --> pdb=" O ALA K 247 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE K 249 " --> pdb=" O TYR K 363 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N PHE K 365 " --> pdb=" O PHE K 249 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE K 251 " --> pdb=" O PHE K 365 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 313 through 314 removed outlier: 6.740A pdb=" N THR L 314 " --> pdb=" O PHE L 342 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE L 291 " --> pdb=" O ILE L 343 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS L 292 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA L 247 " --> pdb=" O GLU L 361 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N TYR L 363 " --> pdb=" O ALA L 247 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE L 249 " --> pdb=" O TYR L 363 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE L 365 " --> pdb=" O PHE L 249 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE L 251 " --> pdb=" O PHE L 365 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 313 through 314 removed outlier: 6.130A pdb=" N THR M 314 " --> pdb=" O PHE M 342 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE M 291 " --> pdb=" O ILE M 343 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS M 292 " --> pdb=" O LEU M 252 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 313 through 314 removed outlier: 6.025A pdb=" N THR N 314 " --> pdb=" O PHE N 342 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE N 291 " --> pdb=" O ILE N 343 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS N 292 " --> pdb=" O LEU N 252 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA N 247 " --> pdb=" O GLU N 361 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TYR N 363 " --> pdb=" O ALA N 247 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE N 249 " --> pdb=" O TYR N 363 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE N 365 " --> pdb=" O PHE N 249 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE N 251 " --> pdb=" O PHE N 365 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 313 through 314 removed outlier: 6.058A pdb=" N THR O 314 " --> pdb=" O PHE O 342 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE O 291 " --> pdb=" O ILE O 343 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS O 292 " --> pdb=" O LEU O 252 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA O 247 " --> pdb=" O GLU O 361 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N TYR O 363 " --> pdb=" O ALA O 247 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE O 249 " --> pdb=" O TYR O 363 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N PHE O 365 " --> pdb=" O PHE O 249 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE O 251 " --> pdb=" O PHE O 365 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N VAL O 380 " --> pdb=" O LYS O 360 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL O 362 " --> pdb=" O VAL O 380 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE O 382 " --> pdb=" O VAL O 362 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN O 364 " --> pdb=" O ILE O 382 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 313 through 314 removed outlier: 6.190A pdb=" N THR P 314 " --> pdb=" O PHE P 342 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE P 291 " --> pdb=" O ILE P 343 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG P 248 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU P 290 " --> pdb=" O ARG P 248 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE P 250 " --> pdb=" O LEU P 290 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N HIS P 292 " --> pdb=" O PHE P 250 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU P 252 " --> pdb=" O HIS P 292 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 313 through 314 removed outlier: 6.311A pdb=" N THR Q 314 " --> pdb=" O PHE Q 342 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE Q 291 " --> pdb=" O ILE Q 343 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 313 through 314 removed outlier: 6.101A pdb=" N THR R 314 " --> pdb=" O PHE R 342 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE R 291 " --> pdb=" O ILE R 343 " (cutoff:3.500A) 1608 hydrogen bonds defined for protein. 4614 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: 15.34 Time building geometry restraints manager: 10.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 14978 1.34 - 1.46: 11189 1.46 - 1.58: 22997 1.58 - 1.71: 6 1.71 - 1.83: 114 Bond restraints: 49284 Sorted by residual: bond pdb=" CB PRO E 265 " pdb=" CG PRO E 265 " ideal model delta sigma weight residual 1.492 1.652 -0.160 5.00e-02 4.00e+02 1.02e+01 bond pdb=" CB PRO B 265 " pdb=" CG PRO B 265 " ideal model delta sigma weight residual 1.492 1.634 -0.142 5.00e-02 4.00e+02 8.12e+00 bond pdb=" CB PRO F 265 " pdb=" CG PRO F 265 " ideal model delta sigma weight residual 1.492 1.605 -0.113 5.00e-02 4.00e+02 5.08e+00 bond pdb=" CB GLU N 253 " pdb=" CG GLU N 253 " ideal model delta sigma weight residual 1.520 1.587 -0.067 3.00e-02 1.11e+03 4.92e+00 bond pdb=" CB LYS G 226 " pdb=" CG LYS G 226 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.86e+00 ... (remaining 49279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 65795 3.34 - 6.68: 562 6.68 - 10.02: 110 10.02 - 13.36: 27 13.36 - 16.70: 4 Bond angle restraints: 66498 Sorted by residual: angle pdb=" CA PRO E 265 " pdb=" N PRO E 265 " pdb=" CD PRO E 265 " ideal model delta sigma weight residual 112.00 99.76 12.24 1.40e+00 5.10e-01 7.65e+01 angle pdb=" CA PRO F 265 " pdb=" N PRO F 265 " pdb=" CD PRO F 265 " ideal model delta sigma weight residual 112.00 101.86 10.14 1.40e+00 5.10e-01 5.25e+01 angle pdb=" CA LYS R 226 " pdb=" CB LYS R 226 " pdb=" CG LYS R 226 " ideal model delta sigma weight residual 114.10 127.97 -13.87 2.00e+00 2.50e-01 4.81e+01 angle pdb=" CA LYS M 226 " pdb=" CB LYS M 226 " pdb=" CG LYS M 226 " ideal model delta sigma weight residual 114.10 127.50 -13.40 2.00e+00 2.50e-01 4.49e+01 angle pdb=" CA PRO B 265 " pdb=" N PRO B 265 " pdb=" CD PRO B 265 " ideal model delta sigma weight residual 112.00 103.65 8.35 1.40e+00 5.10e-01 3.56e+01 ... (remaining 66493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 25263 18.00 - 36.00: 3497 36.00 - 54.00: 939 54.00 - 72.00: 187 72.00 - 89.99: 66 Dihedral angle restraints: 29952 sinusoidal: 12528 harmonic: 17424 Sorted by residual: dihedral pdb=" CA VAL B 504 " pdb=" C VAL B 504 " pdb=" N GLY B 505 " pdb=" CA GLY B 505 " ideal model delta harmonic sigma weight residual -180.00 -155.77 -24.23 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA VAL A 504 " pdb=" C VAL A 504 " pdb=" N GLY A 505 " pdb=" CA GLY A 505 " ideal model delta harmonic sigma weight residual -180.00 -155.88 -24.12 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA GLN J 156 " pdb=" C GLN J 156 " pdb=" N LYS J 157 " pdb=" CA LYS J 157 " ideal model delta harmonic sigma weight residual -180.00 -155.94 -24.06 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 29949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 6332 0.074 - 0.147: 875 0.147 - 0.221: 35 0.221 - 0.295: 3 0.295 - 0.369: 3 Chirality restraints: 7248 Sorted by residual: chirality pdb=" CG LEU A 500 " pdb=" CB LEU A 500 " pdb=" CD1 LEU A 500 " pdb=" CD2 LEU A 500 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CG LEU B 500 " pdb=" CB LEU B 500 " pdb=" CD1 LEU B 500 " pdb=" CD2 LEU B 500 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB ILE A 31 " pdb=" CA ILE A 31 " pdb=" CG1 ILE A 31 " pdb=" CG2 ILE A 31 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 7245 not shown) Planarity restraints: 8610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER F 264 " 0.096 5.00e-02 4.00e+02 1.38e-01 3.03e+01 pdb=" N PRO F 265 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO F 265 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO F 265 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 264 " 0.069 5.00e-02 4.00e+02 9.70e-02 1.50e+01 pdb=" N PRO E 265 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO E 265 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 265 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 264 " -0.062 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO D 265 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO D 265 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 265 " -0.051 5.00e-02 4.00e+02 ... (remaining 8607 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2849 2.73 - 3.27: 47388 3.27 - 3.82: 83312 3.82 - 4.36: 105328 4.36 - 4.90: 177256 Nonbonded interactions: 416133 Sorted by model distance: nonbonded pdb=" O GLN O 271 " pdb=" OG SER O 275 " model vdw 2.191 3.040 nonbonded pdb=" O LYS O 231 " pdb=" OG SER O 235 " model vdw 2.204 3.040 nonbonded pdb=" O ARG C 553 " pdb=" OH TYR E 176 " model vdw 2.205 3.040 nonbonded pdb=" O LYS P 231 " pdb=" OG SER P 235 " model vdw 2.215 3.040 nonbonded pdb=" OE1 GLU C 62 " pdb=" OG SER E 13 " model vdw 2.219 3.040 ... (remaining 416128 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 568) selection = (chain 'B' and resid 5 through 568) selection = (chain 'C' and resid 5 through 568) selection = (chain 'D' and resid 5 through 568) selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 0.030 Extract box with map and model: 1.340 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 77.980 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 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 : 0.004 0.160 49284 Z= 0.283 Angle : 0.838 16.696 66498 Z= 0.434 Chirality : 0.049 0.369 7248 Planarity : 0.007 0.138 8610 Dihedral : 18.055 89.995 18636 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.55 % Allowed : 33.59 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.10), residues: 5850 helix: -2.62 (0.08), residues: 2085 sheet: -0.63 (0.19), residues: 827 loop : -0.86 (0.10), residues: 2938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 568 HIS 0.018 0.001 HIS E 232 PHE 0.043 0.002 PHE J 184 TYR 0.031 0.002 TYR H 173 ARG 0.033 0.001 ARG N 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 747 time to evaluate : 4.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.7564 (mtpp) cc_final: 0.6600 (mtmm) REVERT: A 30 LYS cc_start: 0.6344 (mppt) cc_final: 0.6136 (mppt) REVERT: A 62 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6828 (mp0) REVERT: A 85 LYS cc_start: 0.6891 (ttmm) cc_final: 0.6103 (tttp) REVERT: A 174 GLU cc_start: 0.6968 (tp30) cc_final: 0.6585 (mt-10) REVERT: A 221 GLU cc_start: 0.6221 (mt-10) cc_final: 0.5828 (mt-10) REVERT: A 235 ARG cc_start: 0.6152 (ttp80) cc_final: 0.5875 (ttm110) REVERT: A 342 ASP cc_start: 0.7159 (t0) cc_final: 0.6943 (t0) REVERT: A 445 GLU cc_start: 0.7618 (pt0) cc_final: 0.7360 (pt0) REVERT: A 449 ARG cc_start: 0.6767 (ttt-90) cc_final: 0.6151 (ttt-90) REVERT: A 466 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.6980 (pm20) REVERT: A 467 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6776 (ttp-110) REVERT: A 499 LEU cc_start: 0.8101 (mm) cc_final: 0.7876 (mm) REVERT: B 20 LYS cc_start: 0.7896 (ttmm) cc_final: 0.7016 (mtmt) REVERT: B 27 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6981 (tp30) REVERT: B 85 LYS cc_start: 0.6992 (ttmm) cc_final: 0.6196 (tttp) REVERT: B 101 GLU cc_start: 0.8508 (pt0) cc_final: 0.7863 (pm20) REVERT: B 189 ILE cc_start: 0.7933 (tt) cc_final: 0.7679 (tt) REVERT: B 449 ARG cc_start: 0.6907 (ttt90) cc_final: 0.6674 (ttt-90) REVERT: B 467 ARG cc_start: 0.6788 (ttt90) cc_final: 0.5976 (ptp90) REVERT: B 499 LEU cc_start: 0.8140 (mm) cc_final: 0.7897 (mm) REVERT: C 6 ASP cc_start: 0.6892 (p0) cc_final: 0.5951 (m-30) REVERT: C 20 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7712 (mmmt) REVERT: C 65 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6525 (mp0) REVERT: C 72 MET cc_start: 0.8042 (mmt) cc_final: 0.7765 (mmm) REVERT: C 82 LYS cc_start: 0.7863 (mtpp) cc_final: 0.7053 (mtmm) REVERT: C 88 ARG cc_start: 0.7504 (mmm-85) cc_final: 0.6365 (ttp-110) REVERT: C 101 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7394 (mt-10) REVERT: C 174 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7420 (mm-30) REVERT: C 235 ARG cc_start: 0.6139 (ttm-80) cc_final: 0.5767 (tpp-160) REVERT: C 285 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7101 (pttm) REVERT: C 305 GLU cc_start: 0.7652 (tp30) cc_final: 0.7282 (mp0) REVERT: C 401 GLU cc_start: 0.8018 (pt0) cc_final: 0.7816 (pt0) REVERT: C 436 ASP cc_start: 0.7776 (t0) cc_final: 0.7068 (m-30) REVERT: C 441 ARG cc_start: 0.6278 (ttp80) cc_final: 0.5845 (ttp-110) REVERT: C 536 LYS cc_start: 0.7412 (mppt) cc_final: 0.7150 (mppt) REVERT: D 6 ASP cc_start: 0.6083 (p0) cc_final: 0.5862 (m-30) REVERT: D 30 LYS cc_start: 0.7232 (ttmm) cc_final: 0.6676 (tttp) REVERT: D 62 GLU cc_start: 0.6970 (mm-30) cc_final: 0.5406 (mp0) REVERT: D 65 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6772 (mp0) REVERT: D 68 LYS cc_start: 0.7506 (ttpp) cc_final: 0.7211 (tttp) REVERT: D 74 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6683 (mp0) REVERT: D 82 LYS cc_start: 0.7604 (mtmm) cc_final: 0.7262 (mtpp) REVERT: D 88 ARG cc_start: 0.7495 (mmm-85) cc_final: 0.6348 (ttp-110) REVERT: D 107 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6557 (mt-10) REVERT: D 174 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7450 (mm-30) REVERT: D 235 ARG cc_start: 0.6097 (ttm170) cc_final: 0.5659 (tpp-160) REVERT: D 253 ASP cc_start: 0.7566 (p0) cc_final: 0.7162 (p0) REVERT: D 300 PHE cc_start: 0.8033 (p90) cc_final: 0.7432 (p90) REVERT: D 305 GLU cc_start: 0.8019 (pt0) cc_final: 0.7533 (tm-30) REVERT: D 309 ARG cc_start: 0.7946 (mtm110) cc_final: 0.7448 (ptm160) REVERT: D 436 ASP cc_start: 0.7746 (t0) cc_final: 0.7330 (m-30) REVERT: D 441 ARG cc_start: 0.6363 (ttp80) cc_final: 0.5935 (ttp-110) REVERT: D 516 GLU cc_start: 0.7491 (tp30) cc_final: 0.6975 (mm-30) REVERT: E 28 GLU cc_start: 0.7079 (tp30) cc_final: 0.6691 (tt0) REVERT: E 30 LYS cc_start: 0.7734 (mmmm) cc_final: 0.7371 (tppt) REVERT: E 99 LYS cc_start: 0.7936 (ptmm) cc_final: 0.7490 (pptt) REVERT: E 101 GLU cc_start: 0.7701 (pm20) cc_final: 0.7228 (pm20) REVERT: E 106 ASP cc_start: 0.6817 (p0) cc_final: 0.6337 (m-30) REVERT: E 473 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7003 (mm-30) REVERT: F 28 GLU cc_start: 0.7201 (tp30) cc_final: 0.6749 (tt0) REVERT: F 30 LYS cc_start: 0.7683 (mmmm) cc_final: 0.7278 (tppt) REVERT: F 70 LYS cc_start: 0.7467 (ttmm) cc_final: 0.7266 (ttmm) REVERT: F 82 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7472 (mttm) REVERT: F 106 ASP cc_start: 0.6723 (p0) cc_final: 0.6270 (m-30) REVERT: F 119 ASN cc_start: 0.7590 (t0) cc_final: 0.7192 (t0) REVERT: F 194 GLU cc_start: 0.7277 (tt0) cc_final: 0.7062 (tt0) REVERT: F 474 THR cc_start: 0.8406 (p) cc_final: 0.8024 (t) REVERT: G 231 LYS cc_start: 0.7525 (mtpp) cc_final: 0.7298 (mtpp) REVERT: G 283 ARG cc_start: 0.7239 (mtt90) cc_final: 0.5930 (mmm160) REVERT: G 327 LYS cc_start: 0.7940 (ttpp) cc_final: 0.7716 (pttp) REVERT: G 337 GLU cc_start: 0.8266 (mp0) cc_final: 0.7290 (mm-30) REVERT: G 367 THR cc_start: 0.7703 (m) cc_final: 0.7468 (p) REVERT: H 231 LYS cc_start: 0.7887 (tptm) cc_final: 0.7622 (tptm) REVERT: H 279 LYS cc_start: 0.7336 (pttt) cc_final: 0.7131 (pttm) REVERT: H 335 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7671 (t0) REVERT: H 379 GLN cc_start: 0.8450 (mt0) cc_final: 0.8173 (mt0) REVERT: I 231 LYS cc_start: 0.7487 (pttp) cc_final: 0.6995 (pptt) REVERT: I 238 ARG cc_start: 0.7886 (ptp-110) cc_final: 0.7301 (mtm-85) REVERT: I 359 ARG cc_start: 0.7913 (ttt-90) cc_final: 0.7551 (tpt-90) REVERT: J 359 ARG cc_start: 0.7446 (mtp85) cc_final: 0.7020 (ttt-90) REVERT: K 337 GLU cc_start: 0.8266 (mp0) cc_final: 0.7291 (mm-30) REVERT: L 279 LYS cc_start: 0.7387 (pttt) cc_final: 0.6478 (mtmt) REVERT: M 259 ASP cc_start: 0.7730 (t0) cc_final: 0.6890 (m-30) REVERT: M 283 ARG cc_start: 0.7406 (mtm-85) cc_final: 0.7191 (mtm180) REVERT: M 312 ILE cc_start: 0.7671 (mt) cc_final: 0.7274 (mm) REVERT: M 337 GLU cc_start: 0.7752 (mp0) cc_final: 0.7238 (mp0) REVERT: M 363 TYR cc_start: 0.8220 (m-80) cc_final: 0.8019 (m-80) REVERT: N 282 ASP cc_start: 0.7387 (p0) cc_final: 0.7090 (p0) REVERT: N 337 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7376 (mm-30) REVERT: O 337 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7401 (mm-30) REVERT: O 361 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7095 (mp0) REVERT: P 279 LYS cc_start: 0.7562 (pttp) cc_final: 0.6865 (mptp) REVERT: P 317 TYR cc_start: 0.8663 (m-80) cc_final: 0.8411 (m-80) REVERT: P 372 ASP cc_start: 0.7348 (t0) cc_final: 0.6659 (OUTLIER) REVERT: Q 279 LYS cc_start: 0.7651 (pttp) cc_final: 0.7016 (mptp) REVERT: Q 351 GLU cc_start: 0.7456 (tt0) cc_final: 0.7078 (tt0) REVERT: R 283 ARG cc_start: 0.7448 (mtm-85) cc_final: 0.7169 (mtm110) REVERT: R 312 ILE cc_start: 0.7700 (mt) cc_final: 0.7300 (mp) REVERT: R 327 LYS cc_start: 0.7196 (ttpt) cc_final: 0.6680 (tttt) outliers start: 30 outliers final: 6 residues processed: 772 average time/residue: 1.2704 time to fit residues: 1230.7911 Evaluate side-chains 651 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 642 time to evaluate : 4.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain H residue 335 ASN Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain P residue 244 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 491 optimal weight: 3.9990 chunk 441 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 297 optimal weight: 8.9990 chunk 235 optimal weight: 0.8980 chunk 456 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 277 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 chunk 528 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 199 ASN A 263 HIS A 405 HIS ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN C 282 ASN C 466 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN D 306 ASN D 466 GLN E 67 GLN F 67 GLN G 162 GLN H 177 HIS I 255 GLN I 350 ASN J 193 ASN J 305 GLN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 ASN M 381 ASN N 335 ASN O 292 HIS O 335 ASN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 369 ASN R 379 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.154374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111792 restraints weight = 56613.683| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.07 r_work: 0.3099 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 49284 Z= 0.477 Angle : 0.672 11.253 66498 Z= 0.355 Chirality : 0.049 0.234 7248 Planarity : 0.005 0.071 8610 Dihedral : 5.122 33.489 6361 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.37 % Allowed : 26.11 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.10), residues: 5850 helix: -0.99 (0.10), residues: 2224 sheet: -0.89 (0.17), residues: 937 loop : -0.69 (0.12), residues: 2689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 274 HIS 0.009 0.001 HIS E 232 PHE 0.020 0.002 PHE A 250 TYR 0.025 0.002 TYR F 495 ARG 0.007 0.001 ARG R 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 294 poor density : 649 time to evaluate : 4.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.8829 (m110) cc_final: 0.8537 (m110) REVERT: A 20 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8452 (mtmm) REVERT: A 30 LYS cc_start: 0.8355 (mppt) cc_final: 0.7942 (mptt) REVERT: A 85 LYS cc_start: 0.8518 (ttmm) cc_final: 0.7891 (tttp) REVERT: A 141 ARG cc_start: 0.8284 (mtm-85) cc_final: 0.8038 (mpp80) REVERT: A 145 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7136 (mtpt) REVERT: A 174 GLU cc_start: 0.7170 (tp30) cc_final: 0.6538 (mt-10) REVERT: A 239 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7645 (mmt90) REVERT: A 412 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.5902 (pptt) REVERT: A 474 THR cc_start: 0.9424 (OUTLIER) cc_final: 0.9171 (p) REVERT: B 85 LYS cc_start: 0.8541 (ttmm) cc_final: 0.7914 (tttp) REVERT: B 145 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7335 (mtpt) REVERT: B 293 TRP cc_start: 0.7536 (m100) cc_final: 0.7292 (m-90) REVERT: B 320 SER cc_start: 0.7157 (OUTLIER) cc_final: 0.6783 (m) REVERT: B 449 ARG cc_start: 0.8394 (ttt90) cc_final: 0.8022 (ttt-90) REVERT: B 467 ARG cc_start: 0.8222 (ttt90) cc_final: 0.7628 (ttp-110) REVERT: B 470 GLU cc_start: 0.8470 (mp0) cc_final: 0.8190 (pm20) REVERT: C 5 ASN cc_start: 0.6415 (t0) cc_final: 0.5989 (t160) REVERT: C 6 ASP cc_start: 0.7475 (p0) cc_final: 0.7134 (m-30) REVERT: C 30 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8192 (mtpp) REVERT: C 88 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7524 (ttm110) REVERT: C 104 LYS cc_start: 0.7815 (pttp) cc_final: 0.7599 (pttt) REVERT: C 174 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7698 (mm-30) REVERT: C 204 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8229 (p0) REVERT: C 206 ASP cc_start: 0.8754 (m-30) cc_final: 0.8337 (m-30) REVERT: C 377 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8926 (mp) REVERT: C 436 ASP cc_start: 0.7876 (t0) cc_final: 0.7486 (m-30) REVERT: C 445 GLU cc_start: 0.8159 (mp0) cc_final: 0.7928 (tt0) REVERT: C 536 LYS cc_start: 0.8052 (mppt) cc_final: 0.7613 (mppt) REVERT: D 30 LYS cc_start: 0.8524 (ttmm) cc_final: 0.7731 (mtmm) REVERT: D 82 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8359 (mtpt) REVERT: D 88 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7700 (ttp-110) REVERT: D 144 ASN cc_start: 0.8490 (p0) cc_final: 0.8233 (p0) REVERT: D 206 ASP cc_start: 0.8788 (m-30) cc_final: 0.8543 (m-30) REVERT: D 309 ARG cc_start: 0.8568 (mtm180) cc_final: 0.8365 (mtm180) REVERT: D 335 ARG cc_start: 0.8579 (tpp80) cc_final: 0.8334 (tpm170) REVERT: D 377 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8957 (mp) REVERT: D 436 ASP cc_start: 0.7796 (t0) cc_final: 0.7502 (m-30) REVERT: D 485 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.8147 (mmm) REVERT: D 536 LYS cc_start: 0.7849 (mppt) cc_final: 0.7533 (mmtm) REVERT: E 27 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: E 30 LYS cc_start: 0.8542 (mmmm) cc_final: 0.8197 (tppt) REVERT: E 74 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8405 (mt-10) REVERT: E 101 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8060 (pm20) REVERT: E 362 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8379 (mt) REVERT: F 27 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: F 28 GLU cc_start: 0.8064 (tp30) cc_final: 0.7686 (tt0) REVERT: F 118 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8959 (tp) REVERT: F 235 ARG cc_start: 0.7553 (tpt-90) cc_final: 0.7287 (mtp-110) REVERT: F 330 LEU cc_start: 0.8184 (tp) cc_final: 0.7969 (mt) REVERT: F 362 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8366 (mt) REVERT: F 473 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: G 226 LYS cc_start: 0.8181 (ttmt) cc_final: 0.7949 (ttmm) REVERT: G 283 ARG cc_start: 0.8561 (mtt90) cc_final: 0.7760 (mmm160) REVERT: G 286 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8534 (p) REVERT: G 337 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8487 (mm-30) REVERT: H 176 GLU cc_start: 0.6993 (tm-30) cc_final: 0.6591 (tm-30) REVERT: H 255 GLN cc_start: 0.7730 (mt0) cc_final: 0.7423 (mt0) REVERT: H 301 GLU cc_start: 0.8677 (tp30) cc_final: 0.8322 (tp30) REVERT: I 230 ARG cc_start: 0.7508 (ttp-110) cc_final: 0.6805 (ttp-110) REVERT: I 231 LYS cc_start: 0.8233 (pttp) cc_final: 0.7798 (pptt) REVERT: I 238 ARG cc_start: 0.8407 (ptp-110) cc_final: 0.8014 (mtm-85) REVERT: J 185 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6671 (ttt180) REVERT: J 238 ARG cc_start: 0.8497 (mtm110) cc_final: 0.8123 (mtm180) REVERT: K 279 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8443 (ptpp) REVERT: K 283 ARG cc_start: 0.8341 (mmm160) cc_final: 0.8019 (mtp85) REVERT: L 220 TYR cc_start: 0.7421 (t80) cc_final: 0.6831 (t80) REVERT: L 279 LYS cc_start: 0.8552 (pttt) cc_final: 0.8091 (mtmt) REVERT: L 366 TYR cc_start: 0.8495 (p90) cc_final: 0.8269 (p90) REVERT: M 257 LYS cc_start: 0.8719 (pttp) cc_final: 0.8122 (ptpp) REVERT: M 302 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9026 (tm) REVERT: M 312 ILE cc_start: 0.8752 (mt) cc_final: 0.8509 (mp) REVERT: M 337 GLU cc_start: 0.8255 (mp0) cc_final: 0.7717 (mp0) REVERT: M 383 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: N 254 PHE cc_start: 0.8281 (t80) cc_final: 0.7905 (t80) REVERT: N 337 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8048 (mm-30) REVERT: O 337 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8080 (mm-30) REVERT: P 228 TYR cc_start: 0.4305 (OUTLIER) cc_final: 0.3733 (m-80) REVERT: P 253 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: P 279 LYS cc_start: 0.8000 (pttp) cc_final: 0.7530 (mptp) REVERT: Q 279 LYS cc_start: 0.8079 (pttp) cc_final: 0.7705 (tptt) REVERT: Q 299 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8562 (tp) REVERT: R 312 ILE cc_start: 0.8708 (mt) cc_final: 0.8504 (mm) REVERT: R 327 LYS cc_start: 0.8295 (ttpt) cc_final: 0.7900 (tttt) outliers start: 294 outliers final: 89 residues processed: 861 average time/residue: 1.3243 time to fit residues: 1412.5384 Evaluate side-chains 701 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 584 time to evaluate : 4.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 5 ASN Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 473 GLU Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 194 LYS Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 379 GLN Chi-restraints excluded: chain J residue 185 ARG Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 192 CYS Chi-restraints excluded: chain K residue 262 THR Chi-restraints excluded: chain K residue 279 LYS Chi-restraints excluded: chain K residue 325 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 165 LYS Chi-restraints excluded: chain L residue 347 ASP Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain M residue 227 GLU Chi-restraints excluded: chain M residue 229 LEU Chi-restraints excluded: chain M residue 243 THR Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 255 GLN Chi-restraints excluded: chain M residue 286 SER Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 243 THR Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain P residue 228 TYR Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain P residue 244 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 310 ASP Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 334 SER Chi-restraints excluded: chain P residue 335 ASN Chi-restraints excluded: chain P residue 367 THR Chi-restraints excluded: chain P residue 379 GLN Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain Q residue 243 THR Chi-restraints excluded: chain Q residue 244 SER Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 380 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 472 optimal weight: 0.8980 chunk 513 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 369 optimal weight: 0.6980 chunk 417 optimal weight: 2.9990 chunk 547 optimal weight: 2.9990 chunk 387 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 266 optimal weight: 0.8980 chunk 273 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 236 ASN A 263 HIS A 466 GLN A 493 GLN B 138 ASN C 234 GLN C 245 ASN C 331 ASN C 509 ASN D 48 GLN D 230 ASN D 234 GLN D 331 ASN D 466 GLN E 232 HIS E 251 GLN E 278 ASN F 58 ASN F 232 HIS ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 GLN F 308 HIS H 379 GLN I 292 HIS ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 216 ASN M 273 ASN M 364 GLN O 273 ASN O 305 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 364 GLN Q 255 GLN R 292 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119852 restraints weight = 57048.113| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.97 r_work: 0.3129 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 49284 Z= 0.206 Angle : 0.515 9.180 66498 Z= 0.273 Chirality : 0.044 0.240 7248 Planarity : 0.004 0.061 8610 Dihedral : 4.608 32.751 6345 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.97 % Allowed : 27.16 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.11), residues: 5850 helix: -0.17 (0.11), residues: 2216 sheet: -0.94 (0.18), residues: 878 loop : -0.54 (0.12), residues: 2756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 274 HIS 0.008 0.001 HIS F 232 PHE 0.019 0.001 PHE H 215 TYR 0.018 0.001 TYR G 188 ARG 0.007 0.001 ARG N 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 659 time to evaluate : 4.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8305 (mtmm) REVERT: A 85 LYS cc_start: 0.8429 (ttmm) cc_final: 0.7937 (tttp) REVERT: A 174 GLU cc_start: 0.6869 (tp30) cc_final: 0.6586 (mt-10) REVERT: A 412 LYS cc_start: 0.6311 (OUTLIER) cc_final: 0.5794 (pptt) REVERT: A 441 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7526 (ttp80) REVERT: B 85 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8014 (tttp) REVERT: B 449 ARG cc_start: 0.8364 (ttt90) cc_final: 0.8131 (ttt-90) REVERT: B 467 ARG cc_start: 0.8082 (ttt90) cc_final: 0.7756 (ttp-110) REVERT: B 560 GLU cc_start: 0.7618 (tt0) cc_final: 0.7347 (tt0) REVERT: C 5 ASN cc_start: 0.6600 (t0) cc_final: 0.6294 (t0) REVERT: C 6 ASP cc_start: 0.7429 (p0) cc_final: 0.7179 (m-30) REVERT: C 30 LYS cc_start: 0.8289 (ttmm) cc_final: 0.7744 (mptp) REVERT: C 70 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8140 (tttm) REVERT: C 88 ARG cc_start: 0.8019 (mmm-85) cc_final: 0.7347 (ttm110) REVERT: C 204 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8092 (p0) REVERT: C 436 ASP cc_start: 0.7746 (t0) cc_final: 0.7449 (m-30) REVERT: C 536 LYS cc_start: 0.8002 (mppt) cc_final: 0.7700 (mppt) REVERT: D 30 LYS cc_start: 0.8329 (ttmm) cc_final: 0.7740 (mptp) REVERT: D 62 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7532 (mm-30) REVERT: D 68 LYS cc_start: 0.8087 (ttpp) cc_final: 0.7871 (ttpp) REVERT: D 82 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8471 (mtpt) REVERT: D 88 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7441 (ttm110) REVERT: D 118 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8539 (tp) REVERT: D 141 ARG cc_start: 0.8526 (mtt90) cc_final: 0.8251 (mtm-85) REVERT: D 206 ASP cc_start: 0.8701 (m-30) cc_final: 0.8482 (m-30) REVERT: D 407 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.7935 (ptpp) REVERT: D 445 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: E 28 GLU cc_start: 0.7958 (tp30) cc_final: 0.7686 (tp30) REVERT: E 30 LYS cc_start: 0.8580 (mmmm) cc_final: 0.8342 (tppt) REVERT: E 74 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8191 (mt-10) REVERT: E 101 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8020 (pm20) REVERT: E 330 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7877 (tp) REVERT: E 362 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8328 (mt) REVERT: F 26 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8143 (tm) REVERT: F 28 GLU cc_start: 0.8036 (tp30) cc_final: 0.7758 (tp30) REVERT: F 118 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8939 (tp) REVERT: F 235 ARG cc_start: 0.7551 (tpt-90) cc_final: 0.7232 (mtp-110) REVERT: F 362 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8364 (mt) REVERT: F 473 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: G 226 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7984 (ttmm) REVERT: G 283 ARG cc_start: 0.8519 (mtt90) cc_final: 0.8259 (mtp85) REVERT: G 286 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8349 (p) REVERT: H 176 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6682 (tm-30) REVERT: H 255 GLN cc_start: 0.7652 (mt0) cc_final: 0.7311 (mt0) REVERT: H 260 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7181 (tp) REVERT: I 154 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7724 (p0) REVERT: I 231 LYS cc_start: 0.8325 (pttp) cc_final: 0.7864 (pptt) REVERT: I 238 ARG cc_start: 0.8284 (ptp-110) cc_final: 0.8003 (mtm180) REVERT: J 185 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6740 (ttt180) REVERT: J 230 ARG cc_start: 0.7856 (ttp-110) cc_final: 0.7491 (ttp-110) REVERT: J 238 ARG cc_start: 0.8508 (mtm110) cc_final: 0.8139 (mtm-85) REVERT: K 174 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6750 (tt0) REVERT: K 223 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7170 (mm-30) REVERT: K 238 ARG cc_start: 0.8012 (ptp-110) cc_final: 0.7225 (ptp90) REVERT: K 334 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8650 (m) REVERT: L 220 TYR cc_start: 0.7478 (t80) cc_final: 0.7088 (t80) REVERT: L 279 LYS cc_start: 0.8513 (pttt) cc_final: 0.8168 (mtmt) REVERT: L 366 TYR cc_start: 0.8362 (p90) cc_final: 0.8139 (p90) REVERT: M 257 LYS cc_start: 0.8706 (pttp) cc_final: 0.8465 (pptt) REVERT: M 277 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8844 (mt) REVERT: M 302 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9070 (tm) REVERT: M 309 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8579 (mt-10) REVERT: M 312 ILE cc_start: 0.8696 (mt) cc_final: 0.8496 (mp) REVERT: M 337 GLU cc_start: 0.8186 (mp0) cc_final: 0.7637 (mp0) REVERT: M 383 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: N 254 PHE cc_start: 0.8367 (t80) cc_final: 0.7991 (t80) REVERT: N 337 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8045 (mm-30) REVERT: O 257 LYS cc_start: 0.8208 (ptpt) cc_final: 0.7966 (pptt) REVERT: O 337 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8117 (mm-30) REVERT: P 253 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: P 279 LYS cc_start: 0.7920 (pttp) cc_final: 0.7564 (mptp) REVERT: Q 253 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7967 (tt0) REVERT: Q 279 LYS cc_start: 0.7891 (pttp) cc_final: 0.7643 (mptp) REVERT: Q 299 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8590 (tp) REVERT: R 277 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8857 (mt) REVERT: R 327 LYS cc_start: 0.8353 (ttpt) cc_final: 0.8068 (tttt) outliers start: 217 outliers final: 74 residues processed: 821 average time/residue: 1.3223 time to fit residues: 1344.8094 Evaluate side-chains 685 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 582 time to evaluate : 4.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 278 ASN Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 192 GLU Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 473 GLU Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain H residue 260 ILE Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 315 ASP Chi-restraints excluded: chain J residue 185 ARG Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 315 ASP Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain K residue 181 SER Chi-restraints excluded: chain K residue 192 CYS Chi-restraints excluded: chain K residue 223 GLU Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 260 ILE Chi-restraints excluded: chain K residue 262 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 165 LYS Chi-restraints excluded: chain L residue 347 ASP Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain M residue 227 GLU Chi-restraints excluded: chain M residue 229 LEU Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 255 GLN Chi-restraints excluded: chain M residue 277 LEU Chi-restraints excluded: chain M residue 286 SER Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 244 SER Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 243 THR Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain P residue 229 LEU Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 286 SER Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 335 ASN Chi-restraints excluded: chain P residue 379 GLN Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 257 LYS Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 380 VAL Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 212 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 296 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 491 optimal weight: 5.9990 chunk 323 optimal weight: 6.9990 chunk 553 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 199 ASN A 466 GLN C 48 GLN C 234 GLN C 245 ASN C 286 ASN C 466 GLN C 509 ASN D 5 ASN D 8 ASN D 48 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 ASN D 466 GLN E 232 HIS E 278 ASN E 308 HIS F 67 GLN F 232 HIS ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 305 GLN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 255 GLN M 273 ASN M 364 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.153159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.113131 restraints weight = 56777.538| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.91 r_work: 0.3083 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 49284 Z= 0.306 Angle : 0.537 9.560 66498 Z= 0.284 Chirality : 0.045 0.209 7248 Planarity : 0.004 0.061 8610 Dihedral : 4.589 32.419 6343 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.93 % Allowed : 26.61 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.11), residues: 5850 helix: 0.09 (0.11), residues: 2220 sheet: -1.14 (0.17), residues: 927 loop : -0.42 (0.12), residues: 2703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 568 HIS 0.009 0.001 HIS F 232 PHE 0.022 0.001 PHE L 184 TYR 0.022 0.002 TYR J 188 ARG 0.007 0.001 ARG N 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 270 poor density : 608 time to evaluate : 4.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8602 (mtpp) cc_final: 0.8310 (mtmt) REVERT: A 30 LYS cc_start: 0.8220 (mptp) cc_final: 0.7827 (mptt) REVERT: A 85 LYS cc_start: 0.8434 (ttmm) cc_final: 0.7920 (tttp) REVERT: A 174 GLU cc_start: 0.7001 (tp30) cc_final: 0.6540 (mt-10) REVERT: A 412 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.5819 (pptt) REVERT: A 441 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7531 (ttp80) REVERT: A 466 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8290 (pm20) REVERT: B 85 LYS cc_start: 0.8499 (ttmm) cc_final: 0.7998 (tttp) REVERT: B 235 ARG cc_start: 0.7647 (ttm110) cc_final: 0.7392 (ttm-80) REVERT: B 449 ARG cc_start: 0.8403 (ttt90) cc_final: 0.8176 (ttt-90) REVERT: B 500 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7104 (mt) REVERT: B 560 GLU cc_start: 0.7589 (tt0) cc_final: 0.7337 (tt0) REVERT: C 5 ASN cc_start: 0.6552 (t0) cc_final: 0.6313 (t0) REVERT: C 6 ASP cc_start: 0.7431 (p0) cc_final: 0.7128 (m-30) REVERT: C 30 LYS cc_start: 0.8417 (ttmm) cc_final: 0.7842 (mptp) REVERT: C 68 LYS cc_start: 0.8313 (ttpp) cc_final: 0.8101 (ttpp) REVERT: C 88 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7495 (ttm110) REVERT: C 141 ARG cc_start: 0.8597 (mtt90) cc_final: 0.8310 (mtm-85) REVERT: C 174 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7092 (mm-30) REVERT: C 204 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8148 (p0) REVERT: C 300 PHE cc_start: 0.8135 (p90) cc_final: 0.7778 (p90) REVERT: C 303 ASP cc_start: 0.8190 (p0) cc_final: 0.7838 (p0) REVERT: C 309 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7804 (ptm160) REVERT: C 354 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8706 (mtmm) REVERT: C 377 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8776 (mp) REVERT: C 436 ASP cc_start: 0.7884 (t0) cc_final: 0.7660 (t0) REVERT: C 536 LYS cc_start: 0.8115 (mppt) cc_final: 0.7714 (mppt) REVERT: D 30 LYS cc_start: 0.8433 (ttmm) cc_final: 0.7852 (mtmm) REVERT: D 62 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7552 (mm-30) REVERT: D 70 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7722 (pttm) REVERT: D 88 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7716 (ttp-110) REVERT: D 118 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8549 (tp) REVERT: D 141 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8283 (mtm-85) REVERT: D 206 ASP cc_start: 0.8724 (m-30) cc_final: 0.8499 (m-30) REVERT: D 309 ARG cc_start: 0.8576 (mtm180) cc_final: 0.8340 (mtm180) REVERT: D 377 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8824 (mp) REVERT: D 386 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8699 (mp0) REVERT: D 407 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8014 (ptpp) REVERT: D 445 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: D 485 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.8093 (mmm) REVERT: E 28 GLU cc_start: 0.8017 (tp30) cc_final: 0.7743 (tp30) REVERT: E 30 LYS cc_start: 0.8528 (mmmm) cc_final: 0.8285 (tppt) REVERT: E 101 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8010 (pm20) REVERT: E 330 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7883 (tp) REVERT: E 362 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8375 (mt) REVERT: F 26 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8222 (tm) REVERT: F 27 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: F 28 GLU cc_start: 0.8067 (tp30) cc_final: 0.7778 (tp30) REVERT: F 30 LYS cc_start: 0.8519 (mmmm) cc_final: 0.8285 (tppt) REVERT: F 118 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8921 (tp) REVERT: F 235 ARG cc_start: 0.7552 (tpt-90) cc_final: 0.7323 (mtp-110) REVERT: F 312 LYS cc_start: 0.7957 (mmtm) cc_final: 0.7572 (mmmt) REVERT: F 321 SER cc_start: 0.5558 (OUTLIER) cc_final: 0.5241 (p) REVERT: F 362 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8400 (mt) REVERT: F 473 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: F 547 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8045 (mttm) REVERT: G 226 LYS cc_start: 0.8215 (ttmt) cc_final: 0.8000 (ttmm) REVERT: G 231 LYS cc_start: 0.8254 (mtpm) cc_final: 0.7942 (mtpp) REVERT: G 283 ARG cc_start: 0.8574 (mtt90) cc_final: 0.8319 (mtp85) REVERT: G 286 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8402 (p) REVERT: H 176 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6765 (tm-30) REVERT: H 253 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: H 260 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7237 (tp) REVERT: I 227 GLU cc_start: 0.8105 (tp30) cc_final: 0.7778 (tp30) REVERT: I 231 LYS cc_start: 0.8289 (pttp) cc_final: 0.7860 (pptt) REVERT: I 238 ARG cc_start: 0.8299 (ptp-110) cc_final: 0.8047 (mtm-85) REVERT: J 185 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6637 (ttt180) REVERT: J 230 ARG cc_start: 0.7873 (ttp-110) cc_final: 0.7431 (ttp-110) REVERT: J 238 ARG cc_start: 0.8479 (mtm110) cc_final: 0.8196 (mtm180) REVERT: J 368 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: K 174 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6750 (tt0) REVERT: K 223 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7292 (mm-30) REVERT: K 334 SER cc_start: 0.8954 (OUTLIER) cc_final: 0.8642 (m) REVERT: L 165 LYS cc_start: 0.6546 (OUTLIER) cc_final: 0.6156 (tmtt) REVERT: L 220 TYR cc_start: 0.7546 (t80) cc_final: 0.7175 (t80) REVERT: L 231 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8399 (tptm) REVERT: L 279 LYS cc_start: 0.8561 (pttt) cc_final: 0.8178 (mtmt) REVERT: L 366 TYR cc_start: 0.8402 (p90) cc_final: 0.8194 (p90) REVERT: M 257 LYS cc_start: 0.8715 (pttp) cc_final: 0.8376 (pptt) REVERT: M 277 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8899 (mt) REVERT: M 309 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8694 (mt-10) REVERT: M 312 ILE cc_start: 0.8753 (mt) cc_final: 0.8545 (mp) REVERT: M 337 GLU cc_start: 0.8279 (mp0) cc_final: 0.7733 (mp0) REVERT: M 383 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: N 254 PHE cc_start: 0.8617 (t80) cc_final: 0.8248 (t80) REVERT: N 337 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8024 (mm-30) REVERT: O 253 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7236 (tm-30) REVERT: P 253 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: P 279 LYS cc_start: 0.8008 (pttp) cc_final: 0.7612 (mptp) REVERT: P 385 LYS cc_start: 0.7663 (mppt) cc_final: 0.7451 (mppt) REVERT: Q 253 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: Q 279 LYS cc_start: 0.8027 (pttp) cc_final: 0.7754 (mptp) REVERT: Q 299 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8642 (tp) REVERT: R 327 LYS cc_start: 0.8401 (ttpt) cc_final: 0.8126 (tttt) outliers start: 270 outliers final: 112 residues processed: 813 average time/residue: 1.2910 time to fit residues: 1309.7183 Evaluate side-chains 731 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 575 time to evaluate : 4.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 192 GLU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 321 SER Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 466 GLN Chi-restraints excluded: chain F residue 473 GLU Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 547 LYS Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 260 ILE Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 185 ARG Chi-restraints excluded: chain J residue 315 ASP Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 368 GLU Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain K residue 181 SER Chi-restraints excluded: chain K residue 192 CYS Chi-restraints excluded: chain K residue 207 SER Chi-restraints excluded: chain K residue 223 GLU Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 262 THR Chi-restraints excluded: chain K residue 325 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 165 LYS Chi-restraints excluded: chain L residue 206 GLU Chi-restraints excluded: chain L residue 231 LYS Chi-restraints excluded: chain L residue 347 ASP Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain M residue 229 LEU Chi-restraints excluded: chain M residue 243 THR Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 255 GLN Chi-restraints excluded: chain M residue 277 LEU Chi-restraints excluded: chain M residue 286 SER Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 244 SER Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 243 THR Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain P residue 244 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 286 SER Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 334 SER Chi-restraints excluded: chain P residue 335 ASN Chi-restraints excluded: chain P residue 367 THR Chi-restraints excluded: chain P residue 379 GLN Chi-restraints excluded: chain Q residue 243 THR Chi-restraints excluded: chain Q residue 244 SER Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 257 LYS Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 367 THR Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 380 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 513 optimal weight: 3.9990 chunk 269 optimal weight: 3.9990 chunk 383 optimal weight: 7.9990 chunk 240 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 chunk 477 optimal weight: 4.9990 chunk 210 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 468 optimal weight: 6.9990 chunk 464 optimal weight: 0.9980 chunk 291 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 263 HIS A 331 ASN A 466 GLN A 480 ASN C 234 GLN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN C 509 ASN D 48 GLN D 263 HIS D 331 ASN D 466 GLN E 67 GLN E 232 HIS E 308 HIS F 232 HIS ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 GLN H 364 GLN I 344 ASN I 354 ASN J 167 HIS ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.152815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116865 restraints weight = 57283.891| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.15 r_work: 0.3079 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 49284 Z= 0.307 Angle : 0.534 12.336 66498 Z= 0.281 Chirality : 0.045 0.201 7248 Planarity : 0.004 0.060 8610 Dihedral : 4.559 32.910 6343 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.97 % Allowed : 26.61 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.11), residues: 5850 helix: 0.22 (0.11), residues: 2230 sheet: -1.25 (0.17), residues: 940 loop : -0.32 (0.12), residues: 2680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 274 HIS 0.009 0.001 HIS F 232 PHE 0.022 0.001 PHE D 300 TYR 0.021 0.002 TYR J 188 ARG 0.009 0.001 ARG H 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 272 poor density : 591 time to evaluate : 4.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8354 (mtmt) REVERT: A 30 LYS cc_start: 0.8192 (mptp) cc_final: 0.7748 (mptt) REVERT: A 85 LYS cc_start: 0.8427 (ttmm) cc_final: 0.7904 (tttp) REVERT: A 174 GLU cc_start: 0.7038 (tp30) cc_final: 0.6556 (mt-10) REVERT: A 412 LYS cc_start: 0.6376 (OUTLIER) cc_final: 0.5860 (pptt) REVERT: A 441 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7499 (ttp80) REVERT: B 85 LYS cc_start: 0.8485 (ttmm) cc_final: 0.7937 (tttp) REVERT: B 192 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8309 (mt-10) REVERT: B 235 ARG cc_start: 0.7628 (ttm110) cc_final: 0.7385 (ttm-80) REVERT: B 372 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.9029 (mmtm) REVERT: B 467 ARG cc_start: 0.8349 (ttt90) cc_final: 0.7886 (ttp-110) REVERT: B 560 GLU cc_start: 0.7616 (tt0) cc_final: 0.7289 (tt0) REVERT: C 5 ASN cc_start: 0.6544 (t0) cc_final: 0.6216 (t0) REVERT: C 6 ASP cc_start: 0.7480 (p0) cc_final: 0.7095 (m-30) REVERT: C 18 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8534 (ttpp) REVERT: C 30 LYS cc_start: 0.8420 (ttmm) cc_final: 0.7818 (mptp) REVERT: C 88 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7404 (ttm110) REVERT: C 141 ARG cc_start: 0.8608 (mtt90) cc_final: 0.8314 (mtm-85) REVERT: C 204 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8137 (p0) REVERT: C 309 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7856 (ptm160) REVERT: C 354 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8719 (mtmm) REVERT: C 377 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8792 (mp) REVERT: C 436 ASP cc_start: 0.7921 (t0) cc_final: 0.7676 (t0) REVERT: C 445 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: C 536 LYS cc_start: 0.8177 (mppt) cc_final: 0.7844 (mppt) REVERT: D 30 LYS cc_start: 0.8461 (ttmm) cc_final: 0.7858 (mtmm) REVERT: D 62 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7607 (mm-30) REVERT: D 68 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7804 (ttpp) REVERT: D 70 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7742 (pttm) REVERT: D 72 MET cc_start: 0.8988 (mmt) cc_final: 0.8784 (mmm) REVERT: D 88 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7475 (ttm110) REVERT: D 118 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8568 (tp) REVERT: D 141 ARG cc_start: 0.8612 (mtt90) cc_final: 0.8340 (mtm-85) REVERT: D 309 ARG cc_start: 0.8586 (mtm180) cc_final: 0.8380 (mtm180) REVERT: D 377 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8839 (mp) REVERT: D 386 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8655 (mp0) REVERT: D 407 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8067 (ptpp) REVERT: D 411 ARG cc_start: 0.5391 (OUTLIER) cc_final: 0.5115 (mmt180) REVERT: D 445 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: D 485 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.8144 (mmm) REVERT: E 27 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: E 28 GLU cc_start: 0.8096 (tp30) cc_final: 0.7804 (tp30) REVERT: E 30 LYS cc_start: 0.8558 (mmmm) cc_final: 0.8287 (tppt) REVERT: E 101 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: E 118 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9023 (tp) REVERT: E 330 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7894 (tp) REVERT: E 362 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8384 (mt) REVERT: F 28 GLU cc_start: 0.8112 (tp30) cc_final: 0.7791 (tp30) REVERT: F 30 LYS cc_start: 0.8548 (mmmm) cc_final: 0.8287 (tppt) REVERT: F 64 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8243 (ttmt) REVERT: F 118 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8929 (tp) REVERT: F 235 ARG cc_start: 0.7583 (tpt-90) cc_final: 0.7348 (mtp-110) REVERT: F 312 LYS cc_start: 0.7913 (mmtm) cc_final: 0.7553 (mmmt) REVERT: F 321 SER cc_start: 0.5527 (OUTLIER) cc_final: 0.5219 (p) REVERT: F 330 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7960 (mt) REVERT: F 362 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8398 (mt) REVERT: G 223 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7369 (mm-30) REVERT: G 226 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7986 (ttmm) REVERT: G 283 ARG cc_start: 0.8601 (mtt90) cc_final: 0.8315 (mtp85) REVERT: G 286 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8399 (p) REVERT: H 158 LYS cc_start: 0.5857 (pmtt) cc_final: 0.5212 (pmtt) REVERT: H 176 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6843 (tm-30) REVERT: H 231 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8584 (tptm) REVERT: H 253 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: I 231 LYS cc_start: 0.8281 (pttp) cc_final: 0.7954 (pptt) REVERT: I 238 ARG cc_start: 0.8319 (ptp-110) cc_final: 0.8008 (mtm180) REVERT: J 185 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6783 (ttt180) REVERT: J 230 ARG cc_start: 0.7834 (ttp-110) cc_final: 0.7389 (ttp-170) REVERT: J 238 ARG cc_start: 0.8452 (mtm110) cc_final: 0.8162 (mtm180) REVERT: J 368 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: K 171 GLU cc_start: 0.6727 (pm20) cc_final: 0.6451 (pm20) REVERT: K 174 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6580 (tt0) REVERT: K 223 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7297 (mm-30) REVERT: K 238 ARG cc_start: 0.8061 (ptp-110) cc_final: 0.7311 (ptp90) REVERT: K 283 ARG cc_start: 0.8365 (mmm160) cc_final: 0.8119 (mtp85) REVERT: L 220 TYR cc_start: 0.7516 (t80) cc_final: 0.7173 (t80) REVERT: L 279 LYS cc_start: 0.8590 (pttt) cc_final: 0.8186 (mttt) REVERT: L 366 TYR cc_start: 0.8416 (p90) cc_final: 0.8180 (p90) REVERT: M 257 LYS cc_start: 0.8696 (pttp) cc_final: 0.8147 (ptpp) REVERT: M 277 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8857 (mt) REVERT: M 312 ILE cc_start: 0.8757 (mt) cc_final: 0.8543 (mp) REVERT: M 337 GLU cc_start: 0.8409 (mp0) cc_final: 0.7863 (mp0) REVERT: M 383 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: N 254 PHE cc_start: 0.8648 (t80) cc_final: 0.8361 (t80) REVERT: N 337 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7981 (mm-30) REVERT: O 253 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: O 257 LYS cc_start: 0.8296 (ptpt) cc_final: 0.7911 (pptt) REVERT: P 253 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: P 279 LYS cc_start: 0.7995 (pttp) cc_final: 0.7597 (mptp) REVERT: Q 253 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8008 (tt0) REVERT: Q 279 LYS cc_start: 0.8000 (pttp) cc_final: 0.7728 (mptp) REVERT: Q 299 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8651 (tp) REVERT: R 314 THR cc_start: 0.9107 (p) cc_final: 0.8847 (t) REVERT: R 327 LYS cc_start: 0.8433 (ttpt) cc_final: 0.8130 (tttt) outliers start: 272 outliers final: 120 residues processed: 789 average time/residue: 1.3562 time to fit residues: 1337.0920 Evaluate side-chains 711 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 545 time to evaluate : 4.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 411 ARG Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 192 GLU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 321 SER Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 466 GLN Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain H residue 231 LYS Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain J residue 185 ARG Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 315 ASP Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 368 GLU Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain K residue 181 SER Chi-restraints excluded: chain K residue 192 CYS Chi-restraints excluded: chain K residue 207 SER Chi-restraints excluded: chain K residue 223 GLU Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 260 ILE Chi-restraints excluded: chain K residue 262 THR Chi-restraints excluded: chain K residue 325 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 206 GLU Chi-restraints excluded: chain L residue 347 ASP Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain M residue 227 GLU Chi-restraints excluded: chain M residue 229 LEU Chi-restraints excluded: chain M residue 243 THR Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 255 GLN Chi-restraints excluded: chain M residue 277 LEU Chi-restraints excluded: chain M residue 286 SER Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 244 SER Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 243 THR Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain P residue 244 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 258 THR Chi-restraints excluded: chain P residue 286 SER Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 334 SER Chi-restraints excluded: chain P residue 335 ASN Chi-restraints excluded: chain P residue 367 THR Chi-restraints excluded: chain Q residue 243 THR Chi-restraints excluded: chain Q residue 244 SER Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 257 LYS Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 367 THR Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 380 VAL Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 334 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 475 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 469 optimal weight: 2.9990 chunk 565 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 405 HIS A 480 ASN C 58 ASN C 234 GLN C 331 ASN C 466 GLN C 509 ASN D 48 GLN D 67 GLN D 234 GLN D 331 ASN D 466 GLN E 67 GLN E 232 HIS E 251 GLN E 306 ASN E 308 HIS F 232 HIS ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 354 ASN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 GLN L 255 GLN L 383 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.152661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116569 restraints weight = 57099.364| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.09 r_work: 0.3074 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 49284 Z= 0.314 Angle : 0.533 11.843 66498 Z= 0.280 Chirality : 0.045 0.204 7248 Planarity : 0.004 0.062 8610 Dihedral : 4.556 33.373 6343 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.95 % Allowed : 26.55 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.11), residues: 5850 helix: 0.31 (0.11), residues: 2230 sheet: -1.21 (0.17), residues: 926 loop : -0.34 (0.12), residues: 2694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 213 HIS 0.009 0.001 HIS F 232 PHE 0.026 0.001 PHE L 184 TYR 0.024 0.002 TYR J 188 ARG 0.011 0.001 ARG E 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 271 poor density : 587 time to evaluate : 4.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8649 (mtpp) cc_final: 0.8446 (mppt) REVERT: A 30 LYS cc_start: 0.8206 (mptp) cc_final: 0.7751 (mptt) REVERT: A 85 LYS cc_start: 0.8436 (ttmm) cc_final: 0.7824 (tttm) REVERT: A 408 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7839 (mtpt) REVERT: A 412 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.5903 (pptt) REVERT: A 441 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7395 (ttp80) REVERT: A 445 GLU cc_start: 0.8431 (pt0) cc_final: 0.8105 (mm-30) REVERT: B 20 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8343 (mppt) REVERT: B 30 LYS cc_start: 0.8287 (mptp) cc_final: 0.7804 (mptt) REVERT: B 85 LYS cc_start: 0.8460 (ttmm) cc_final: 0.7922 (tttp) REVERT: B 132 LYS cc_start: 0.9085 (mtpp) cc_final: 0.8858 (mtmt) REVERT: B 192 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8307 (mt-10) REVERT: B 235 ARG cc_start: 0.7639 (ttm110) cc_final: 0.7395 (ttm-80) REVERT: B 372 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.9018 (mmtm) REVERT: B 449 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8113 (ttt-90) REVERT: B 467 ARG cc_start: 0.8365 (ttt90) cc_final: 0.7935 (ttm-80) REVERT: B 560 GLU cc_start: 0.7614 (tt0) cc_final: 0.7283 (tt0) REVERT: C 5 ASN cc_start: 0.6545 (t0) cc_final: 0.6307 (t160) REVERT: C 6 ASP cc_start: 0.7494 (p0) cc_final: 0.7017 (m-30) REVERT: C 18 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8552 (ttpp) REVERT: C 30 LYS cc_start: 0.8423 (ttmm) cc_final: 0.7837 (mptp) REVERT: C 88 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7466 (ttm110) REVERT: C 141 ARG cc_start: 0.8610 (mtt90) cc_final: 0.8290 (mtm-85) REVERT: C 174 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6986 (mm-30) REVERT: C 204 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8140 (p0) REVERT: C 309 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7843 (ptm160) REVERT: C 331 ASN cc_start: 0.8577 (m110) cc_final: 0.8323 (m-40) REVERT: C 354 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8623 (mtmm) REVERT: C 377 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8806 (mp) REVERT: C 445 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: C 536 LYS cc_start: 0.8188 (mppt) cc_final: 0.7765 (mppt) REVERT: D 30 LYS cc_start: 0.8474 (ttmm) cc_final: 0.7870 (mtmm) REVERT: D 62 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7590 (mm-30) REVERT: D 70 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7750 (pttm) REVERT: D 88 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7688 (ttp-110) REVERT: D 118 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8573 (tp) REVERT: D 141 ARG cc_start: 0.8571 (mtt90) cc_final: 0.8335 (mtm-85) REVERT: D 309 ARG cc_start: 0.8599 (mtm180) cc_final: 0.8387 (mtm180) REVERT: D 377 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8850 (mp) REVERT: D 407 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8027 (ptpp) REVERT: D 411 ARG cc_start: 0.5377 (OUTLIER) cc_final: 0.5051 (mmt180) REVERT: D 485 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.8156 (mmm) REVERT: E 27 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: E 28 GLU cc_start: 0.8137 (tp30) cc_final: 0.7853 (tp30) REVERT: E 101 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8044 (pm20) REVERT: E 118 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9009 (tp) REVERT: E 235 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7090 (ttt180) REVERT: E 312 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7868 (mmmt) REVERT: E 321 SER cc_start: 0.5833 (OUTLIER) cc_final: 0.5430 (p) REVERT: E 362 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8378 (mt) REVERT: E 521 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8805 (mm) REVERT: F 28 GLU cc_start: 0.8110 (tp30) cc_final: 0.7796 (tp30) REVERT: F 30 LYS cc_start: 0.8542 (mmmm) cc_final: 0.8286 (tppt) REVERT: F 64 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8258 (ttmt) REVERT: F 80 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9092 (tp) REVERT: F 118 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8928 (tp) REVERT: F 235 ARG cc_start: 0.7632 (tpt-90) cc_final: 0.7389 (mtp-110) REVERT: F 312 LYS cc_start: 0.7871 (mmtm) cc_final: 0.7569 (mmmt) REVERT: F 321 SER cc_start: 0.5517 (OUTLIER) cc_final: 0.5213 (p) REVERT: F 330 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7994 (mt) REVERT: F 362 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8386 (mt) REVERT: G 223 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: G 226 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7964 (ttmm) REVERT: G 231 LYS cc_start: 0.8222 (mtpm) cc_final: 0.7839 (mtpp) REVERT: G 283 ARG cc_start: 0.8605 (mtt90) cc_final: 0.8327 (mtp85) REVERT: G 286 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8391 (p) REVERT: H 176 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6796 (tm-30) REVERT: H 230 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7421 (ttp80) REVERT: H 231 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8595 (tptm) REVERT: H 253 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: I 231 LYS cc_start: 0.8335 (pttp) cc_final: 0.7988 (pptt) REVERT: I 238 ARG cc_start: 0.8329 (ptp-110) cc_final: 0.8026 (mtm-85) REVERT: J 185 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6723 (ttt180) REVERT: J 230 ARG cc_start: 0.7854 (ttp-110) cc_final: 0.7406 (ttp-170) REVERT: J 238 ARG cc_start: 0.8453 (mtm110) cc_final: 0.8186 (mtm180) REVERT: J 368 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: K 171 GLU cc_start: 0.6844 (pm20) cc_final: 0.6545 (pm20) REVERT: K 174 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6581 (tt0) REVERT: K 223 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7207 (mt-10) REVERT: L 165 LYS cc_start: 0.6596 (OUTLIER) cc_final: 0.6163 (tmtt) REVERT: L 220 TYR cc_start: 0.7548 (t80) cc_final: 0.7217 (t80) REVERT: L 279 LYS cc_start: 0.8582 (pttt) cc_final: 0.8178 (mttt) REVERT: L 366 TYR cc_start: 0.8510 (p90) cc_final: 0.8252 (p90) REVERT: L 379 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7874 (mp-120) REVERT: M 257 LYS cc_start: 0.8652 (pttp) cc_final: 0.8202 (ptpp) REVERT: M 277 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8842 (mt) REVERT: M 312 ILE cc_start: 0.8751 (mt) cc_final: 0.8531 (mp) REVERT: M 337 GLU cc_start: 0.8355 (mp0) cc_final: 0.7804 (mp0) REVERT: M 383 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: N 254 PHE cc_start: 0.8740 (t80) cc_final: 0.8485 (t80) REVERT: N 337 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7974 (mm-30) REVERT: N 392 GLU cc_start: 0.8134 (mp0) cc_final: 0.7564 (mp0) REVERT: O 253 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: O 346 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8123 (mm) REVERT: P 253 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: P 279 LYS cc_start: 0.8050 (pttp) cc_final: 0.7611 (mptp) REVERT: P 299 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8631 (tm) REVERT: Q 253 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: Q 279 LYS cc_start: 0.8028 (pttp) cc_final: 0.7770 (tptt) REVERT: Q 299 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8679 (tp) REVERT: R 314 THR cc_start: 0.9115 (p) cc_final: 0.8892 (t) REVERT: R 327 LYS cc_start: 0.8461 (ttpt) cc_final: 0.8153 (tttt) outliers start: 271 outliers final: 135 residues processed: 789 average time/residue: 1.3357 time to fit residues: 1306.3326 Evaluate side-chains 751 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 564 time to evaluate : 4.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 411 ARG Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 521 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 192 GLU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 321 SER Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 466 GLN Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain H residue 231 LYS Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain I residue 379 GLN Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 185 ARG Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 368 GLU Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain K residue 161 ILE Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain K residue 181 SER Chi-restraints excluded: chain K residue 192 CYS Chi-restraints excluded: chain K residue 207 SER Chi-restraints excluded: chain K residue 223 GLU Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 260 ILE Chi-restraints excluded: chain K residue 262 THR Chi-restraints excluded: chain K residue 325 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 165 LYS Chi-restraints excluded: chain L residue 347 ASP Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 379 GLN Chi-restraints excluded: chain M residue 227 GLU Chi-restraints excluded: chain M residue 229 LEU Chi-restraints excluded: chain M residue 243 THR Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 255 GLN Chi-restraints excluded: chain M residue 277 LEU Chi-restraints excluded: chain M residue 286 SER Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 244 SER Chi-restraints excluded: chain N residue 299 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 243 THR Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain O residue 346 ILE Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain P residue 229 LEU Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain P residue 244 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 258 THR Chi-restraints excluded: chain P residue 286 SER Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 299 LEU Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 334 SER Chi-restraints excluded: chain P residue 335 ASN Chi-restraints excluded: chain P residue 367 THR Chi-restraints excluded: chain P residue 379 GLN Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 243 THR Chi-restraints excluded: chain Q residue 244 SER Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 257 LYS Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 367 THR Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 380 VAL Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 221 optimal weight: 6.9990 chunk 466 optimal weight: 7.9990 chunk 538 optimal weight: 7.9990 chunk 281 optimal weight: 0.7980 chunk 478 optimal weight: 20.0000 chunk 68 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 385 optimal weight: 10.0000 chunk 304 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 480 ASN C 234 GLN C 466 GLN C 509 ASN D 48 GLN D 58 ASN D 234 GLN D 331 ASN D 466 GLN E 67 GLN E 232 HIS E 308 HIS F 232 HIS F 240 GLN ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 HIS I 354 ASN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 GLN L 383 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.152995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116925 restraints weight = 56995.484| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.07 r_work: 0.3076 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 49284 Z= 0.282 Angle : 0.523 11.539 66498 Z= 0.276 Chirality : 0.045 0.200 7248 Planarity : 0.004 0.063 8610 Dihedral : 4.521 33.373 6343 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.66 % Allowed : 26.94 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.11), residues: 5850 helix: 0.41 (0.11), residues: 2230 sheet: -1.22 (0.17), residues: 926 loop : -0.31 (0.12), residues: 2694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 213 HIS 0.009 0.001 HIS F 232 PHE 0.029 0.001 PHE H 184 TYR 0.044 0.002 TYR H 188 ARG 0.011 0.001 ARG H 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 255 poor density : 589 time to evaluate : 4.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8185 (mptp) cc_final: 0.7767 (mptt) REVERT: A 85 LYS cc_start: 0.8429 (ttmm) cc_final: 0.7879 (tttp) REVERT: A 174 GLU cc_start: 0.7189 (tp30) cc_final: 0.6506 (mt-10) REVERT: A 412 LYS cc_start: 0.6515 (OUTLIER) cc_final: 0.5971 (pptt) REVERT: A 441 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7395 (ttp80) REVERT: A 445 GLU cc_start: 0.8406 (pt0) cc_final: 0.8124 (mm-30) REVERT: A 467 ARG cc_start: 0.8659 (ttm-80) cc_final: 0.8273 (ttp-110) REVERT: A 498 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8242 (ttp80) REVERT: B 85 LYS cc_start: 0.8437 (ttmm) cc_final: 0.7910 (tttp) REVERT: B 132 LYS cc_start: 0.9074 (mtpp) cc_final: 0.8849 (mtmt) REVERT: B 192 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8286 (mt-10) REVERT: B 235 ARG cc_start: 0.7635 (ttm110) cc_final: 0.7374 (ttm-80) REVERT: B 467 ARG cc_start: 0.8303 (ttt90) cc_final: 0.7941 (ttm-80) REVERT: B 560 GLU cc_start: 0.7601 (tt0) cc_final: 0.7279 (tt0) REVERT: C 5 ASN cc_start: 0.6489 (t0) cc_final: 0.6256 (t160) REVERT: C 6 ASP cc_start: 0.7568 (p0) cc_final: 0.7014 (m-30) REVERT: C 18 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8531 (ttpp) REVERT: C 30 LYS cc_start: 0.8408 (ttmm) cc_final: 0.7864 (mptp) REVERT: C 88 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7404 (ttm110) REVERT: C 141 ARG cc_start: 0.8616 (mtt90) cc_final: 0.8306 (mtm-85) REVERT: C 300 PHE cc_start: 0.8152 (p90) cc_final: 0.7870 (p90) REVERT: C 309 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7849 (ptm160) REVERT: C 377 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8781 (mp) REVERT: C 445 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: C 485 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.8122 (mmm) REVERT: C 536 LYS cc_start: 0.8191 (mppt) cc_final: 0.7757 (mppt) REVERT: D 30 LYS cc_start: 0.8437 (ttmm) cc_final: 0.7845 (mtmm) REVERT: D 62 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7569 (mm-30) REVERT: D 70 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7759 (pttm) REVERT: D 88 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7456 (ttm110) REVERT: D 118 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8568 (tp) REVERT: D 141 ARG cc_start: 0.8570 (mtt90) cc_final: 0.8339 (mtm-85) REVERT: D 331 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7812 (m-40) REVERT: D 377 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8535 (mm) REVERT: D 407 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8020 (ptpp) REVERT: D 411 ARG cc_start: 0.5342 (OUTLIER) cc_final: 0.5038 (mmt180) REVERT: E 27 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: E 28 GLU cc_start: 0.8126 (tp30) cc_final: 0.7821 (tp30) REVERT: E 30 LYS cc_start: 0.8612 (mmmm) cc_final: 0.8338 (tppt) REVERT: E 101 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: E 118 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8992 (tp) REVERT: E 312 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7888 (mmmt) REVERT: E 321 SER cc_start: 0.5834 (OUTLIER) cc_final: 0.5434 (p) REVERT: E 362 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8339 (mt) REVERT: E 439 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.6658 (pttp) REVERT: E 521 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8743 (mm) REVERT: F 28 GLU cc_start: 0.8120 (tp30) cc_final: 0.7812 (tp30) REVERT: F 64 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8236 (ttmt) REVERT: F 80 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9089 (tp) REVERT: F 88 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7998 (ttm170) REVERT: F 118 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8921 (tp) REVERT: F 235 ARG cc_start: 0.7629 (tpt-90) cc_final: 0.7380 (mtp-110) REVERT: F 312 LYS cc_start: 0.7879 (mmtm) cc_final: 0.7601 (mmmt) REVERT: F 321 SER cc_start: 0.5521 (OUTLIER) cc_final: 0.5220 (p) REVERT: F 330 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7993 (mt) REVERT: F 362 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8393 (mt) REVERT: F 439 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6709 (pttp) REVERT: G 223 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7395 (mm-30) REVERT: G 226 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7969 (ttmm) REVERT: G 283 ARG cc_start: 0.8598 (mtt90) cc_final: 0.8319 (mtp85) REVERT: G 286 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8304 (p) REVERT: H 176 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6777 (tm-30) REVERT: H 230 ARG cc_start: 0.7660 (ttp80) cc_final: 0.7406 (ttp80) REVERT: H 231 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8582 (tptm) REVERT: H 253 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: I 231 LYS cc_start: 0.8277 (pttp) cc_final: 0.7931 (pptt) REVERT: I 238 ARG cc_start: 0.8315 (ptp-110) cc_final: 0.8007 (mtm-85) REVERT: J 185 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6748 (ttt180) REVERT: J 230 ARG cc_start: 0.7821 (ttp-110) cc_final: 0.7358 (ttp-170) REVERT: J 238 ARG cc_start: 0.8440 (mtm110) cc_final: 0.8176 (mtm180) REVERT: J 368 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: K 171 GLU cc_start: 0.6917 (pm20) cc_final: 0.6588 (pm20) REVERT: K 174 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6543 (tt0) REVERT: K 223 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7197 (mt-10) REVERT: K 238 ARG cc_start: 0.8184 (ptm160) cc_final: 0.7955 (ptp-110) REVERT: K 283 ARG cc_start: 0.8681 (mtp85) cc_final: 0.8091 (mmm160) REVERT: L 165 LYS cc_start: 0.6577 (OUTLIER) cc_final: 0.6176 (tmtt) REVERT: L 220 TYR cc_start: 0.7538 (t80) cc_final: 0.7211 (t80) REVERT: L 279 LYS cc_start: 0.8580 (pttt) cc_final: 0.8177 (mttt) REVERT: L 379 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7879 (mp-120) REVERT: M 257 LYS cc_start: 0.8652 (pttp) cc_final: 0.8238 (ptpp) REVERT: M 277 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8853 (mt) REVERT: M 312 ILE cc_start: 0.8742 (mt) cc_final: 0.8522 (mp) REVERT: M 337 GLU cc_start: 0.8330 (mp0) cc_final: 0.7769 (mp0) REVERT: M 383 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: N 254 PHE cc_start: 0.8780 (t80) cc_final: 0.8546 (t80) REVERT: N 299 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8074 (tp) REVERT: N 337 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7978 (mm-30) REVERT: N 392 GLU cc_start: 0.8133 (mp0) cc_final: 0.7558 (mp0) REVERT: O 253 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: O 346 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8081 (mm) REVERT: P 253 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: P 279 LYS cc_start: 0.8051 (pttp) cc_final: 0.7632 (mptp) REVERT: P 299 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8647 (tm) REVERT: Q 253 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: Q 279 LYS cc_start: 0.8049 (pttp) cc_final: 0.7732 (mptp) REVERT: Q 299 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8713 (tp) REVERT: R 314 THR cc_start: 0.9105 (p) cc_final: 0.8880 (t) REVERT: R 327 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8154 (tttt) outliers start: 255 outliers final: 133 residues processed: 775 average time/residue: 1.3358 time to fit residues: 1289.7418 Evaluate side-chains 740 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 555 time to evaluate : 4.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 411 ARG Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 521 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 192 GLU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 321 SER Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 439 LYS Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain H residue 231 LYS Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain I residue 379 GLN Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 185 ARG Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 368 GLU Chi-restraints excluded: chain K residue 161 ILE Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain K residue 181 SER Chi-restraints excluded: chain K residue 192 CYS Chi-restraints excluded: chain K residue 207 SER Chi-restraints excluded: chain K residue 223 GLU Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 260 ILE Chi-restraints excluded: chain K residue 262 THR Chi-restraints excluded: chain K residue 325 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 165 LYS Chi-restraints excluded: chain L residue 244 SER Chi-restraints excluded: chain L residue 347 ASP Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 379 GLN Chi-restraints excluded: chain M residue 227 GLU Chi-restraints excluded: chain M residue 229 LEU Chi-restraints excluded: chain M residue 243 THR Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 277 LEU Chi-restraints excluded: chain M residue 286 SER Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 244 SER Chi-restraints excluded: chain N residue 299 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 243 THR Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain O residue 346 ILE Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain P residue 229 LEU Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain P residue 244 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 258 THR Chi-restraints excluded: chain P residue 286 SER Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 299 LEU Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 334 SER Chi-restraints excluded: chain P residue 335 ASN Chi-restraints excluded: chain P residue 367 THR Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 243 THR Chi-restraints excluded: chain Q residue 244 SER Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 257 LYS Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 367 THR Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 380 VAL Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 317 optimal weight: 4.9990 chunk 539 optimal weight: 5.9990 chunk 438 optimal weight: 0.5980 chunk 451 optimal weight: 6.9990 chunk 399 optimal weight: 6.9990 chunk 65 optimal weight: 0.1980 chunk 298 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 517 optimal weight: 7.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 ASN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 466 GLN C 509 ASN D 48 GLN D 67 GLN D 234 GLN ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 ASN D 466 GLN E 232 HIS E 308 HIS F 232 HIS ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 HIS G 177 HIS I 354 ASN J 167 HIS ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 GLN L 255 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117934 restraints weight = 57155.181| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.05 r_work: 0.3084 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 49284 Z= 0.222 Angle : 0.505 11.308 66498 Z= 0.267 Chirality : 0.044 0.196 7248 Planarity : 0.004 0.062 8610 Dihedral : 4.426 32.881 6343 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.20 % Allowed : 27.69 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.11), residues: 5850 helix: 0.54 (0.11), residues: 2238 sheet: -1.11 (0.17), residues: 896 loop : -0.33 (0.12), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 213 HIS 0.009 0.001 HIS F 232 PHE 0.027 0.001 PHE L 184 TYR 0.032 0.001 TYR H 188 ARG 0.016 0.001 ARG E 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 581 time to evaluate : 4.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8163 (mptp) cc_final: 0.7749 (mptt) REVERT: A 85 LYS cc_start: 0.8425 (ttmm) cc_final: 0.7887 (tttp) REVERT: A 174 GLU cc_start: 0.7099 (tp30) cc_final: 0.6477 (mt-10) REVERT: A 412 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.5967 (pptt) REVERT: A 441 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7364 (ttp80) REVERT: A 445 GLU cc_start: 0.8363 (pt0) cc_final: 0.8105 (mm-30) REVERT: A 498 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8214 (ttp80) REVERT: A 560 GLU cc_start: 0.7507 (tt0) cc_final: 0.7088 (tt0) REVERT: B 20 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8334 (mppt) REVERT: B 30 LYS cc_start: 0.8267 (mptp) cc_final: 0.7811 (mptt) REVERT: B 85 LYS cc_start: 0.8433 (ttmm) cc_final: 0.7919 (tttp) REVERT: B 192 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: B 235 ARG cc_start: 0.7657 (ttm110) cc_final: 0.7422 (ttm-80) REVERT: B 408 LYS cc_start: 0.8052 (pttm) cc_final: 0.7722 (pttp) REVERT: B 445 GLU cc_start: 0.8295 (pt0) cc_final: 0.8090 (mm-30) REVERT: B 467 ARG cc_start: 0.8280 (ttt90) cc_final: 0.7993 (ttm-80) REVERT: B 560 GLU cc_start: 0.7594 (tt0) cc_final: 0.7266 (tt0) REVERT: C 6 ASP cc_start: 0.7700 (p0) cc_final: 0.7062 (m-30) REVERT: C 18 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8505 (ttpp) REVERT: C 30 LYS cc_start: 0.8393 (ttmm) cc_final: 0.7852 (mptp) REVERT: C 88 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7438 (ttm110) REVERT: C 104 LYS cc_start: 0.7992 (pttt) cc_final: 0.7750 (pttt) REVERT: C 174 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6927 (mm-30) REVERT: C 204 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8097 (p0) REVERT: C 309 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7834 (ptm160) REVERT: C 312 LYS cc_start: 0.8460 (mmmm) cc_final: 0.8253 (mmmt) REVERT: C 445 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: C 485 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.8113 (mmm) REVERT: C 536 LYS cc_start: 0.8171 (mppt) cc_final: 0.7741 (mppt) REVERT: D 30 LYS cc_start: 0.8395 (ttmm) cc_final: 0.7784 (mptp) REVERT: D 62 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7500 (mm-30) REVERT: D 70 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7770 (pttm) REVERT: D 88 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7580 (ttp-110) REVERT: D 118 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8562 (tp) REVERT: D 141 ARG cc_start: 0.8543 (mtt90) cc_final: 0.8341 (mtm-85) REVERT: D 377 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8773 (mp) REVERT: D 407 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8074 (ptpp) REVERT: D 411 ARG cc_start: 0.5283 (OUTLIER) cc_final: 0.4987 (mmt180) REVERT: D 485 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8100 (mmm) REVERT: E 28 GLU cc_start: 0.8119 (tp30) cc_final: 0.7812 (tp30) REVERT: E 30 LYS cc_start: 0.8575 (mmmm) cc_final: 0.8317 (tppt) REVERT: E 118 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.8978 (tp) REVERT: E 312 LYS cc_start: 0.8156 (mmtm) cc_final: 0.7880 (mmmt) REVERT: E 362 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8366 (mt) REVERT: E 366 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8247 (mm) REVERT: E 439 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6661 (pttp) REVERT: E 521 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8731 (mm) REVERT: F 28 GLU cc_start: 0.8109 (tp30) cc_final: 0.7783 (tp30) REVERT: F 30 LYS cc_start: 0.8586 (mmmm) cc_final: 0.8354 (tppt) REVERT: F 118 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8910 (tp) REVERT: F 235 ARG cc_start: 0.7601 (tpt-90) cc_final: 0.7374 (mtp-110) REVERT: F 330 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8010 (mt) REVERT: F 362 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8387 (mt) REVERT: G 223 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7405 (mm-30) REVERT: G 226 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7952 (ttmm) REVERT: G 283 ARG cc_start: 0.8580 (mtt90) cc_final: 0.8300 (mtp85) REVERT: G 286 SER cc_start: 0.8662 (OUTLIER) cc_final: 0.8254 (p) REVERT: H 158 LYS cc_start: 0.5825 (pmtt) cc_final: 0.5545 (ttpp) REVERT: H 176 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6671 (tm-30) REVERT: H 231 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8556 (tptm) REVERT: H 253 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: I 231 LYS cc_start: 0.8274 (pttp) cc_final: 0.7935 (pptt) REVERT: I 238 ARG cc_start: 0.8255 (ptp-110) cc_final: 0.7949 (mtm-85) REVERT: J 185 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6771 (ttt180) REVERT: J 230 ARG cc_start: 0.7835 (ttp-110) cc_final: 0.7375 (ttp-170) REVERT: J 238 ARG cc_start: 0.8433 (mtm110) cc_final: 0.8186 (mtm180) REVERT: J 368 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8016 (mt-10) REVERT: K 171 GLU cc_start: 0.6905 (pm20) cc_final: 0.6573 (pm20) REVERT: K 174 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6486 (tt0) REVERT: K 223 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7220 (mt-10) REVERT: K 283 ARG cc_start: 0.8661 (mtp85) cc_final: 0.8081 (mmm160) REVERT: K 334 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8680 (m) REVERT: L 165 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.6169 (tmtt) REVERT: L 220 TYR cc_start: 0.7478 (t80) cc_final: 0.7192 (t80) REVERT: L 279 LYS cc_start: 0.8585 (pttt) cc_final: 0.8180 (mttt) REVERT: L 379 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7799 (mp-120) REVERT: M 256 ASP cc_start: 0.7114 (m-30) cc_final: 0.6582 (p0) REVERT: M 257 LYS cc_start: 0.8664 (pttp) cc_final: 0.8214 (ptpp) REVERT: M 277 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8873 (mt) REVERT: M 312 ILE cc_start: 0.8721 (mt) cc_final: 0.8499 (mp) REVERT: M 337 GLU cc_start: 0.8308 (mp0) cc_final: 0.7765 (mp0) REVERT: M 383 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7477 (tm-30) REVERT: N 254 PHE cc_start: 0.8826 (t80) cc_final: 0.8587 (t80) REVERT: N 299 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8093 (tp) REVERT: N 337 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7944 (mm-30) REVERT: O 253 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.6880 (tm-30) REVERT: O 346 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8075 (mm) REVERT: P 253 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: P 279 LYS cc_start: 0.8036 (pttp) cc_final: 0.7627 (mptp) REVERT: Q 253 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: Q 279 LYS cc_start: 0.8016 (pttp) cc_final: 0.7718 (mptp) REVERT: Q 299 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8686 (tp) REVERT: R 314 THR cc_start: 0.9084 (p) cc_final: 0.8846 (t) REVERT: R 327 LYS cc_start: 0.8456 (ttpt) cc_final: 0.8157 (tttt) outliers start: 230 outliers final: 115 residues processed: 746 average time/residue: 1.3737 time to fit residues: 1292.6640 Evaluate side-chains 718 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 557 time to evaluate : 4.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 411 ARG Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 521 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain H residue 231 LYS Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 185 ARG Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 368 GLU Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain K residue 161 ILE Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain K residue 181 SER Chi-restraints excluded: chain K residue 192 CYS Chi-restraints excluded: chain K residue 223 GLU Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 260 ILE Chi-restraints excluded: chain K residue 262 THR Chi-restraints excluded: chain K residue 325 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 165 LYS Chi-restraints excluded: chain L residue 206 GLU Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 379 GLN Chi-restraints excluded: chain M residue 227 GLU Chi-restraints excluded: chain M residue 243 THR Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 277 LEU Chi-restraints excluded: chain M residue 286 SER Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 244 SER Chi-restraints excluded: chain N residue 299 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 243 THR Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 302 LEU Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain O residue 346 ILE Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain P residue 229 LEU Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain P residue 244 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 258 THR Chi-restraints excluded: chain P residue 286 SER Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 335 ASN Chi-restraints excluded: chain P residue 367 THR Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 243 THR Chi-restraints excluded: chain Q residue 244 SER Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 367 THR Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 380 VAL Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 301 optimal weight: 0.7980 chunk 213 optimal weight: 2.9990 chunk 357 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 263 HIS A 480 ASN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN C 234 GLN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN C 509 ASN D 5 ASN D 48 GLN D 67 GLN D 234 GLN D 466 GLN E 67 GLN E 232 HIS ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 HIS F 232 HIS ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 GLN F 308 HIS J 167 HIS ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 344 ASN L 221 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 364 GLN ** Q 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118785 restraints weight = 57004.527| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.01 r_work: 0.3111 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 49284 Z= 0.202 Angle : 0.503 10.956 66498 Z= 0.266 Chirality : 0.044 0.196 7248 Planarity : 0.004 0.063 8610 Dihedral : 4.342 32.205 6343 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.76 % Allowed : 28.27 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.11), residues: 5850 helix: 0.64 (0.11), residues: 2250 sheet: -1.19 (0.17), residues: 856 loop : -0.29 (0.12), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 213 HIS 0.010 0.001 HIS F 232 PHE 0.024 0.001 PHE D 300 TYR 0.030 0.001 TYR H 188 ARG 0.013 0.001 ARG H 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 606 time to evaluate : 4.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8141 (mptp) cc_final: 0.7907 (mptp) REVERT: A 85 LYS cc_start: 0.8412 (ttmm) cc_final: 0.7868 (tttp) REVERT: A 174 GLU cc_start: 0.7040 (tp30) cc_final: 0.6493 (mt-10) REVERT: A 412 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.5914 (pptt) REVERT: A 441 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7341 (ttp80) REVERT: A 445 GLU cc_start: 0.8342 (pt0) cc_final: 0.8113 (mm-30) REVERT: A 467 ARG cc_start: 0.8609 (ttp-110) cc_final: 0.8312 (ttp-110) REVERT: A 560 GLU cc_start: 0.7565 (tt0) cc_final: 0.7147 (tt0) REVERT: B 20 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8293 (mppt) REVERT: B 30 LYS cc_start: 0.8234 (mptp) cc_final: 0.7745 (mptt) REVERT: B 85 LYS cc_start: 0.8424 (ttmm) cc_final: 0.7876 (tttp) REVERT: B 192 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: B 235 ARG cc_start: 0.7625 (ttm110) cc_final: 0.7391 (ttm-80) REVERT: B 408 LYS cc_start: 0.7983 (pttm) cc_final: 0.7749 (pttp) REVERT: B 467 ARG cc_start: 0.8269 (ttt90) cc_final: 0.7972 (ttp-110) REVERT: B 560 GLU cc_start: 0.7586 (tt0) cc_final: 0.7240 (tt0) REVERT: C 5 ASN cc_start: 0.6467 (t0) cc_final: 0.6218 (t0) REVERT: C 6 ASP cc_start: 0.7688 (p0) cc_final: 0.7059 (m-30) REVERT: C 30 LYS cc_start: 0.8346 (ttmm) cc_final: 0.7820 (mptp) REVERT: C 88 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7501 (ttp-110) REVERT: C 104 LYS cc_start: 0.8007 (pttt) cc_final: 0.7729 (pttt) REVERT: C 174 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6988 (mm-30) REVERT: C 204 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8067 (p0) REVERT: C 300 PHE cc_start: 0.8208 (p90) cc_final: 0.7805 (p90) REVERT: C 309 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7898 (ptm160) REVERT: C 331 ASN cc_start: 0.7989 (m110) cc_final: 0.7415 (m-40) REVERT: C 445 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: C 536 LYS cc_start: 0.8153 (mppt) cc_final: 0.7727 (mppt) REVERT: D 30 LYS cc_start: 0.8325 (ttmm) cc_final: 0.7716 (mptp) REVERT: D 70 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7764 (pttm) REVERT: D 88 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7339 (ttm110) REVERT: D 118 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8548 (tp) REVERT: D 141 ARG cc_start: 0.8527 (mtt90) cc_final: 0.8326 (mtm-85) REVERT: D 407 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8071 (ptpp) REVERT: D 411 ARG cc_start: 0.5264 (OUTLIER) cc_final: 0.4988 (mmt180) REVERT: D 485 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.8097 (mmm) REVERT: E 28 GLU cc_start: 0.8077 (tp30) cc_final: 0.7768 (tp30) REVERT: E 30 LYS cc_start: 0.8519 (mmmm) cc_final: 0.8276 (tppt) REVERT: E 118 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.8962 (tp) REVERT: E 235 ARG cc_start: 0.7598 (mtp85) cc_final: 0.7151 (ttt180) REVERT: E 362 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8353 (mt) REVERT: E 366 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8246 (mm) REVERT: E 439 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6663 (pttp) REVERT: E 521 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8718 (mm) REVERT: F 7 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8240 (tp) REVERT: F 26 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8143 (tm) REVERT: F 28 GLU cc_start: 0.8103 (tp30) cc_final: 0.7785 (tp30) REVERT: F 30 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8320 (tppt) REVERT: F 118 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8907 (tp) REVERT: F 235 ARG cc_start: 0.7546 (tpt-90) cc_final: 0.7336 (mtp-110) REVERT: F 330 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8016 (mt) REVERT: F 362 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8374 (mt) REVERT: F 439 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6734 (pttp) REVERT: G 223 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7360 (mm-30) REVERT: G 226 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7938 (ttmm) REVERT: G 231 LYS cc_start: 0.8250 (mtpm) cc_final: 0.7941 (mtpp) REVERT: G 283 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8278 (mtp85) REVERT: G 286 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8175 (p) REVERT: H 158 LYS cc_start: 0.5834 (pmtt) cc_final: 0.5247 (ttpp) REVERT: H 176 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6639 (tm-30) REVERT: H 226 LYS cc_start: 0.8375 (ttpt) cc_final: 0.7771 (ttmt) REVERT: H 231 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8528 (tptm) REVERT: H 253 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8277 (tt0) REVERT: I 231 LYS cc_start: 0.8241 (pttp) cc_final: 0.7833 (pptt) REVERT: I 238 ARG cc_start: 0.8222 (ptp-110) cc_final: 0.7896 (mtm-85) REVERT: J 230 ARG cc_start: 0.7808 (ttp-110) cc_final: 0.7346 (ttp-170) REVERT: J 238 ARG cc_start: 0.8419 (mtm110) cc_final: 0.8084 (mtm-85) REVERT: K 171 GLU cc_start: 0.6918 (pm20) cc_final: 0.6527 (pm20) REVERT: K 174 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6349 (tt0) REVERT: K 223 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: K 283 ARG cc_start: 0.8632 (mtp85) cc_final: 0.8070 (mmm160) REVERT: K 334 SER cc_start: 0.8958 (OUTLIER) cc_final: 0.8710 (m) REVERT: L 165 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.6166 (tmtt) REVERT: L 220 TYR cc_start: 0.7430 (t80) cc_final: 0.7151 (t80) REVERT: L 279 LYS cc_start: 0.8582 (pttt) cc_final: 0.8155 (mttt) REVERT: L 379 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7782 (mp-120) REVERT: M 255 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7716 (mt0) REVERT: M 256 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6653 (p0) REVERT: M 257 LYS cc_start: 0.8647 (pttp) cc_final: 0.8167 (ptpp) REVERT: M 312 ILE cc_start: 0.8720 (mt) cc_final: 0.8492 (mp) REVERT: M 337 GLU cc_start: 0.8295 (mp0) cc_final: 0.7722 (mp0) REVERT: M 383 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: N 254 PHE cc_start: 0.8814 (t80) cc_final: 0.8590 (t80) REVERT: N 299 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8088 (tp) REVERT: N 337 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7950 (mm-30) REVERT: O 253 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.6830 (tm-30) REVERT: O 257 LYS cc_start: 0.8325 (ptpt) cc_final: 0.7958 (pptt) REVERT: O 346 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8087 (mm) REVERT: P 233 LYS cc_start: 0.7712 (tttp) cc_final: 0.7456 (tttp) REVERT: P 253 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: P 279 LYS cc_start: 0.8035 (pttp) cc_final: 0.7613 (mptp) REVERT: P 299 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8660 (tm) REVERT: Q 253 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: Q 279 LYS cc_start: 0.8096 (pttp) cc_final: 0.7763 (mptp) REVERT: Q 299 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8678 (tp) REVERT: R 314 THR cc_start: 0.9057 (p) cc_final: 0.8814 (t) REVERT: R 327 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8137 (tttt) outliers start: 206 outliers final: 106 residues processed: 752 average time/residue: 1.2697 time to fit residues: 1193.2159 Evaluate side-chains 707 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 557 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 411 ARG Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 521 ILE Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 439 LYS Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain H residue 231 LYS Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain K residue 161 ILE Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain K residue 181 SER Chi-restraints excluded: chain K residue 192 CYS Chi-restraints excluded: chain K residue 223 GLU Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 260 ILE Chi-restraints excluded: chain K residue 262 THR Chi-restraints excluded: chain K residue 325 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 165 LYS Chi-restraints excluded: chain L residue 244 SER Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 379 GLN Chi-restraints excluded: chain M residue 227 GLU Chi-restraints excluded: chain M residue 243 THR Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 255 GLN Chi-restraints excluded: chain M residue 256 ASP Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 244 SER Chi-restraints excluded: chain N residue 299 LEU Chi-restraints excluded: chain N residue 330 ILE Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 243 THR Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 302 LEU Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain O residue 346 ILE Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain P residue 229 LEU Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain P residue 244 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 258 THR Chi-restraints excluded: chain P residue 286 SER Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 299 LEU Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 335 ASN Chi-restraints excluded: chain P residue 367 THR Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 244 SER Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 367 THR Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 380 VAL Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 83 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 323 optimal weight: 9.9990 chunk 365 optimal weight: 7.9990 chunk 574 optimal weight: 6.9990 chunk 565 optimal weight: 0.8980 chunk 389 optimal weight: 0.9980 chunk 328 optimal weight: 2.9990 chunk 417 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 263 HIS A 374 ASN A 480 ASN B 480 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN D 48 GLN D 67 GLN D 234 GLN D 466 GLN E 232 HIS ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 HIS F 232 HIS ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 HIS ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 GLN L 255 GLN O 273 ASN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.152898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116963 restraints weight = 57055.176| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.09 r_work: 0.3077 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 49284 Z= 0.312 Angle : 0.547 10.951 66498 Z= 0.287 Chirality : 0.045 0.236 7248 Planarity : 0.004 0.074 8610 Dihedral : 4.476 33.085 6343 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.42 % Allowed : 28.87 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.11), residues: 5850 helix: 0.57 (0.11), residues: 2246 sheet: -1.29 (0.17), residues: 926 loop : -0.30 (0.12), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 213 HIS 0.010 0.001 HIS E 232 PHE 0.030 0.001 PHE C 332 TYR 0.030 0.002 TYR L 188 ARG 0.015 0.001 ARG H 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 570 time to evaluate : 4.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8205 (mptp) cc_final: 0.7833 (mptt) REVERT: A 85 LYS cc_start: 0.8413 (ttmm) cc_final: 0.7868 (tttp) REVERT: A 174 GLU cc_start: 0.7182 (tp30) cc_final: 0.6453 (mt-10) REVERT: A 408 LYS cc_start: 0.8190 (mtpt) cc_final: 0.7905 (mtpp) REVERT: A 412 LYS cc_start: 0.6439 (OUTLIER) cc_final: 0.5902 (pptt) REVERT: A 441 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7377 (ttp80) REVERT: A 445 GLU cc_start: 0.8365 (pt0) cc_final: 0.8137 (mm-30) REVERT: A 560 GLU cc_start: 0.7492 (tt0) cc_final: 0.7064 (tt0) REVERT: B 20 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8315 (mppt) REVERT: B 85 LYS cc_start: 0.8396 (ttmm) cc_final: 0.7864 (tttp) REVERT: B 192 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8233 (mt-10) REVERT: B 235 ARG cc_start: 0.7624 (ttm110) cc_final: 0.7414 (ttm-80) REVERT: B 408 LYS cc_start: 0.7993 (pttm) cc_final: 0.7748 (pttp) REVERT: B 467 ARG cc_start: 0.8247 (ttt90) cc_final: 0.7984 (ttp-110) REVERT: B 498 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8157 (ttp80) REVERT: B 560 GLU cc_start: 0.7629 (tt0) cc_final: 0.7315 (tt0) REVERT: C 5 ASN cc_start: 0.6482 (t0) cc_final: 0.6277 (t0) REVERT: C 6 ASP cc_start: 0.7833 (p0) cc_final: 0.7130 (m-30) REVERT: C 30 LYS cc_start: 0.8422 (ttmm) cc_final: 0.7867 (mptp) REVERT: C 88 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7553 (ttm110) REVERT: C 104 LYS cc_start: 0.8005 (pttt) cc_final: 0.7764 (pttt) REVERT: C 204 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8109 (p0) REVERT: C 309 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7914 (ptm160) REVERT: C 445 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: C 485 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.8088 (mmm) REVERT: C 536 LYS cc_start: 0.8164 (mppt) cc_final: 0.7744 (mppt) REVERT: D 30 LYS cc_start: 0.8397 (ttmm) cc_final: 0.7810 (mtmm) REVERT: D 62 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7449 (mm-30) REVERT: D 70 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7722 (pttm) REVERT: D 88 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7687 (ttp-110) REVERT: D 118 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8563 (tp) REVERT: D 141 ARG cc_start: 0.8563 (mtt90) cc_final: 0.8357 (mtm-85) REVERT: D 407 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8046 (ptpp) REVERT: D 411 ARG cc_start: 0.5293 (OUTLIER) cc_final: 0.5000 (mmt180) REVERT: D 485 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.8085 (mmm) REVERT: E 28 GLU cc_start: 0.8117 (tp30) cc_final: 0.7817 (tp30) REVERT: E 118 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8941 (tp) REVERT: E 218 ASP cc_start: 0.8546 (m-30) cc_final: 0.8338 (m-30) REVERT: E 235 ARG cc_start: 0.7761 (mtp85) cc_final: 0.7221 (ttt180) REVERT: E 321 SER cc_start: 0.5868 (OUTLIER) cc_final: 0.5463 (p) REVERT: E 362 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8390 (mt) REVERT: E 366 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8308 (mm) REVERT: E 439 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6675 (pttp) REVERT: F 20 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8644 (tptt) REVERT: F 28 GLU cc_start: 0.8124 (tp30) cc_final: 0.7798 (tp30) REVERT: F 30 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8319 (tppt) REVERT: F 118 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.8929 (tp) REVERT: F 235 ARG cc_start: 0.7638 (tpt-90) cc_final: 0.7414 (mtp-110) REVERT: F 302 PHE cc_start: 0.7914 (t80) cc_final: 0.7665 (t80) REVERT: F 330 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8002 (mt) REVERT: F 362 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8405 (mt) REVERT: F 439 LYS cc_start: 0.7375 (OUTLIER) cc_final: 0.6778 (pttp) REVERT: G 223 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: G 226 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7942 (ttmm) REVERT: G 231 LYS cc_start: 0.8268 (mtpm) cc_final: 0.7950 (mtpp) REVERT: G 283 ARG cc_start: 0.8604 (mtt90) cc_final: 0.8323 (mtp85) REVERT: G 286 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.8283 (p) REVERT: H 158 LYS cc_start: 0.5953 (pmtt) cc_final: 0.5298 (ttpp) REVERT: H 230 ARG cc_start: 0.7621 (ttp80) cc_final: 0.7355 (ttp80) REVERT: H 231 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8572 (tptm) REVERT: H 253 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: I 231 LYS cc_start: 0.8244 (pttp) cc_final: 0.7912 (pptt) REVERT: I 238 ARG cc_start: 0.8241 (ptp-110) cc_final: 0.7924 (mtm-85) REVERT: J 230 ARG cc_start: 0.7847 (ttp-110) cc_final: 0.7375 (ttp-170) REVERT: J 238 ARG cc_start: 0.8427 (mtm110) cc_final: 0.8127 (mtm180) REVERT: K 171 GLU cc_start: 0.6953 (pm20) cc_final: 0.6567 (pm20) REVERT: K 174 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6478 (tt0) REVERT: K 223 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7332 (mt-10) REVERT: K 283 ARG cc_start: 0.8684 (mtp85) cc_final: 0.8098 (mmm160) REVERT: K 334 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8685 (m) REVERT: L 220 TYR cc_start: 0.7488 (t80) cc_final: 0.7213 (t80) REVERT: L 279 LYS cc_start: 0.8567 (pttt) cc_final: 0.8172 (mttt) REVERT: L 379 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7921 (mp-120) REVERT: M 255 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7712 (mt0) REVERT: M 257 LYS cc_start: 0.8677 (pttp) cc_final: 0.8251 (ptpp) REVERT: M 312 ILE cc_start: 0.8733 (mt) cc_final: 0.8500 (mp) REVERT: M 337 GLU cc_start: 0.8299 (mp0) cc_final: 0.7722 (mp0) REVERT: M 383 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: N 299 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8108 (tp) REVERT: N 337 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7969 (mm-30) REVERT: O 253 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.6887 (tm-30) REVERT: O 346 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8098 (mm) REVERT: P 233 LYS cc_start: 0.7727 (tttp) cc_final: 0.7453 (tttp) REVERT: P 253 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: P 279 LYS cc_start: 0.8061 (pttp) cc_final: 0.7641 (mptp) REVERT: P 299 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8639 (tm) REVERT: Q 253 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: Q 279 LYS cc_start: 0.8139 (pttp) cc_final: 0.7775 (mptp) REVERT: Q 299 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8712 (tp) REVERT: R 314 THR cc_start: 0.9055 (p) cc_final: 0.8813 (t) REVERT: R 327 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8158 (tttt) outliers start: 187 outliers final: 120 residues processed: 703 average time/residue: 1.2972 time to fit residues: 1135.9461 Evaluate side-chains 737 residues out of total 5472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 573 time to evaluate : 4.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 411 ARG Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 308 HIS Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 439 LYS Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain H residue 231 LYS Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain K residue 161 ILE Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain K residue 181 SER Chi-restraints excluded: chain K residue 192 CYS Chi-restraints excluded: chain K residue 223 GLU Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 260 ILE Chi-restraints excluded: chain K residue 262 THR Chi-restraints excluded: chain K residue 325 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 206 GLU Chi-restraints excluded: chain L residue 244 SER Chi-restraints excluded: chain L residue 347 ASP Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 379 GLN Chi-restraints excluded: chain M residue 227 GLU Chi-restraints excluded: chain M residue 243 THR Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 255 GLN Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 244 SER Chi-restraints excluded: chain N residue 279 LYS Chi-restraints excluded: chain N residue 299 LEU Chi-restraints excluded: chain N residue 330 ILE Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 243 THR Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 302 LEU Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain O residue 346 ILE Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain P residue 229 LEU Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain P residue 244 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 258 THR Chi-restraints excluded: chain P residue 286 SER Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 299 LEU Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 335 ASN Chi-restraints excluded: chain P residue 367 THR Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 243 THR Chi-restraints excluded: chain Q residue 244 SER Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 367 THR Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 380 VAL Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 388 optimal weight: 9.9990 chunk 485 optimal weight: 7.9990 chunk 391 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 498 optimal weight: 9.9990 chunk 503 optimal weight: 0.0570 chunk 500 optimal weight: 0.3980 chunk 284 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 263 HIS A 291 HIS A 374 ASN A 480 ASN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 466 GLN D 48 GLN D 67 GLN D 234 GLN D 466 GLN E 67 GLN E 232 HIS ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 HIS F 232 HIS F 308 HIS J 167 HIS ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.119618 restraints weight = 56955.813| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.98 r_work: 0.3122 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 49284 Z= 0.183 Angle : 0.499 10.907 66498 Z= 0.264 Chirality : 0.044 0.227 7248 Planarity : 0.004 0.068 8610 Dihedral : 4.327 32.287 6343 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.96 % Allowed : 29.51 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.11), residues: 5850 helix: 0.68 (0.11), residues: 2262 sheet: -1.20 (0.17), residues: 876 loop : -0.26 (0.12), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 556 HIS 0.010 0.001 HIS F 232 PHE 0.025 0.001 PHE H 215 TYR 0.030 0.001 TYR G 188 ARG 0.014 0.001 ARG H 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31622.90 seconds wall clock time: 541 minutes 37.79 seconds (32497.79 seconds total)