Starting phenix.real_space_refine on Mon Sep 23 21:08:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xav_38204/09_2024/8xav_38204.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xav_38204/09_2024/8xav_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xav_38204/09_2024/8xav_38204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xav_38204/09_2024/8xav_38204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xav_38204/09_2024/8xav_38204.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xav_38204/09_2024/8xav_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 20.20, 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: 8.16 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: 4.31 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: 16.97 Time building geometry restraints manager: 9.91 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: 0.00 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: 0.060 Extract box with map and model: 1.380 Check model and map are aligned: 0.280 Set scattering table: 0.340 Process input model: 80.200 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:10.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.380 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 30 poor density : 747 time to evaluate : 4.267 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: 1.2197 time to fit residues: 1183.0668 Evaluate side-chains 651 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 642 time to evaluate : 4.118 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 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 fitting. rotamer outliers: 294 poor density : 649 time to evaluate : 4.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.7818 (m110) cc_final: 0.7235 (m110) REVERT: A 20 LYS cc_start: 0.7770 (mtpp) cc_final: 0.6784 (mtmm) REVERT: A 30 LYS cc_start: 0.7020 (mppt) cc_final: 0.6473 (mptt) REVERT: A 85 LYS cc_start: 0.7044 (ttmm) cc_final: 0.6067 (tttp) REVERT: A 141 ARG cc_start: 0.6758 (mtm-85) cc_final: 0.6415 (mpp80) REVERT: A 145 LYS cc_start: 0.6623 (OUTLIER) cc_final: 0.6097 (mtpt) REVERT: A 152 SER cc_start: 0.7441 (m) cc_final: 0.7140 (p) REVERT: A 174 GLU cc_start: 0.7165 (tp30) cc_final: 0.6256 (mt-10) REVERT: A 412 LYS cc_start: 0.6462 (OUTLIER) cc_final: 0.5818 (pptt) REVERT: B 85 LYS cc_start: 0.7047 (ttmm) cc_final: 0.6074 (tttp) REVERT: B 141 ARG cc_start: 0.7539 (mtm-85) cc_final: 0.7289 (mtm-85) REVERT: B 145 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6416 (mtpt) REVERT: B 152 SER cc_start: 0.7069 (m) cc_final: 0.6835 (p) REVERT: B 320 SER cc_start: 0.7487 (OUTLIER) cc_final: 0.7234 (m) REVERT: B 351 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7424 (mm-30) REVERT: B 449 ARG cc_start: 0.6863 (ttt90) cc_final: 0.6179 (ttt-90) REVERT: B 467 ARG cc_start: 0.6675 (ttt90) cc_final: 0.5511 (ttp-110) REVERT: B 470 GLU cc_start: 0.7718 (mp0) cc_final: 0.6987 (pm20) REVERT: B 560 GLU cc_start: 0.6784 (tt0) cc_final: 0.6522 (tt0) REVERT: C 5 ASN cc_start: 0.5280 (t0) cc_final: 0.4759 (t160) REVERT: C 6 ASP cc_start: 0.6794 (p0) cc_final: 0.5920 (m-30) REVERT: C 30 LYS cc_start: 0.7137 (ttmm) cc_final: 0.6763 (mtpp) REVERT: C 88 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.6524 (ttm110) REVERT: C 104 LYS cc_start: 0.6394 (pttp) cc_final: 0.6018 (pttt) REVERT: C 174 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7418 (mm-30) REVERT: C 204 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7025 (p0) REVERT: C 206 ASP cc_start: 0.8135 (m-30) cc_final: 0.7729 (m-30) REVERT: C 377 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7992 (mp) REVERT: C 436 ASP cc_start: 0.7931 (t0) cc_final: 0.7233 (m-30) REVERT: C 445 GLU cc_start: 0.6522 (mp0) cc_final: 0.6025 (tt0) REVERT: C 470 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7213 (mm-30) REVERT: C 509 ASN cc_start: 0.7279 (t0) cc_final: 0.6989 (m110) REVERT: C 536 LYS cc_start: 0.7489 (mppt) cc_final: 0.6978 (mppt) REVERT: D 6 ASP cc_start: 0.6482 (p0) cc_final: 0.5861 (m-30) REVERT: D 8 ASN cc_start: 0.7955 (m-40) cc_final: 0.7712 (m-40) REVERT: D 30 LYS cc_start: 0.7216 (ttmm) cc_final: 0.6218 (mtmm) REVERT: D 67 GLN cc_start: 0.6743 (mm-40) cc_final: 0.6462 (mm-40) REVERT: D 82 LYS cc_start: 0.7533 (mtmm) cc_final: 0.7053 (mtpt) REVERT: D 88 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.6880 (ttp-110) REVERT: D 101 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: D 104 LYS cc_start: 0.6834 (pttp) cc_final: 0.6525 (pttt) REVERT: D 144 ASN cc_start: 0.8082 (p0) cc_final: 0.7690 (p0) REVERT: D 174 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7387 (mm-30) REVERT: D 253 ASP cc_start: 0.6703 (p0) cc_final: 0.6452 (p0) REVERT: D 309 ARG cc_start: 0.8096 (mtm180) cc_final: 0.7885 (mtm180) REVERT: D 335 ARG cc_start: 0.7472 (tpp80) cc_final: 0.7198 (tpm170) REVERT: D 377 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8086 (mp) REVERT: D 436 ASP cc_start: 0.7818 (t0) cc_final: 0.7247 (m-30) REVERT: D 485 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.7424 (mmm) REVERT: D 536 LYS cc_start: 0.7349 (mppt) cc_final: 0.6777 (mmtm) REVERT: E 27 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.5964 (mp0) REVERT: E 30 LYS cc_start: 0.7158 (mmmm) cc_final: 0.6748 (tppt) REVERT: E 74 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7424 (mt-10) REVERT: E 99 LYS cc_start: 0.7848 (ptmm) cc_final: 0.7618 (tttp) REVERT: E 101 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6927 (pm20) REVERT: E 106 ASP cc_start: 0.6451 (p0) cc_final: 0.6036 (m-30) REVERT: E 412 LYS cc_start: 0.5363 (OUTLIER) cc_final: 0.5140 (mmtm) REVERT: F 27 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6078 (mp0) REVERT: F 28 GLU cc_start: 0.7081 (tp30) cc_final: 0.6566 (tt0) REVERT: F 52 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8417 (mt) REVERT: F 62 GLU cc_start: 0.6983 (tp30) cc_final: 0.6769 (mp0) REVERT: F 70 LYS cc_start: 0.7833 (ttmm) cc_final: 0.7616 (ttmm) REVERT: F 106 ASP cc_start: 0.6442 (p0) cc_final: 0.6161 (m-30) REVERT: F 118 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8225 (tp) REVERT: F 177 LYS cc_start: 0.7754 (pttt) cc_final: 0.7536 (pmmt) REVERT: F 473 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: G 219 PHE cc_start: 0.7729 (m-80) cc_final: 0.7513 (m-80) REVERT: G 279 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7272 (ptpp) REVERT: G 283 ARG cc_start: 0.7304 (mtt90) cc_final: 0.6056 (mmm160) REVERT: G 286 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.7797 (p) REVERT: G 327 LYS cc_start: 0.7841 (ttpp) cc_final: 0.7633 (ttpp) REVERT: G 337 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: G 357 ASN cc_start: 0.8195 (p0) cc_final: 0.7855 (m-40) REVERT: H 176 GLU cc_start: 0.6397 (tm-30) cc_final: 0.6069 (tm-30) REVERT: H 255 GLN cc_start: 0.7910 (mt0) cc_final: 0.7614 (mt0) REVERT: H 279 LYS cc_start: 0.7469 (pttt) cc_final: 0.7262 (pttm) REVERT: H 301 GLU cc_start: 0.8061 (tp30) cc_final: 0.7560 (tp30) REVERT: H 385 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7383 (mtpt) REVERT: I 230 ARG cc_start: 0.6650 (ttp-110) cc_final: 0.5976 (ttp-110) REVERT: I 231 LYS cc_start: 0.7450 (pttp) cc_final: 0.6995 (pptt) REVERT: I 238 ARG cc_start: 0.7837 (ptp-110) cc_final: 0.7283 (mtm-85) REVERT: J 185 ARG cc_start: 0.6241 (OUTLIER) cc_final: 0.5977 (ttt180) REVERT: J 238 ARG cc_start: 0.7948 (mtm110) cc_final: 0.7441 (mtm180) REVERT: K 279 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7243 (ptpp) REVERT: K 283 ARG cc_start: 0.7113 (mmm160) cc_final: 0.6820 (mtp85) REVERT: K 337 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7540 (mm-30) REVERT: L 220 TYR cc_start: 0.7058 (t80) cc_final: 0.6475 (t80) REVERT: L 279 LYS cc_start: 0.7467 (pttt) cc_final: 0.6614 (mtmt) REVERT: L 366 TYR cc_start: 0.8292 (p90) cc_final: 0.8034 (p90) REVERT: M 257 LYS cc_start: 0.8393 (pttp) cc_final: 0.7906 (ptpp) REVERT: M 283 ARG cc_start: 0.7419 (mtm-85) cc_final: 0.7128 (mtm110) REVERT: M 312 ILE cc_start: 0.7754 (mt) cc_final: 0.7331 (mp) REVERT: M 337 GLU cc_start: 0.7786 (mp0) cc_final: 0.6943 (mp0) REVERT: M 383 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: N 317 TYR cc_start: 0.8581 (m-80) cc_final: 0.8278 (m-80) REVERT: N 337 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7537 (mm-30) REVERT: O 317 TYR cc_start: 0.8519 (m-80) cc_final: 0.8222 (m-80) REVERT: O 337 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7334 (mm-30) REVERT: P 228 TYR cc_start: 0.4532 (OUTLIER) cc_final: 0.4041 (m-80) REVERT: P 234 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: P 253 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: P 279 LYS cc_start: 0.7730 (pttp) cc_final: 0.7043 (mptp) REVERT: P 301 GLU cc_start: 0.7529 (tp30) cc_final: 0.7328 (tp30) REVERT: Q 234 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7369 (tt0) REVERT: Q 279 LYS cc_start: 0.7840 (pttp) cc_final: 0.7199 (tptt) REVERT: Q 299 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7082 (tp) REVERT: Q 301 GLU cc_start: 0.7158 (tp30) cc_final: 0.6923 (tp30) REVERT: R 283 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7413 (mtm110) REVERT: R 312 ILE cc_start: 0.7852 (mt) cc_final: 0.7445 (mm) REVERT: R 327 LYS cc_start: 0.7138 (ttpt) cc_final: 0.6600 (tttt) outliers start: 294 outliers final: 89 residues processed: 861 average time/residue: 1.3173 time to fit residues: 1408.1774 Evaluate side-chains 713 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 593 time to evaluate : 4.222 ------------------------------------------------------------------------------- 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 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 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 101 GLU 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 412 LYS Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 52 LEU 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 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 279 LYS 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 H residue 385 LYS 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 337 GLU 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 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 234 GLU 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 234 GLU 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 293 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 439 optimal weight: 10.0000 chunk 359 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 529 optimal weight: 4.9990 chunk 571 optimal weight: 1.9990 chunk 471 optimal weight: 1.9990 chunk 525 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 424 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 C 234 GLN C 245 ASN C 331 ASN D 230 ASN D 234 GLN 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: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 49284 Z= 0.244 Angle : 0.528 9.652 66498 Z= 0.280 Chirality : 0.045 0.240 7248 Planarity : 0.004 0.061 8610 Dihedral : 4.657 33.321 6345 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.42 % Allowed : 26.75 % Favored : 68.82 % 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: -0.83 (0.11), residues: 5850 helix: -0.20 (0.11), residues: 2212 sheet: -0.99 (0.17), residues: 883 loop : -0.54 (0.12), residues: 2755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 274 HIS 0.009 0.001 HIS F 232 PHE 0.017 0.001 PHE A 250 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 905 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 663 time to evaluate : 4.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.7872 (m110) cc_final: 0.7335 (m110) REVERT: A 20 LYS cc_start: 0.7625 (mtpp) cc_final: 0.6646 (mtmm) REVERT: A 30 LYS cc_start: 0.6876 (mppt) cc_final: 0.6540 (mptp) REVERT: A 85 LYS cc_start: 0.6949 (ttmm) cc_final: 0.5966 (tttp) REVERT: A 145 LYS cc_start: 0.6595 (OUTLIER) cc_final: 0.6135 (mtpt) REVERT: A 152 SER cc_start: 0.7333 (m) cc_final: 0.7072 (p) REVERT: A 174 GLU cc_start: 0.7098 (tp30) cc_final: 0.6334 (mt-10) REVERT: A 208 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6940 (tt) REVERT: A 235 ARG cc_start: 0.6557 (ttm110) cc_final: 0.6246 (ttm110) REVERT: A 239 ARG cc_start: 0.5806 (mmt90) cc_final: 0.5520 (mmt90) REVERT: A 412 LYS cc_start: 0.6481 (OUTLIER) cc_final: 0.5818 (pptt) REVERT: A 441 ARG cc_start: 0.6614 (OUTLIER) cc_final: 0.6186 (ttp80) REVERT: B 30 LYS cc_start: 0.6386 (mptp) cc_final: 0.6042 (mptp) REVERT: B 85 LYS cc_start: 0.6942 (ttmm) cc_final: 0.5976 (tttp) REVERT: B 141 ARG cc_start: 0.7453 (mtm-85) cc_final: 0.7176 (mtm-85) REVERT: B 145 LYS cc_start: 0.6796 (OUTLIER) cc_final: 0.6348 (mtpt) REVERT: B 152 SER cc_start: 0.7176 (m) cc_final: 0.6862 (p) REVERT: B 207 THR cc_start: 0.8209 (m) cc_final: 0.7984 (p) REVERT: B 339 LYS cc_start: 0.7498 (mmtt) cc_final: 0.7284 (mmtp) REVERT: B 351 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7319 (mm-30) REVERT: B 372 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8380 (mmtm) REVERT: B 449 ARG cc_start: 0.6936 (ttt90) cc_final: 0.6246 (ttt-90) REVERT: B 467 ARG cc_start: 0.6837 (ttt90) cc_final: 0.5640 (ttp-110) REVERT: B 470 GLU cc_start: 0.7934 (mp0) cc_final: 0.7047 (pm20) REVERT: B 560 GLU cc_start: 0.6827 (tt0) cc_final: 0.6478 (tt0) REVERT: C 5 ASN cc_start: 0.5523 (t0) cc_final: 0.5096 (t0) REVERT: C 6 ASP cc_start: 0.6640 (p0) cc_final: 0.5851 (m-30) REVERT: C 26 LEU cc_start: 0.7009 (tp) cc_final: 0.6785 (tm) REVERT: C 30 LYS cc_start: 0.7095 (ttmm) cc_final: 0.6097 (mptp) REVERT: C 65 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6786 (tp30) REVERT: C 67 GLN cc_start: 0.6447 (mm-40) cc_final: 0.6220 (mm-40) REVERT: C 88 ARG cc_start: 0.7862 (mmm-85) cc_final: 0.6498 (ttm110) REVERT: C 104 LYS cc_start: 0.6381 (pttp) cc_final: 0.5997 (pttt) REVERT: C 174 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7435 (mm-30) REVERT: C 204 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.6842 (p0) REVERT: C 235 ARG cc_start: 0.6217 (ttm170) cc_final: 0.5908 (ttm-80) REVERT: C 309 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7720 (ptm160) REVERT: C 436 ASP cc_start: 0.7926 (t0) cc_final: 0.7220 (m-30) REVERT: C 445 GLU cc_start: 0.6476 (mp0) cc_final: 0.6077 (tt0) REVERT: C 470 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7247 (mm-30) REVERT: C 536 LYS cc_start: 0.7487 (mppt) cc_final: 0.7095 (mppt) REVERT: D 5 ASN cc_start: 0.5449 (OUTLIER) cc_final: 0.4893 (t0) REVERT: D 6 ASP cc_start: 0.6487 (p0) cc_final: 0.5805 (m-30) REVERT: D 8 ASN cc_start: 0.7874 (m-40) cc_final: 0.7482 (m-40) REVERT: D 30 LYS cc_start: 0.7117 (ttmm) cc_final: 0.6041 (mptp) REVERT: D 62 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6455 (mm-30) REVERT: D 70 LYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6064 (pttp) REVERT: D 72 MET cc_start: 0.8087 (mmt) cc_final: 0.7743 (mmm) REVERT: D 82 LYS cc_start: 0.7542 (mtmm) cc_final: 0.7125 (mtpt) REVERT: D 88 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.6624 (ttm110) REVERT: D 101 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: D 104 LYS cc_start: 0.6850 (pttp) cc_final: 0.6514 (pttt) REVERT: D 141 ARG cc_start: 0.7495 (mtt90) cc_final: 0.6890 (mtm-85) REVERT: D 144 ASN cc_start: 0.8051 (p0) cc_final: 0.7843 (p0) REVERT: D 174 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7356 (mm-30) REVERT: D 230 ASN cc_start: 0.4962 (OUTLIER) cc_final: 0.4424 (t0) REVERT: D 309 ARG cc_start: 0.8055 (mtm180) cc_final: 0.7722 (mtm180) REVERT: D 335 ARG cc_start: 0.7409 (tpp80) cc_final: 0.7130 (tpm170) REVERT: D 407 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6655 (ptpp) REVERT: D 436 ASP cc_start: 0.7820 (t0) cc_final: 0.7262 (m-30) REVERT: D 445 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.5911 (tt0) REVERT: D 536 LYS cc_start: 0.7284 (mppt) cc_final: 0.6693 (mmtm) REVERT: E 27 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.5933 (mp0) REVERT: E 28 GLU cc_start: 0.7012 (tp30) cc_final: 0.6592 (tp30) REVERT: E 30 LYS cc_start: 0.7276 (mmmm) cc_final: 0.6800 (tppt) REVERT: E 74 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7329 (mt-10) REVERT: E 99 LYS cc_start: 0.7839 (ptmm) cc_final: 0.7614 (tttp) REVERT: E 106 ASP cc_start: 0.6418 (p0) cc_final: 0.6031 (m-30) REVERT: E 330 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7229 (tp) REVERT: E 412 LYS cc_start: 0.5405 (OUTLIER) cc_final: 0.5140 (mmtm) REVERT: F 27 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6104 (mp0) REVERT: F 28 GLU cc_start: 0.7079 (tp30) cc_final: 0.6685 (tp30) REVERT: F 62 GLU cc_start: 0.6956 (tp30) cc_final: 0.6693 (mp0) REVERT: F 82 LYS cc_start: 0.8106 (ttmm) cc_final: 0.7867 (mtmt) REVERT: F 106 ASP cc_start: 0.6422 (p0) cc_final: 0.6137 (m-30) REVERT: F 118 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8201 (tp) REVERT: F 330 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7228 (tp) REVERT: F 473 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7288 (mt-10) REVERT: G 219 PHE cc_start: 0.7760 (m-80) cc_final: 0.7504 (m-80) REVERT: G 279 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7358 (ptpt) REVERT: G 283 ARG cc_start: 0.7304 (mtt90) cc_final: 0.6626 (mtp85) REVERT: G 286 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.7668 (p) REVERT: G 337 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7537 (mm-30) REVERT: G 357 ASN cc_start: 0.8252 (p0) cc_final: 0.7904 (m-40) REVERT: H 176 GLU cc_start: 0.6401 (tm-30) cc_final: 0.6037 (tm-30) REVERT: H 255 GLN cc_start: 0.7980 (mt0) cc_final: 0.7552 (mt0) REVERT: H 260 ILE cc_start: 0.6820 (OUTLIER) cc_final: 0.6437 (tp) REVERT: H 279 LYS cc_start: 0.7497 (pttt) cc_final: 0.7293 (pttm) REVERT: H 301 GLU cc_start: 0.8000 (tp30) cc_final: 0.7791 (tp30) REVERT: H 386 ASP cc_start: 0.7048 (m-30) cc_final: 0.6391 (p0) REVERT: I 154 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7686 (p0) REVERT: I 227 GLU cc_start: 0.7703 (tp30) cc_final: 0.7316 (tp30) REVERT: I 231 LYS cc_start: 0.7452 (pttp) cc_final: 0.6932 (pptt) REVERT: I 238 ARG cc_start: 0.7736 (ptp-110) cc_final: 0.7157 (mtm180) REVERT: I 289 LEU cc_start: 0.8552 (mm) cc_final: 0.8251 (mt) REVERT: I 368 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: J 185 ARG cc_start: 0.6137 (OUTLIER) cc_final: 0.5920 (ttt180) REVERT: J 230 ARG cc_start: 0.6690 (ttp-110) cc_final: 0.6292 (ttp-110) REVERT: J 238 ARG cc_start: 0.7854 (mtm110) cc_final: 0.7308 (mtm-85) REVERT: J 289 LEU cc_start: 0.8463 (mm) cc_final: 0.8209 (mt) REVERT: K 174 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6460 (tt0) REVERT: K 223 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6652 (mm-30) REVERT: K 279 LYS cc_start: 0.7836 (pmtt) cc_final: 0.7195 (ptpt) REVERT: K 337 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: L 220 TYR cc_start: 0.7072 (t80) cc_final: 0.6701 (t80) REVERT: L 279 LYS cc_start: 0.7436 (pttt) cc_final: 0.6538 (mtmt) REVERT: L 366 TYR cc_start: 0.8188 (p90) cc_final: 0.7944 (p90) REVERT: L 379 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7623 (mp-120) REVERT: M 256 ASP cc_start: 0.6580 (m-30) cc_final: 0.6197 (p0) REVERT: M 257 LYS cc_start: 0.8374 (pttp) cc_final: 0.7940 (pptt) REVERT: M 277 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7827 (mt) REVERT: M 283 ARG cc_start: 0.7417 (mtm-85) cc_final: 0.7169 (mtm110) REVERT: M 312 ILE cc_start: 0.7716 (mt) cc_final: 0.7309 (mp) REVERT: M 337 GLU cc_start: 0.7824 (mp0) cc_final: 0.6899 (mp0) REVERT: M 363 TYR cc_start: 0.8426 (m-80) cc_final: 0.8181 (m-80) REVERT: M 383 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: N 337 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7579 (mm-30) REVERT: O 257 LYS cc_start: 0.8079 (ptpt) cc_final: 0.7636 (pptt) REVERT: O 269 LYS cc_start: 0.7188 (tppt) cc_final: 0.6927 (tppp) REVERT: O 337 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7361 (mm-30) REVERT: P 253 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7059 (tt0) REVERT: P 279 LYS cc_start: 0.7724 (pttp) cc_final: 0.7031 (mptp) REVERT: P 301 GLU cc_start: 0.7483 (tp30) cc_final: 0.7275 (tp30) REVERT: Q 234 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: Q 253 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6820 (tt0) REVERT: Q 274 TRP cc_start: 0.8022 (m100) cc_final: 0.7715 (m100) REVERT: Q 279 LYS cc_start: 0.7708 (pttp) cc_final: 0.7106 (mptp) REVERT: Q 301 GLU cc_start: 0.7182 (tp30) cc_final: 0.6860 (tp30) REVERT: R 283 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7414 (mtm110) REVERT: R 312 ILE cc_start: 0.7850 (mt) cc_final: 0.7448 (mp) REVERT: R 327 LYS cc_start: 0.7176 (ttpt) cc_final: 0.6643 (tttt) outliers start: 242 outliers final: 80 residues processed: 842 average time/residue: 1.3498 time to fit residues: 1406.9467 Evaluate side-chains 718 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 598 time to evaluate : 4.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 208 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 466 GLN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 372 LYS 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 65 GLU 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 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 5 ASN 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 101 GLU Chi-restraints excluded: chain D residue 230 ASN 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 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 27 GLU Chi-restraints excluded: chain E residue 52 LEU 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 393 SER Chi-restraints excluded: chain E residue 412 LYS 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 27 GLU 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 330 LEU Chi-restraints excluded: chain F residue 393 SER 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 279 LYS 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 260 ILE Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain J residue 185 ARG Chi-restraints excluded: chain J residue 199 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 262 THR Chi-restraints excluded: chain K residue 325 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 337 GLU 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 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 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 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 380 VAL Chi-restraints excluded: chain Q residue 234 GLU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 523 optimal weight: 0.9990 chunk 398 optimal weight: 10.0000 chunk 274 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 252 optimal weight: 20.0000 chunk 355 optimal weight: 3.9990 chunk 531 optimal weight: 6.9990 chunk 562 optimal weight: 8.9990 chunk 277 optimal weight: 8.9990 chunk 503 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN C 234 GLN C 286 ASN C 308 HIS C 466 GLN D 234 GLN D 263 HIS D 466 GLN E 67 GLN E 232 HIS E 278 ASN E 308 HIS 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 49284 Z= 0.424 Angle : 0.589 10.045 66498 Z= 0.309 Chirality : 0.047 0.207 7248 Planarity : 0.005 0.069 8610 Dihedral : 4.785 33.270 6343 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.72 % Allowed : 25.93 % Favored : 68.35 % 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: -0.80 (0.11), residues: 5850 helix: -0.08 (0.11), residues: 2244 sheet: -1.29 (0.17), residues: 940 loop : -0.46 (0.12), residues: 2666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 274 HIS 0.009 0.001 HIS E 232 PHE 0.023 0.002 PHE L 184 TYR 0.023 0.002 TYR J 188 ARG 0.010 0.001 ARG A 467 *********************** 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 916 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 603 time to evaluate : 4.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.7685 (mtpp) cc_final: 0.6659 (mtmm) REVERT: A 30 LYS cc_start: 0.7048 (mppt) cc_final: 0.6598 (mptp) REVERT: A 85 LYS cc_start: 0.6819 (ttmm) cc_final: 0.5799 (tttp) REVERT: A 145 LYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6288 (mtpt) REVERT: A 152 SER cc_start: 0.7333 (m) cc_final: 0.7027 (p) REVERT: A 235 ARG cc_start: 0.6536 (ttm110) cc_final: 0.6264 (ttm110) REVERT: A 412 LYS cc_start: 0.6726 (OUTLIER) cc_final: 0.5975 (pptt) REVERT: A 441 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.6185 (ttp80) REVERT: B 30 LYS cc_start: 0.6624 (mptp) cc_final: 0.5952 (mptt) REVERT: B 85 LYS cc_start: 0.6879 (ttmm) cc_final: 0.5857 (tttp) REVERT: B 141 ARG cc_start: 0.7592 (mtm-85) cc_final: 0.7319 (mtm-85) REVERT: B 145 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.6290 (mtpt) REVERT: B 152 SER cc_start: 0.7396 (m) cc_final: 0.7020 (p) REVERT: B 207 THR cc_start: 0.8196 (m) cc_final: 0.7938 (p) REVERT: B 351 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7430 (mm-30) REVERT: B 449 ARG cc_start: 0.6871 (ttt90) cc_final: 0.6200 (ttt-90) REVERT: B 467 ARG cc_start: 0.6815 (ttt90) cc_final: 0.5691 (ttp-110) REVERT: B 470 GLU cc_start: 0.8035 (mp0) cc_final: 0.7262 (pm20) REVERT: C 5 ASN cc_start: 0.5509 (t0) cc_final: 0.5145 (t0) REVERT: C 6 ASP cc_start: 0.6757 (p0) cc_final: 0.5860 (m-30) REVERT: C 15 SER cc_start: 0.8099 (OUTLIER) cc_final: 0.7887 (t) REVERT: C 30 LYS cc_start: 0.7156 (ttmm) cc_final: 0.6145 (mptp) REVERT: C 67 GLN cc_start: 0.6557 (mm-40) cc_final: 0.6270 (mm-40) REVERT: C 88 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6787 (ttp-110) REVERT: C 104 LYS cc_start: 0.6417 (pttp) cc_final: 0.5976 (pttt) REVERT: C 141 ARG cc_start: 0.7608 (mtt90) cc_final: 0.7009 (mtm-85) REVERT: C 174 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7404 (mm-30) REVERT: C 204 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.6951 (p0) REVERT: C 300 PHE cc_start: 0.7359 (p90) cc_final: 0.6995 (p90) REVERT: C 303 ASP cc_start: 0.7476 (p0) cc_final: 0.7263 (p0) REVERT: C 305 GLU cc_start: 0.7685 (tp30) cc_final: 0.7334 (mp0) REVERT: C 309 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7249 (ptm160) REVERT: C 377 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.8030 (mp) REVERT: C 436 ASP cc_start: 0.8011 (t0) cc_final: 0.7654 (t0) REVERT: C 445 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6291 (tt0) REVERT: C 470 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7377 (mm-30) REVERT: C 509 ASN cc_start: 0.7270 (t0) cc_final: 0.6986 (m110) REVERT: C 536 LYS cc_start: 0.7515 (mppt) cc_final: 0.7103 (mppt) REVERT: D 5 ASN cc_start: 0.5237 (OUTLIER) cc_final: 0.4772 (t0) REVERT: D 6 ASP cc_start: 0.6619 (p0) cc_final: 0.5777 (m-30) REVERT: D 8 ASN cc_start: 0.7963 (m-40) cc_final: 0.7620 (m-40) REVERT: D 15 SER cc_start: 0.8187 (OUTLIER) cc_final: 0.7984 (t) REVERT: D 30 LYS cc_start: 0.7243 (ttmm) cc_final: 0.6306 (mtmm) REVERT: D 62 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6419 (mm-30) REVERT: D 65 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6195 (mp0) REVERT: D 67 GLN cc_start: 0.6665 (mm-40) cc_final: 0.6368 (mm-40) REVERT: D 70 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6007 (pttp) REVERT: D 82 LYS cc_start: 0.7525 (mtmm) cc_final: 0.7128 (mtpt) REVERT: D 88 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.6870 (ttp-110) REVERT: D 104 LYS cc_start: 0.6650 (pttp) cc_final: 0.6218 (pttt) REVERT: D 141 ARG cc_start: 0.7617 (mtt90) cc_final: 0.6968 (mtm-85) REVERT: D 174 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7357 (mm-30) REVERT: D 309 ARG cc_start: 0.8065 (mtm180) cc_final: 0.7827 (mtm180) REVERT: D 335 ARG cc_start: 0.7467 (tpp80) cc_final: 0.7215 (tpm170) REVERT: D 377 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8142 (mp) REVERT: D 407 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6630 (ptpp) REVERT: D 436 ASP cc_start: 0.7832 (t0) cc_final: 0.7253 (m-30) REVERT: D 445 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.5993 (tt0) REVERT: D 485 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.7419 (mmm) REVERT: D 536 LYS cc_start: 0.7398 (mppt) cc_final: 0.6752 (mmtm) REVERT: E 27 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.5928 (mp0) REVERT: E 28 GLU cc_start: 0.7059 (tp30) cc_final: 0.6578 (tp30) REVERT: E 74 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7439 (mt-10) REVERT: E 99 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7528 (tttp) REVERT: E 101 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7441 (pm20) REVERT: E 106 ASP cc_start: 0.6334 (p0) cc_final: 0.6121 (m-30) REVERT: E 118 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8178 (tp) REVERT: E 362 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7081 (mt) REVERT: E 412 LYS cc_start: 0.5452 (OUTLIER) cc_final: 0.5155 (mmtm) REVERT: F 27 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6123 (mp0) REVERT: F 28 GLU cc_start: 0.7084 (tp30) cc_final: 0.6644 (tp30) REVERT: F 30 LYS cc_start: 0.7244 (mmmm) cc_final: 0.6790 (tppt) REVERT: F 62 GLU cc_start: 0.7029 (tp30) cc_final: 0.6825 (mp0) REVERT: F 74 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7220 (mt-10) REVERT: F 82 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7859 (mtmt) REVERT: F 118 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8120 (tp) REVERT: F 312 LYS cc_start: 0.6833 (mmtm) cc_final: 0.6618 (mmmt) REVERT: F 321 SER cc_start: 0.5741 (OUTLIER) cc_final: 0.5476 (p) REVERT: F 362 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7175 (mt) REVERT: F 473 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: G 219 PHE cc_start: 0.7713 (m-80) cc_final: 0.7430 (m-80) REVERT: G 279 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7337 (ptpp) REVERT: G 283 ARG cc_start: 0.7314 (mtt90) cc_final: 0.6599 (mtp85) REVERT: G 286 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.7752 (p) REVERT: G 337 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7550 (mm-30) REVERT: G 357 ASN cc_start: 0.8139 (p0) cc_final: 0.7796 (m-40) REVERT: H 158 LYS cc_start: 0.6160 (ptpt) cc_final: 0.5736 (mtmm) REVERT: H 176 GLU cc_start: 0.6722 (tm-30) cc_final: 0.6361 (tm-30) REVERT: H 253 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8008 (tt0) REVERT: H 301 GLU cc_start: 0.7984 (tp30) cc_final: 0.7721 (tp30) REVERT: H 385 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7427 (mtpt) REVERT: I 227 GLU cc_start: 0.7685 (tp30) cc_final: 0.7379 (tp30) REVERT: I 231 LYS cc_start: 0.7444 (pttp) cc_final: 0.6933 (pptt) REVERT: I 238 ARG cc_start: 0.7728 (ptp-110) cc_final: 0.7157 (mtm-85) REVERT: I 368 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: J 185 ARG cc_start: 0.6141 (OUTLIER) cc_final: 0.5913 (ttt180) REVERT: J 230 ARG cc_start: 0.6581 (ttp-110) cc_final: 0.6149 (ttp-170) REVERT: J 238 ARG cc_start: 0.7862 (mtm110) cc_final: 0.7364 (mtm180) REVERT: K 171 GLU cc_start: 0.6827 (pm20) cc_final: 0.6369 (pm20) REVERT: K 174 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6237 (tt0) REVERT: K 223 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6659 (mt-10) REVERT: K 279 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7206 (ptpp) REVERT: K 283 ARG cc_start: 0.7081 (mmm160) cc_final: 0.6756 (mtp85) REVERT: K 337 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: L 220 TYR cc_start: 0.7122 (t80) cc_final: 0.6699 (t80) REVERT: L 231 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7286 (tptm) REVERT: L 279 LYS cc_start: 0.7455 (pttt) cc_final: 0.6548 (mttt) REVERT: L 366 TYR cc_start: 0.8263 (p90) cc_final: 0.7981 (p90) REVERT: M 256 ASP cc_start: 0.6759 (m-30) cc_final: 0.6350 (p0) REVERT: M 277 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7834 (mt) REVERT: M 283 ARG cc_start: 0.7563 (mtm-85) cc_final: 0.7284 (mtm110) REVERT: M 312 ILE cc_start: 0.7756 (mt) cc_final: 0.7351 (mp) REVERT: M 337 GLU cc_start: 0.7781 (mp0) cc_final: 0.6870 (mp0) REVERT: M 383 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: N 317 TYR cc_start: 0.8543 (m-80) cc_final: 0.8284 (m-80) REVERT: N 337 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7355 (mm-30) REVERT: O 253 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.5957 (tm-30) REVERT: O 337 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7414 (mm-30) REVERT: P 253 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: P 279 LYS cc_start: 0.7758 (pttp) cc_final: 0.7029 (mptp) REVERT: P 301 GLU cc_start: 0.7479 (tp30) cc_final: 0.7190 (tp30) REVERT: Q 234 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7342 (tt0) REVERT: Q 253 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: Q 279 LYS cc_start: 0.7789 (pttp) cc_final: 0.7192 (mmtt) REVERT: R 312 ILE cc_start: 0.7880 (mt) cc_final: 0.7470 (mp) REVERT: R 327 LYS cc_start: 0.7250 (ttpt) cc_final: 0.6719 (tttt) outliers start: 313 outliers final: 126 residues processed: 835 average time/residue: 1.3998 time to fit residues: 1461.7591 Evaluate side-chains 749 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 575 time to evaluate : 4.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 145 LYS 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 430 LYS Chi-restraints excluded: chain A residue 441 ARG 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 145 LYS Chi-restraints excluded: chain B residue 169 VAL 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 496 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 562 ASP 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 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 377 ILE Chi-restraints excluded: chain C residue 386 GLU 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 5 ASN 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 153 THR Chi-restraints excluded: chain D residue 330 LEU 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 389 SER 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 27 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 118 ILE 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 412 LYS 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 17 ASN 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 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 473 GLU Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 279 LYS 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 253 GLU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 385 LYS Chi-restraints excluded: chain I residue 315 ASP Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain J residue 185 ARG 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 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 279 LYS Chi-restraints excluded: chain K residue 325 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 337 GLU Chi-restraints excluded: chain K residue 370 CYS Chi-restraints excluded: chain L residue 231 LYS Chi-restraints excluded: chain L residue 347 ASP 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 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 P residue 380 VAL Chi-restraints excluded: chain Q residue 234 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 468 optimal weight: 4.9990 chunk 319 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 418 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 480 optimal weight: 4.9990 chunk 388 optimal weight: 20.0000 chunk 0 optimal weight: 1.9990 chunk 287 optimal weight: 0.0170 chunk 504 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- 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 405 HIS A 480 ASN A 493 GLN C 58 ASN C 234 GLN C 245 ASN C 263 HIS C 466 GLN D 58 ASN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 GLN E 67 GLN E 232 HIS E 278 ASN E 308 HIS F 232 HIS F 240 GLN ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 GLN G 177 HIS I 354 ASN J 167 HIS ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 255 GLN M 364 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 383 GLN R 364 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 49284 Z= 0.232 Angle : 0.511 9.293 66498 Z= 0.271 Chirality : 0.044 0.195 7248 Planarity : 0.004 0.059 8610 Dihedral : 4.564 32.887 6343 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.39 % Allowed : 27.30 % Favored : 68.31 % 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: -0.54 (0.11), residues: 5850 helix: 0.22 (0.11), residues: 2232 sheet: -1.19 (0.17), residues: 908 loop : -0.39 (0.12), residues: 2710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 274 HIS 0.008 0.001 HIS E 232 PHE 0.025 0.001 PHE H 184 TYR 0.022 0.001 TYR J 188 ARG 0.010 0.001 ARG F 235 *********************** 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 858 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 618 time to evaluate : 4.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.7851 (m110) cc_final: 0.7298 (m110) REVERT: A 20 LYS cc_start: 0.7652 (mtpp) cc_final: 0.6603 (mppt) REVERT: A 30 LYS cc_start: 0.6928 (mppt) cc_final: 0.6551 (mptp) REVERT: A 85 LYS cc_start: 0.6825 (ttmm) cc_final: 0.5827 (tttp) REVERT: A 152 SER cc_start: 0.7288 (m) cc_final: 0.7045 (p) REVERT: A 174 GLU cc_start: 0.7257 (tp30) cc_final: 0.6348 (mt-10) REVERT: A 351 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7342 (mm-30) REVERT: A 412 LYS cc_start: 0.6696 (OUTLIER) cc_final: 0.5975 (pptt) REVERT: A 467 ARG cc_start: 0.7182 (ttm-80) cc_final: 0.6574 (ttp-110) REVERT: A 470 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6796 (mt-10) REVERT: B 30 LYS cc_start: 0.6489 (mptp) cc_final: 0.6093 (mptp) REVERT: B 85 LYS cc_start: 0.6874 (ttmm) cc_final: 0.5839 (tttp) REVERT: B 141 ARG cc_start: 0.7456 (mtm-85) cc_final: 0.7191 (mtm-85) REVERT: B 145 LYS cc_start: 0.6716 (OUTLIER) cc_final: 0.6218 (mtpt) REVERT: B 152 SER cc_start: 0.7233 (m) cc_final: 0.6979 (p) REVERT: B 192 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: B 207 THR cc_start: 0.8189 (m) cc_final: 0.7972 (p) REVERT: B 351 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7357 (mm-30) REVERT: B 449 ARG cc_start: 0.6921 (ttt90) cc_final: 0.6332 (ttt-90) REVERT: B 467 ARG cc_start: 0.6723 (ttt90) cc_final: 0.5745 (ttp-110) REVERT: B 470 GLU cc_start: 0.7993 (mp0) cc_final: 0.6679 (pt0) REVERT: C 5 ASN cc_start: 0.5584 (t0) cc_final: 0.5129 (t0) REVERT: C 6 ASP cc_start: 0.6682 (p0) cc_final: 0.5714 (m-30) REVERT: C 18 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.6675 (ttpp) REVERT: C 30 LYS cc_start: 0.7109 (ttmm) cc_final: 0.6144 (mptp) REVERT: C 65 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6278 (mp0) REVERT: C 67 GLN cc_start: 0.6595 (mm-40) cc_final: 0.6311 (mm-40) REVERT: C 88 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.6389 (ttm110) REVERT: C 104 LYS cc_start: 0.6411 (pttp) cc_final: 0.5981 (pttt) REVERT: C 174 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7380 (mm-30) REVERT: C 303 ASP cc_start: 0.7461 (p0) cc_final: 0.7227 (p0) REVERT: C 305 GLU cc_start: 0.7761 (tp30) cc_final: 0.7481 (mp0) REVERT: C 309 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7149 (ptm160) REVERT: C 377 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7815 (mp) REVERT: C 386 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: C 436 ASP cc_start: 0.7910 (t0) cc_final: 0.7540 (t0) REVERT: C 445 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6136 (tt0) REVERT: C 470 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7214 (mm-30) REVERT: C 536 LYS cc_start: 0.7566 (mppt) cc_final: 0.7136 (mppt) REVERT: C 548 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.5928 (t80) REVERT: D 5 ASN cc_start: 0.5181 (OUTLIER) cc_final: 0.4712 (t0) REVERT: D 6 ASP cc_start: 0.6562 (p0) cc_final: 0.5731 (m-30) REVERT: D 8 ASN cc_start: 0.7912 (m-40) cc_final: 0.7545 (m-40) REVERT: D 30 LYS cc_start: 0.7150 (ttmm) cc_final: 0.6124 (mptp) REVERT: D 65 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6187 (mp0) REVERT: D 70 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6247 (tttm) REVERT: D 72 MET cc_start: 0.8128 (mmt) cc_final: 0.7747 (mmm) REVERT: D 82 LYS cc_start: 0.7543 (mtmm) cc_final: 0.7131 (mtpt) REVERT: D 88 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.6610 (ttm110) REVERT: D 101 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8014 (mt-10) REVERT: D 104 LYS cc_start: 0.6675 (pttp) cc_final: 0.6240 (pttt) REVERT: D 141 ARG cc_start: 0.7519 (mtt90) cc_final: 0.6944 (mtm-85) REVERT: D 174 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7371 (mm-30) REVERT: D 309 ARG cc_start: 0.8081 (mtm180) cc_final: 0.7786 (mtm180) REVERT: D 335 ARG cc_start: 0.7383 (tpp80) cc_final: 0.7114 (tpm170) REVERT: D 377 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7790 (mm) REVERT: D 407 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6748 (ptpp) REVERT: D 436 ASP cc_start: 0.7859 (t0) cc_final: 0.7226 (m-30) REVERT: D 445 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.5889 (tt0) REVERT: D 536 LYS cc_start: 0.7304 (mppt) cc_final: 0.6609 (mmtm) REVERT: E 27 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.5906 (mp0) REVERT: E 28 GLU cc_start: 0.7084 (tp30) cc_final: 0.6606 (tp30) REVERT: E 74 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7411 (mt-10) REVERT: E 82 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7728 (mtmt) REVERT: E 106 ASP cc_start: 0.6341 (p0) cc_final: 0.6102 (m-30) REVERT: E 321 SER cc_start: 0.5941 (OUTLIER) cc_final: 0.5595 (p) REVERT: E 362 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7099 (mt) REVERT: E 412 LYS cc_start: 0.5394 (OUTLIER) cc_final: 0.5009 (mmtm) REVERT: F 28 GLU cc_start: 0.7083 (tp30) cc_final: 0.6639 (tp30) REVERT: F 30 LYS cc_start: 0.7305 (mmmm) cc_final: 0.7071 (mmmm) REVERT: F 74 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7038 (mt-10) REVERT: F 82 LYS cc_start: 0.8124 (ttmm) cc_final: 0.7874 (mtmt) REVERT: F 118 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8089 (tp) REVERT: F 235 ARG cc_start: 0.6443 (mtp-110) cc_final: 0.5703 (ttt180) REVERT: F 321 SER cc_start: 0.5739 (OUTLIER) cc_final: 0.5474 (p) REVERT: F 330 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7171 (tp) REVERT: F 362 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7163 (mt) REVERT: F 473 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7318 (mt-10) REVERT: F 522 MET cc_start: 0.8482 (ptp) cc_final: 0.8054 (ptp) REVERT: G 219 PHE cc_start: 0.7747 (m-80) cc_final: 0.7464 (m-80) REVERT: G 223 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6855 (mm-30) REVERT: G 279 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7296 (ptpp) REVERT: G 283 ARG cc_start: 0.7291 (mtt90) cc_final: 0.6616 (mtp85) REVERT: G 286 SER cc_start: 0.8325 (OUTLIER) cc_final: 0.7635 (p) REVERT: G 337 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7633 (mm-30) REVERT: G 357 ASN cc_start: 0.8147 (p0) cc_final: 0.7786 (m-40) REVERT: H 176 GLU cc_start: 0.6690 (tm-30) cc_final: 0.6235 (tm-30) REVERT: H 231 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7671 (tptm) REVERT: H 301 GLU cc_start: 0.7799 (tp30) cc_final: 0.7547 (tp30) REVERT: H 366 TYR cc_start: 0.7952 (p90) cc_final: 0.7703 (p90) REVERT: H 386 ASP cc_start: 0.6937 (m-30) cc_final: 0.6392 (p0) REVERT: I 227 GLU cc_start: 0.7716 (tp30) cc_final: 0.7389 (tp30) REVERT: I 231 LYS cc_start: 0.7351 (pttp) cc_final: 0.6915 (pptt) REVERT: I 238 ARG cc_start: 0.7698 (ptp-110) cc_final: 0.7106 (mtm180) REVERT: I 289 LEU cc_start: 0.8515 (mm) cc_final: 0.8186 (mt) REVERT: J 230 ARG cc_start: 0.6547 (ttp-110) cc_final: 0.6125 (ttp-170) REVERT: J 238 ARG cc_start: 0.7829 (mtm110) cc_final: 0.7439 (mtm180) REVERT: J 289 LEU cc_start: 0.8470 (mm) cc_final: 0.8149 (mt) REVERT: K 171 GLU cc_start: 0.6914 (pm20) cc_final: 0.6463 (pm20) REVERT: K 174 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6280 (tt0) REVERT: K 223 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6666 (mm-30) REVERT: K 238 ARG cc_start: 0.7134 (ptp-110) cc_final: 0.6224 (ptp90) REVERT: K 279 LYS cc_start: 0.7739 (pmtt) cc_final: 0.7136 (ptpp) REVERT: K 283 ARG cc_start: 0.7072 (mmm160) cc_final: 0.6716 (mtp85) REVERT: K 337 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7578 (mm-30) REVERT: L 165 LYS cc_start: 0.6280 (OUTLIER) cc_final: 0.5878 (tmtt) REVERT: L 220 TYR cc_start: 0.7083 (t80) cc_final: 0.6664 (t80) REVERT: L 279 LYS cc_start: 0.7460 (pttt) cc_final: 0.6536 (mttt) REVERT: L 366 TYR cc_start: 0.8185 (p90) cc_final: 0.7906 (p90) REVERT: M 256 ASP cc_start: 0.6636 (m-30) cc_final: 0.6257 (p0) REVERT: M 257 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8212 (pttp) REVERT: M 277 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7759 (mt) REVERT: M 283 ARG cc_start: 0.7552 (mtm-85) cc_final: 0.7302 (mtm110) REVERT: M 312 ILE cc_start: 0.7739 (mt) cc_final: 0.7327 (mp) REVERT: M 337 GLU cc_start: 0.7754 (mp0) cc_final: 0.6815 (mp0) REVERT: M 383 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: N 337 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7372 (mm-30) REVERT: O 253 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.5842 (tm-30) REVERT: O 269 LYS cc_start: 0.7210 (tppt) cc_final: 0.6934 (tppp) REVERT: O 337 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7477 (mm-30) REVERT: P 253 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7172 (tt0) REVERT: P 279 LYS cc_start: 0.7780 (pttp) cc_final: 0.7069 (mptp) REVERT: P 301 GLU cc_start: 0.7496 (tp30) cc_final: 0.7136 (tp30) REVERT: Q 234 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7300 (tt0) REVERT: Q 253 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6988 (tt0) REVERT: Q 279 LYS cc_start: 0.7759 (pttp) cc_final: 0.7171 (mptp) REVERT: Q 301 GLU cc_start: 0.7383 (tp30) cc_final: 0.6941 (tp30) REVERT: R 312 ILE cc_start: 0.7884 (mt) cc_final: 0.7475 (mp) REVERT: R 314 THR cc_start: 0.8211 (p) cc_final: 0.7943 (t) REVERT: R 327 LYS cc_start: 0.7250 (ttpt) cc_final: 0.6724 (tttt) outliers start: 240 outliers final: 109 residues processed: 793 average time/residue: 1.2937 time to fit residues: 1277.8107 Evaluate side-chains 716 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 566 time to evaluate : 4.169 ------------------------------------------------------------------------------- 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 496 VAL Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 145 LYS 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 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 309 ARG Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 386 GLU 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 548 TYR 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 27 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 126 SER Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 377 ILE 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 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 52 LEU 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 192 GLU Chi-restraints excluded: chain E residue 278 ASN 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 412 LYS 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 63 VAL Chi-restraints excluded: chain F residue 66 SER 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 473 GLU Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 279 LYS 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 231 LYS 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 337 GLU 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 257 LYS 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 244 SER 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 330 ILE Chi-restraints excluded: chain O residue 375 SER Chi-restraints excluded: chain O residue 380 VAL 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 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 380 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 234 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 189 optimal weight: 3.9990 chunk 506 optimal weight: 5.9990 chunk 111 optimal weight: 0.0020 chunk 330 optimal weight: 5.9990 chunk 138 optimal weight: 0.5980 chunk 563 optimal weight: 3.9990 chunk 467 optimal weight: 5.9990 chunk 260 optimal weight: 0.0980 chunk 46 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 295 optimal weight: 5.9990 overall best weight: 1.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN C 234 GLN C 306 ASN C 466 GLN D 234 GLN D 466 GLN E 67 GLN E 232 HIS E 251 GLN E 278 ASN E 308 HIS F 232 HIS ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS I 344 ASN I 354 ASN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 344 ASN L 221 GLN L 255 GLN L 383 GLN M 364 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 49284 Z= 0.266 Angle : 0.512 8.995 66498 Z= 0.271 Chirality : 0.044 0.200 7248 Planarity : 0.004 0.059 8610 Dihedral : 4.508 33.173 6343 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.08 % Allowed : 26.59 % Favored : 68.33 % 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: -0.47 (0.11), residues: 5850 helix: 0.33 (0.11), residues: 2238 sheet: -1.32 (0.17), residues: 940 loop : -0.33 (0.12), residues: 2672 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 0.025 0.001 PHE L 184 TYR 0.042 0.001 TYR H 188 ARG 0.010 0.001 ARG H 283 *********************** 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 879 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 601 time to evaluate : 4.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.7838 (m110) cc_final: 0.7277 (m110) REVERT: A 20 LYS cc_start: 0.7632 (mtpp) cc_final: 0.6635 (mppt) REVERT: A 30 LYS cc_start: 0.6918 (mppt) cc_final: 0.6540 (mptp) REVERT: A 85 LYS cc_start: 0.6799 (ttmm) cc_final: 0.5755 (tttp) REVERT: A 145 LYS cc_start: 0.6780 (OUTLIER) cc_final: 0.6339 (mtpt) REVERT: A 152 SER cc_start: 0.7358 (m) cc_final: 0.7030 (p) REVERT: A 174 GLU cc_start: 0.7194 (tp30) cc_final: 0.6222 (mt-10) REVERT: A 351 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7363 (mm-30) REVERT: A 412 LYS cc_start: 0.6730 (OUTLIER) cc_final: 0.5984 (pptt) REVERT: A 441 ARG cc_start: 0.6593 (OUTLIER) cc_final: 0.5849 (ttp80) REVERT: A 445 GLU cc_start: 0.6645 (pt0) cc_final: 0.5798 (mm-30) REVERT: A 467 ARG cc_start: 0.7301 (ttm-80) cc_final: 0.6912 (ttp-110) REVERT: A 515 LYS cc_start: 0.7345 (mtpt) cc_final: 0.7125 (mttm) REVERT: B 20 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.6907 (mppt) REVERT: B 27 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6898 (mm-30) REVERT: B 30 LYS cc_start: 0.6584 (mptp) cc_final: 0.6182 (mptp) REVERT: B 85 LYS cc_start: 0.6869 (ttmm) cc_final: 0.5821 (tttp) REVERT: B 141 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.7213 (mtm-85) REVERT: B 145 LYS cc_start: 0.6761 (OUTLIER) cc_final: 0.6281 (mtpt) REVERT: B 152 SER cc_start: 0.7242 (m) cc_final: 0.6988 (p) REVERT: B 192 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7383 (mt-10) REVERT: B 207 THR cc_start: 0.8176 (m) cc_final: 0.7947 (p) REVERT: B 351 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7356 (mm-30) REVERT: B 449 ARG cc_start: 0.6932 (ttt90) cc_final: 0.6260 (ttt-90) REVERT: B 467 ARG cc_start: 0.6742 (ttt90) cc_final: 0.5740 (ttp-110) REVERT: B 470 GLU cc_start: 0.7931 (mp0) cc_final: 0.6676 (pt0) REVERT: C 5 ASN cc_start: 0.5645 (t0) cc_final: 0.5301 (t160) REVERT: C 6 ASP cc_start: 0.6680 (p0) cc_final: 0.5663 (m-30) REVERT: C 15 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7844 (t) REVERT: C 18 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.6793 (ttpp) REVERT: C 30 LYS cc_start: 0.7092 (ttmm) cc_final: 0.6111 (mptp) REVERT: C 65 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6612 (mp0) REVERT: C 67 GLN cc_start: 0.6590 (mm-40) cc_final: 0.6272 (mm-40) REVERT: C 88 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6530 (ttm110) REVERT: C 104 LYS cc_start: 0.6371 (pttp) cc_final: 0.5984 (pttt) REVERT: C 141 ARG cc_start: 0.7544 (mtt90) cc_final: 0.7121 (mtp180) REVERT: C 174 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7360 (mm-30) REVERT: C 204 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.6836 (p0) REVERT: C 305 GLU cc_start: 0.7783 (tp30) cc_final: 0.7531 (mp0) REVERT: C 377 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7843 (mp) REVERT: C 386 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: C 436 ASP cc_start: 0.7866 (t0) cc_final: 0.7547 (t0) REVERT: C 445 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6136 (tt0) REVERT: C 470 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7196 (mm-30) REVERT: C 536 LYS cc_start: 0.7574 (mppt) cc_final: 0.7067 (mppt) REVERT: C 548 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.5958 (t80) REVERT: D 5 ASN cc_start: 0.5200 (OUTLIER) cc_final: 0.4771 (t0) REVERT: D 6 ASP cc_start: 0.6582 (p0) cc_final: 0.5685 (m-30) REVERT: D 8 ASN cc_start: 0.7943 (m-40) cc_final: 0.7576 (m-40) REVERT: D 15 SER cc_start: 0.8128 (OUTLIER) cc_final: 0.7913 (t) REVERT: D 30 LYS cc_start: 0.7148 (ttmm) cc_final: 0.6117 (mptp) REVERT: D 62 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6496 (mm-30) REVERT: D 65 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6276 (mp0) REVERT: D 70 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6257 (tttm) REVERT: D 82 LYS cc_start: 0.7595 (mtmm) cc_final: 0.7184 (mtpt) REVERT: D 88 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.6786 (ttp-110) REVERT: D 101 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7971 (mt-10) REVERT: D 104 LYS cc_start: 0.6661 (pttp) cc_final: 0.6226 (pttt) REVERT: D 141 ARG cc_start: 0.7510 (mtt90) cc_final: 0.6919 (mtm-85) REVERT: D 144 ASN cc_start: 0.8076 (p0) cc_final: 0.7821 (p0) REVERT: D 309 ARG cc_start: 0.8080 (mtm180) cc_final: 0.7815 (mtm180) REVERT: D 335 ARG cc_start: 0.7364 (tpp80) cc_final: 0.7113 (tpm170) REVERT: D 377 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7836 (mm) REVERT: D 386 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: D 407 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6865 (ptpp) REVERT: D 436 ASP cc_start: 0.7873 (t0) cc_final: 0.7215 (m-30) REVERT: D 445 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.5884 (tt0) REVERT: D 485 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.7341 (mmm) REVERT: D 536 LYS cc_start: 0.7305 (mppt) cc_final: 0.6601 (mmtm) REVERT: E 27 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.5912 (mp0) REVERT: E 28 GLU cc_start: 0.7078 (tp30) cc_final: 0.6574 (tp30) REVERT: E 30 LYS cc_start: 0.7353 (mmmm) cc_final: 0.6828 (tppt) REVERT: E 74 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7425 (mt-10) REVERT: E 82 LYS cc_start: 0.8121 (mtpp) cc_final: 0.7714 (mtmt) REVERT: E 99 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7590 (tttp) REVERT: E 101 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7450 (pm20) REVERT: E 106 ASP cc_start: 0.6334 (p0) cc_final: 0.6110 (m-30) REVERT: E 174 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: E 312 LYS cc_start: 0.7134 (mmtm) cc_final: 0.6927 (mmmt) REVERT: E 321 SER cc_start: 0.5959 (OUTLIER) cc_final: 0.5609 (p) REVERT: E 362 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7141 (mt) REVERT: E 412 LYS cc_start: 0.5344 (OUTLIER) cc_final: 0.4946 (mmtm) REVERT: E 439 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.6208 (pttp) REVERT: F 27 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6184 (mp0) REVERT: F 28 GLU cc_start: 0.7123 (tp30) cc_final: 0.6676 (tp30) REVERT: F 30 LYS cc_start: 0.7314 (mmmm) cc_final: 0.7060 (mmmm) REVERT: F 74 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7017 (mt-10) REVERT: F 82 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7798 (mtmt) REVERT: F 118 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8076 (tp) REVERT: F 177 LYS cc_start: 0.7855 (pttt) cc_final: 0.7507 (pmmt) REVERT: F 321 SER cc_start: 0.5753 (OUTLIER) cc_final: 0.5487 (p) REVERT: F 330 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7146 (tp) REVERT: F 362 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7190 (mt) REVERT: F 439 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.6228 (pttp) REVERT: F 522 MET cc_start: 0.8524 (ptp) cc_final: 0.7956 (ptp) REVERT: G 219 PHE cc_start: 0.7742 (m-80) cc_final: 0.7445 (m-80) REVERT: G 223 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6873 (mm-30) REVERT: G 279 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7283 (ptpp) REVERT: G 283 ARG cc_start: 0.7297 (mtt90) cc_final: 0.6635 (mtp85) REVERT: G 286 SER cc_start: 0.8314 (OUTLIER) cc_final: 0.7652 (p) REVERT: G 337 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7594 (mm-30) REVERT: G 357 ASN cc_start: 0.8148 (p0) cc_final: 0.7779 (m-40) REVERT: H 176 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6199 (tm-30) REVERT: H 231 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7694 (tptm) REVERT: H 253 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: H 301 GLU cc_start: 0.7786 (tp30) cc_final: 0.7524 (tp30) REVERT: H 366 TYR cc_start: 0.7986 (p90) cc_final: 0.7711 (p90) REVERT: H 386 ASP cc_start: 0.7029 (m-30) cc_final: 0.6328 (p0) REVERT: I 227 GLU cc_start: 0.7717 (tp30) cc_final: 0.7376 (tp30) REVERT: I 231 LYS cc_start: 0.7442 (pttp) cc_final: 0.7006 (pptt) REVERT: I 238 ARG cc_start: 0.7702 (ptp-110) cc_final: 0.7152 (mtm-85) REVERT: I 289 LEU cc_start: 0.8542 (mm) cc_final: 0.8227 (mt) REVERT: J 230 ARG cc_start: 0.6557 (ttp-110) cc_final: 0.6122 (ttp-170) REVERT: J 238 ARG cc_start: 0.7802 (mtm110) cc_final: 0.7364 (mtm180) REVERT: J 289 LEU cc_start: 0.8454 (mm) cc_final: 0.8128 (mt) REVERT: K 171 GLU cc_start: 0.6963 (pm20) cc_final: 0.6497 (pm20) REVERT: K 174 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6305 (tt0) REVERT: K 223 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6668 (mt-10) REVERT: K 279 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7485 (pttm) REVERT: K 283 ARG cc_start: 0.7108 (mmm160) cc_final: 0.6738 (mtp85) REVERT: K 337 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7609 (mm-30) REVERT: L 165 LYS cc_start: 0.6208 (OUTLIER) cc_final: 0.5806 (tmtt) REVERT: L 220 TYR cc_start: 0.7061 (t80) cc_final: 0.6735 (t80) REVERT: L 279 LYS cc_start: 0.7458 (pttt) cc_final: 0.6530 (mttt) REVERT: M 256 ASP cc_start: 0.6711 (m-30) cc_final: 0.6350 (p0) REVERT: M 277 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7739 (mt) REVERT: M 283 ARG cc_start: 0.7544 (mtm-85) cc_final: 0.7287 (mtm110) REVERT: M 312 ILE cc_start: 0.7732 (mt) cc_final: 0.7317 (mp) REVERT: M 337 GLU cc_start: 0.7740 (mp0) cc_final: 0.6776 (mp0) REVERT: M 383 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: N 257 LYS cc_start: 0.7810 (pptt) cc_final: 0.7569 (pptt) REVERT: N 299 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6760 (tp) REVERT: N 337 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7382 (mm-30) REVERT: N 392 GLU cc_start: 0.7242 (mp0) cc_final: 0.6568 (mp0) REVERT: O 253 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.5783 (tm-30) REVERT: O 257 LYS cc_start: 0.7957 (ptpt) cc_final: 0.7491 (pptt) REVERT: O 269 LYS cc_start: 0.7248 (tppt) cc_final: 0.6951 (tppp) REVERT: O 317 TYR cc_start: 0.8374 (m-80) cc_final: 0.8162 (m-80) REVERT: O 337 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7462 (mm-30) REVERT: O 346 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7280 (mm) REVERT: P 253 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7057 (tt0) REVERT: P 279 LYS cc_start: 0.7789 (pttp) cc_final: 0.7070 (mptp) REVERT: P 299 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7265 (tm) REVERT: P 301 GLU cc_start: 0.7496 (tp30) cc_final: 0.7182 (tp30) REVERT: Q 234 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7309 (tt0) REVERT: Q 253 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7011 (tt0) REVERT: Q 279 LYS cc_start: 0.7785 (pttp) cc_final: 0.7194 (mptp) REVERT: Q 301 GLU cc_start: 0.7429 (tp30) cc_final: 0.6983 (tp30) REVERT: R 312 ILE cc_start: 0.7897 (mt) cc_final: 0.7488 (mp) REVERT: R 314 THR cc_start: 0.8238 (p) cc_final: 0.7953 (t) REVERT: R 327 LYS cc_start: 0.7288 (ttpt) cc_final: 0.6754 (tttt) outliers start: 278 outliers final: 128 residues processed: 808 average time/residue: 1.2779 time to fit residues: 1288.3862 Evaluate side-chains 762 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 576 time to evaluate : 4.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 145 LYS 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 20 LYS Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 145 LYS 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 409 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 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 153 THR Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 386 GLU 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 504 VAL Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 548 TYR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 5 ASN 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 126 SER Chi-restraints excluded: chain D residue 129 LEU 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 27 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 278 ASN 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 412 LYS 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 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 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 466 GLN Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 279 LYS 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 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 241 VAL Chi-restraints excluded: chain J residue 356 ILE 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 279 LYS Chi-restraints excluded: chain K residue 325 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 337 GLU 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 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 330 ILE Chi-restraints excluded: chain N residue 379 GLN 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 380 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 234 GLU 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 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 542 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 320 optimal weight: 6.9990 chunk 411 optimal weight: 1.9990 chunk 318 optimal weight: 0.9990 chunk 474 optimal weight: 1.9990 chunk 314 optimal weight: 2.9990 chunk 560 optimal weight: 0.6980 chunk 351 optimal weight: 0.9990 chunk 341 optimal weight: 6.9990 chunk 258 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 466 GLN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN D 234 GLN D 466 GLN E 232 HIS E 278 ASN E 308 HIS F 232 HIS ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 379 GLN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 GLN L 383 GLN M 364 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 49284 Z= 0.204 Angle : 0.491 12.735 66498 Z= 0.260 Chirality : 0.044 0.214 7248 Planarity : 0.004 0.059 8610 Dihedral : 4.402 32.764 6343 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.31 % Allowed : 27.58 % 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: -0.31 (0.11), residues: 5850 helix: 0.51 (0.11), residues: 2238 sheet: -1.13 (0.17), residues: 890 loop : -0.35 (0.12), residues: 2722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 556 HIS 0.009 0.001 HIS F 232 PHE 0.023 0.001 PHE D 300 TYR 0.031 0.001 TYR H 188 ARG 0.013 0.001 ARG E 235 *********************** 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 855 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 619 time to evaluate : 4.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.7871 (m110) cc_final: 0.7301 (m110) REVERT: A 20 LYS cc_start: 0.7607 (mtpp) cc_final: 0.6631 (mppt) REVERT: A 30 LYS cc_start: 0.6847 (mppt) cc_final: 0.6523 (mptp) REVERT: A 85 LYS cc_start: 0.6846 (ttmm) cc_final: 0.5886 (tttp) REVERT: A 145 LYS cc_start: 0.6795 (OUTLIER) cc_final: 0.6361 (mtpt) REVERT: A 152 SER cc_start: 0.7397 (m) cc_final: 0.7138 (p) REVERT: A 174 GLU cc_start: 0.7099 (tp30) cc_final: 0.6152 (mt-10) REVERT: A 351 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7169 (mm-30) REVERT: A 408 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.6554 (mttp) REVERT: A 412 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.5964 (pptt) REVERT: A 441 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.5818 (ttp80) REVERT: A 445 GLU cc_start: 0.6488 (pt0) cc_final: 0.5734 (mm-30) REVERT: A 467 ARG cc_start: 0.7230 (ttm-80) cc_final: 0.6733 (ttm110) REVERT: A 470 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6867 (mt-10) REVERT: B 20 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.6908 (mppt) REVERT: B 27 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6878 (mm-30) REVERT: B 30 LYS cc_start: 0.6548 (mptp) cc_final: 0.6127 (mptp) REVERT: B 85 LYS cc_start: 0.6874 (ttmm) cc_final: 0.5834 (tttp) REVERT: B 141 ARG cc_start: 0.7390 (mtm-85) cc_final: 0.7177 (mtm-85) REVERT: B 152 SER cc_start: 0.7210 (m) cc_final: 0.6940 (p) REVERT: B 192 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: B 207 THR cc_start: 0.8206 (m) cc_final: 0.7996 (p) REVERT: B 351 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7364 (mm-30) REVERT: B 445 GLU cc_start: 0.6570 (pt0) cc_final: 0.5793 (mm-30) REVERT: B 449 ARG cc_start: 0.6922 (ttt90) cc_final: 0.6364 (ttt-90) REVERT: B 467 ARG cc_start: 0.6718 (ttt90) cc_final: 0.5899 (ttp-110) REVERT: B 470 GLU cc_start: 0.7895 (mp0) cc_final: 0.7106 (mt-10) REVERT: C 5 ASN cc_start: 0.5607 (t0) cc_final: 0.5242 (t0) REVERT: C 6 ASP cc_start: 0.6774 (p0) cc_final: 0.5670 (m-30) REVERT: C 15 SER cc_start: 0.8011 (OUTLIER) cc_final: 0.7785 (t) REVERT: C 18 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6616 (ttpp) REVERT: C 30 LYS cc_start: 0.7049 (ttmm) cc_final: 0.6103 (mptp) REVERT: C 65 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6609 (mp0) REVERT: C 67 GLN cc_start: 0.6594 (mm-40) cc_final: 0.6223 (mm-40) REVERT: C 70 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6161 (ttpp) REVERT: C 88 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6510 (ttm110) REVERT: C 104 LYS cc_start: 0.6383 (pttp) cc_final: 0.5981 (pttt) REVERT: C 141 ARG cc_start: 0.7537 (mtt90) cc_final: 0.7096 (mtp180) REVERT: C 144 ASN cc_start: 0.7630 (p0) cc_final: 0.7337 (p0) REVERT: C 174 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7373 (mm-30) REVERT: C 204 ASN cc_start: 0.7595 (OUTLIER) cc_final: 0.6816 (p0) REVERT: C 305 GLU cc_start: 0.7778 (tp30) cc_final: 0.7532 (mp0) REVERT: C 386 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: C 436 ASP cc_start: 0.7886 (t0) cc_final: 0.7570 (t0) REVERT: C 445 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6075 (tt0) REVERT: C 470 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7161 (mm-30) REVERT: C 485 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.7433 (mmm) REVERT: C 536 LYS cc_start: 0.7591 (mppt) cc_final: 0.7082 (mppt) REVERT: D 5 ASN cc_start: 0.5186 (OUTLIER) cc_final: 0.4764 (t0) REVERT: D 8 ASN cc_start: 0.7923 (m-40) cc_final: 0.7543 (m-40) REVERT: D 15 SER cc_start: 0.8065 (OUTLIER) cc_final: 0.7845 (t) REVERT: D 30 LYS cc_start: 0.7142 (ttmm) cc_final: 0.6140 (mptp) REVERT: D 65 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6164 (mp0) REVERT: D 70 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6292 (tttm) REVERT: D 82 LYS cc_start: 0.7574 (mtmm) cc_final: 0.7169 (mtpt) REVERT: D 88 ARG cc_start: 0.7935 (mmm-85) cc_final: 0.6583 (ttm110) REVERT: D 101 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7955 (mt-10) REVERT: D 104 LYS cc_start: 0.6669 (pttp) cc_final: 0.6242 (pttt) REVERT: D 141 ARG cc_start: 0.7526 (mtt90) cc_final: 0.6964 (mtm-85) REVERT: D 144 ASN cc_start: 0.8086 (p0) cc_final: 0.7793 (p0) REVERT: D 174 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7346 (mm-30) REVERT: D 309 ARG cc_start: 0.8093 (mtm180) cc_final: 0.7823 (mtm180) REVERT: D 377 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7821 (mm) REVERT: D 386 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: D 407 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6908 (ptpp) REVERT: D 436 ASP cc_start: 0.7884 (t0) cc_final: 0.7203 (m-30) REVERT: D 445 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.5872 (tt0) REVERT: D 536 LYS cc_start: 0.7309 (mppt) cc_final: 0.6654 (mmtm) REVERT: E 27 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5964 (mp0) REVERT: E 28 GLU cc_start: 0.7095 (tp30) cc_final: 0.6582 (tp30) REVERT: E 30 LYS cc_start: 0.7305 (mmmm) cc_final: 0.6760 (tppt) REVERT: E 74 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7390 (mt-10) REVERT: E 82 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7719 (mtmt) REVERT: E 99 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7628 (tttp) REVERT: E 101 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: E 174 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: E 362 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7096 (mt) REVERT: E 412 LYS cc_start: 0.5319 (OUTLIER) cc_final: 0.4920 (mmtm) REVERT: E 521 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7842 (mm) REVERT: F 20 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7199 (tttt) REVERT: F 27 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: F 28 GLU cc_start: 0.7114 (tp30) cc_final: 0.6659 (tp30) REVERT: F 30 LYS cc_start: 0.7336 (mmmm) cc_final: 0.7068 (mmmm) REVERT: F 118 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8071 (tp) REVERT: F 177 LYS cc_start: 0.7799 (pttt) cc_final: 0.7458 (pmmt) REVERT: F 235 ARG cc_start: 0.6414 (mtp85) cc_final: 0.5729 (ttt180) REVERT: F 362 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7170 (mt) REVERT: F 522 MET cc_start: 0.8487 (ptp) cc_final: 0.7928 (ptp) REVERT: G 219 PHE cc_start: 0.7737 (m-80) cc_final: 0.7425 (m-80) REVERT: G 223 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6828 (mm-30) REVERT: G 231 LYS cc_start: 0.7273 (mtpp) cc_final: 0.6925 (mtpp) REVERT: G 279 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7232 (ptpp) REVERT: G 283 ARG cc_start: 0.7259 (mtt90) cc_final: 0.6592 (mtp85) REVERT: G 286 SER cc_start: 0.8225 (OUTLIER) cc_final: 0.7535 (p) REVERT: G 337 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7587 (mm-30) REVERT: G 357 ASN cc_start: 0.8191 (p0) cc_final: 0.7836 (m-40) REVERT: H 176 GLU cc_start: 0.6696 (tm-30) cc_final: 0.6169 (tm-30) REVERT: H 231 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7678 (tptm) REVERT: H 253 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: H 301 GLU cc_start: 0.7755 (tp30) cc_final: 0.7540 (tp30) REVERT: H 366 TYR cc_start: 0.7932 (p90) cc_final: 0.7681 (p90) REVERT: I 227 GLU cc_start: 0.7570 (tp30) cc_final: 0.7249 (tp30) REVERT: I 231 LYS cc_start: 0.7384 (pttp) cc_final: 0.6958 (pptt) REVERT: I 238 ARG cc_start: 0.7573 (ptp-110) cc_final: 0.7013 (mtm-85) REVERT: I 289 LEU cc_start: 0.8555 (mm) cc_final: 0.8258 (mt) REVERT: I 309 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7588 (mt-10) REVERT: J 230 ARG cc_start: 0.6575 (ttp-110) cc_final: 0.6126 (ttp-170) REVERT: J 238 ARG cc_start: 0.7728 (mtm110) cc_final: 0.7290 (mtm180) REVERT: J 289 LEU cc_start: 0.8466 (mm) cc_final: 0.8211 (mt) REVERT: K 171 GLU cc_start: 0.7049 (pm20) cc_final: 0.6544 (pm20) REVERT: K 174 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6251 (tt0) REVERT: K 223 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6642 (mt-10) REVERT: K 279 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7461 (pttm) REVERT: K 337 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7608 (mm-30) REVERT: L 165 LYS cc_start: 0.6217 (OUTLIER) cc_final: 0.5830 (tmtt) REVERT: L 220 TYR cc_start: 0.7056 (t80) cc_final: 0.6735 (t80) REVERT: L 279 LYS cc_start: 0.7472 (pttt) cc_final: 0.6526 (mttt) REVERT: L 301 GLU cc_start: 0.7812 (tp30) cc_final: 0.7595 (tp30) REVERT: M 256 ASP cc_start: 0.6699 (m-30) cc_final: 0.6313 (p0) REVERT: M 283 ARG cc_start: 0.7524 (mtm-85) cc_final: 0.7287 (mtm110) REVERT: M 312 ILE cc_start: 0.7701 (mt) cc_final: 0.7286 (mp) REVERT: M 337 GLU cc_start: 0.7751 (mp0) cc_final: 0.6843 (mp0) REVERT: M 383 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: N 257 LYS cc_start: 0.7795 (pptt) cc_final: 0.7546 (pptt) REVERT: N 299 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6797 (tp) REVERT: N 337 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7408 (mm-30) REVERT: O 253 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.5691 (tm-30) REVERT: O 257 LYS cc_start: 0.7942 (ptpt) cc_final: 0.7510 (pptt) REVERT: O 269 LYS cc_start: 0.7221 (tppt) cc_final: 0.6924 (tppp) REVERT: O 337 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7460 (mm-30) REVERT: O 346 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7246 (mm) REVERT: P 253 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7031 (tt0) REVERT: P 279 LYS cc_start: 0.7785 (pttp) cc_final: 0.7065 (mptp) REVERT: P 301 GLU cc_start: 0.7489 (tp30) cc_final: 0.7198 (tp30) REVERT: Q 234 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7297 (tt0) REVERT: Q 253 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6618 (tt0) REVERT: Q 279 LYS cc_start: 0.7786 (pttp) cc_final: 0.7162 (mptp) REVERT: Q 301 GLU cc_start: 0.7500 (tp30) cc_final: 0.6963 (tp30) REVERT: Q 383 GLN cc_start: 0.7320 (tp-100) cc_final: 0.7022 (mm-40) REVERT: R 312 ILE cc_start: 0.7899 (mt) cc_final: 0.7488 (mp) REVERT: R 314 THR cc_start: 0.8282 (p) cc_final: 0.7993 (t) REVERT: R 327 LYS cc_start: 0.7258 (ttpt) cc_final: 0.6730 (tttt) outliers start: 236 outliers final: 116 residues processed: 792 average time/residue: 1.2928 time to fit residues: 1275.4216 Evaluate side-chains 743 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 578 time to evaluate : 4.185 ------------------------------------------------------------------------------- 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 145 LYS 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 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 20 LYS Chi-restraints excluded: chain B residue 46 ASP 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 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 153 THR Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 386 GLU 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 510 LEU Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 5 ASN 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 70 LYS Chi-restraints excluded: chain D residue 92 SER 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 438 SER 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 E residue 27 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 174 GLU 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 393 SER Chi-restraints excluded: chain E residue 412 LYS Chi-restraints excluded: chain E residue 442 THR 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 27 GLU Chi-restraints excluded: chain F residue 49 ASP 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 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 223 GLU Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 279 LYS 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 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 J residue 315 ASP 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 279 LYS Chi-restraints excluded: chain K residue 325 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 337 GLU 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 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 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 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 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 314 THR Chi-restraints excluded: chain P residue 335 ASN Chi-restraints excluded: chain P residue 367 THR Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 234 GLU 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 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 346 ILE 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 347 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 335 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 356 optimal weight: 0.0000 chunk 382 optimal weight: 0.8980 chunk 277 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 440 optimal weight: 5.9990 overall best weight: 2.5790 ------------------------------------------------------------------------------- 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 466 GLN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN C 466 GLN D 234 GLN 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 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 GLN L 255 GLN M 364 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 49284 Z= 0.351 Angle : 0.549 12.333 66498 Z= 0.288 Chirality : 0.046 0.204 7248 Planarity : 0.004 0.059 8610 Dihedral : 4.546 33.625 6343 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.55 % Allowed : 27.36 % Favored : 68.09 % 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: -0.38 (0.11), residues: 5850 helix: 0.46 (0.11), residues: 2230 sheet: -1.33 (0.17), residues: 928 loop : -0.30 (0.12), residues: 2692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 274 HIS 0.010 0.001 HIS E 232 PHE 0.028 0.002 PHE L 184 TYR 0.027 0.002 TYR H 188 ARG 0.012 0.001 ARG H 283 *********************** 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 837 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 588 time to evaluate : 4.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.7801 (m110) cc_final: 0.7234 (m110) REVERT: A 20 LYS cc_start: 0.7726 (mtpp) cc_final: 0.6722 (mppt) REVERT: A 30 LYS cc_start: 0.7011 (mppt) cc_final: 0.6619 (mptp) REVERT: A 85 LYS cc_start: 0.6796 (ttmm) cc_final: 0.5810 (tttp) REVERT: A 141 ARG cc_start: 0.6668 (mtm-85) cc_final: 0.6382 (mtm-85) REVERT: A 145 LYS cc_start: 0.6781 (OUTLIER) cc_final: 0.6339 (mtpt) REVERT: A 152 SER cc_start: 0.7350 (m) cc_final: 0.7023 (p) REVERT: A 218 ASP cc_start: 0.7060 (m-30) cc_final: 0.6764 (m-30) REVERT: A 308 HIS cc_start: 0.7744 (p90) cc_final: 0.7491 (p90) REVERT: A 351 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7407 (mm-30) REVERT: A 408 LYS cc_start: 0.6849 (OUTLIER) cc_final: 0.6456 (mtpp) REVERT: A 412 LYS cc_start: 0.6716 (OUTLIER) cc_final: 0.5985 (pptt) REVERT: A 441 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.5887 (ttp80) REVERT: A 445 GLU cc_start: 0.6625 (pt0) cc_final: 0.5853 (mm-30) REVERT: A 467 ARG cc_start: 0.7288 (ttm-80) cc_final: 0.6685 (ttm110) REVERT: A 470 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6807 (mt-10) REVERT: A 560 GLU cc_start: 0.7658 (tt0) cc_final: 0.6948 (tt0) REVERT: B 27 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6881 (mm-30) REVERT: B 30 LYS cc_start: 0.6592 (mptp) cc_final: 0.6186 (mptp) REVERT: B 85 LYS cc_start: 0.6851 (ttmm) cc_final: 0.5838 (tttp) REVERT: B 132 LYS cc_start: 0.8808 (mtpp) cc_final: 0.8471 (mtmt) REVERT: B 141 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.7301 (mtm-85) REVERT: B 145 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6362 (mtpt) REVERT: B 152 SER cc_start: 0.7254 (m) cc_final: 0.6980 (p) REVERT: B 192 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: B 207 THR cc_start: 0.8174 (m) cc_final: 0.7925 (p) REVERT: B 351 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7421 (mm-30) REVERT: B 408 LYS cc_start: 0.6541 (pttm) cc_final: 0.6324 (pttp) REVERT: B 449 ARG cc_start: 0.6878 (ttt90) cc_final: 0.6250 (ttt-90) REVERT: B 467 ARG cc_start: 0.6593 (ttt90) cc_final: 0.5844 (ttm-80) REVERT: B 470 GLU cc_start: 0.8049 (mp0) cc_final: 0.7358 (mt-10) REVERT: C 5 ASN cc_start: 0.5583 (t0) cc_final: 0.5180 (t160) REVERT: C 6 ASP cc_start: 0.7024 (p0) cc_final: 0.5840 (m-30) REVERT: C 15 SER cc_start: 0.8126 (OUTLIER) cc_final: 0.7920 (t) REVERT: C 18 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.6888 (ttpp) REVERT: C 30 LYS cc_start: 0.7129 (ttmm) cc_final: 0.6130 (mptp) REVERT: C 65 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6616 (mp0) REVERT: C 67 GLN cc_start: 0.6627 (mm-40) cc_final: 0.6257 (mm-40) REVERT: C 88 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.6502 (ttm110) REVERT: C 104 LYS cc_start: 0.6363 (pttp) cc_final: 0.6003 (pttt) REVERT: C 144 ASN cc_start: 0.7610 (p0) cc_final: 0.7292 (p0) REVERT: C 174 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7422 (mm-30) REVERT: C 204 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.6845 (p0) REVERT: C 235 ARG cc_start: 0.6265 (ttm-80) cc_final: 0.6049 (ttm-80) REVERT: C 305 GLU cc_start: 0.7827 (tp30) cc_final: 0.7595 (mp0) REVERT: C 335 ARG cc_start: 0.7302 (tpp80) cc_final: 0.7054 (tpm170) REVERT: C 377 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7897 (mp) REVERT: C 407 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6625 (ptpp) REVERT: C 436 ASP cc_start: 0.7908 (t0) cc_final: 0.7590 (t0) REVERT: C 445 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6130 (tt0) REVERT: C 470 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7251 (mm-30) REVERT: C 485 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.7380 (mmm) REVERT: C 536 LYS cc_start: 0.7561 (mppt) cc_final: 0.7017 (mppt) REVERT: D 5 ASN cc_start: 0.5131 (OUTLIER) cc_final: 0.4622 (t0) REVERT: D 8 ASN cc_start: 0.7954 (m-40) cc_final: 0.7599 (m-40) REVERT: D 15 SER cc_start: 0.8195 (OUTLIER) cc_final: 0.7992 (t) REVERT: D 30 LYS cc_start: 0.7132 (ttmm) cc_final: 0.6089 (mptp) REVERT: D 62 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6313 (mm-30) REVERT: D 65 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6169 (mp0) REVERT: D 70 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6099 (pttp) REVERT: D 82 LYS cc_start: 0.7577 (mtmm) cc_final: 0.7177 (mtpt) REVERT: D 88 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.6605 (ttm110) REVERT: D 101 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7990 (mt-10) REVERT: D 104 LYS cc_start: 0.6594 (pttp) cc_final: 0.6165 (pttt) REVERT: D 141 ARG cc_start: 0.7549 (mtt90) cc_final: 0.6945 (mtm-85) REVERT: D 144 ASN cc_start: 0.8094 (p0) cc_final: 0.7744 (p0) REVERT: D 174 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7357 (mm-30) REVERT: D 309 ARG cc_start: 0.8081 (mtm180) cc_final: 0.7827 (mtm180) REVERT: D 377 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8070 (mp) REVERT: D 386 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: D 407 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6866 (ptpp) REVERT: D 436 ASP cc_start: 0.7929 (t0) cc_final: 0.7253 (m-30) REVERT: D 445 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.5932 (tt0) REVERT: D 485 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.7351 (mmm) REVERT: D 536 LYS cc_start: 0.7370 (mppt) cc_final: 0.6617 (mmtm) REVERT: E 27 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5967 (mp0) REVERT: E 28 GLU cc_start: 0.7073 (tp30) cc_final: 0.6548 (tp30) REVERT: E 30 LYS cc_start: 0.7285 (mmmm) cc_final: 0.6762 (tppt) REVERT: E 74 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7409 (mt-10) REVERT: E 82 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7672 (mtmt) REVERT: E 99 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7639 (tttp) REVERT: E 101 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: E 118 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7987 (tp) REVERT: E 174 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: E 235 ARG cc_start: 0.6385 (mtp85) cc_final: 0.5782 (ttt180) REVERT: E 362 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7112 (mt) REVERT: E 412 LYS cc_start: 0.5163 (OUTLIER) cc_final: 0.4752 (mmtm) REVERT: E 439 LYS cc_start: 0.6506 (OUTLIER) cc_final: 0.6177 (pttp) REVERT: E 521 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7881 (mm) REVERT: E 555 GLU cc_start: 0.7917 (pt0) cc_final: 0.7050 (tt0) REVERT: F 27 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6238 (mp0) REVERT: F 28 GLU cc_start: 0.7137 (tp30) cc_final: 0.6697 (tp30) REVERT: F 30 LYS cc_start: 0.7287 (mmmm) cc_final: 0.7014 (mmmm) REVERT: F 74 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7242 (mt-10) REVERT: F 118 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8069 (tp) REVERT: F 177 LYS cc_start: 0.7818 (pttt) cc_final: 0.7476 (pmmt) REVERT: F 235 ARG cc_start: 0.6595 (mtp85) cc_final: 0.5737 (ttt180) REVERT: F 321 SER cc_start: 0.5779 (OUTLIER) cc_final: 0.5511 (p) REVERT: F 366 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7464 (mm) REVERT: F 439 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.6238 (pttp) REVERT: F 522 MET cc_start: 0.8563 (ptp) cc_final: 0.7950 (ptp) REVERT: G 219 PHE cc_start: 0.7686 (m-80) cc_final: 0.7366 (m-80) REVERT: G 223 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6885 (mm-30) REVERT: G 231 LYS cc_start: 0.7275 (mtpp) cc_final: 0.6978 (mtpp) REVERT: G 279 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7172 (ptpp) REVERT: G 283 ARG cc_start: 0.7298 (mtt90) cc_final: 0.6634 (mtp85) REVERT: G 286 SER cc_start: 0.8335 (OUTLIER) cc_final: 0.7676 (p) REVERT: G 337 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7639 (mm-30) REVERT: H 176 GLU cc_start: 0.6689 (tm-30) cc_final: 0.6220 (tm-30) REVERT: H 231 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7683 (tptm) REVERT: H 253 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: H 301 GLU cc_start: 0.7760 (tp30) cc_final: 0.7476 (tp30) REVERT: H 366 TYR cc_start: 0.7957 (p90) cc_final: 0.7652 (p90) REVERT: I 227 GLU cc_start: 0.7574 (tp30) cc_final: 0.7225 (tp30) REVERT: I 231 LYS cc_start: 0.7372 (pttp) cc_final: 0.6937 (pptt) REVERT: I 238 ARG cc_start: 0.7670 (ptp-110) cc_final: 0.7113 (mtm-85) REVERT: I 289 LEU cc_start: 0.8568 (mm) cc_final: 0.8232 (mt) REVERT: I 309 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7732 (mt-10) REVERT: J 230 ARG cc_start: 0.6544 (ttp-110) cc_final: 0.6090 (ttp-170) REVERT: J 238 ARG cc_start: 0.7802 (mtm110) cc_final: 0.7395 (mtm180) REVERT: J 289 LEU cc_start: 0.8494 (mm) cc_final: 0.8136 (mt) REVERT: K 153 PHE cc_start: 0.3671 (OUTLIER) cc_final: 0.2990 (t80) REVERT: K 171 GLU cc_start: 0.7101 (pm20) cc_final: 0.6572 (pm20) REVERT: K 174 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6261 (tt0) REVERT: K 223 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6706 (mt-10) REVERT: K 279 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7487 (pttm) REVERT: K 337 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7453 (mm-30) REVERT: L 165 LYS cc_start: 0.6143 (OUTLIER) cc_final: 0.5719 (tmtt) REVERT: L 220 TYR cc_start: 0.7063 (t80) cc_final: 0.6726 (t80) REVERT: L 279 LYS cc_start: 0.7464 (pttt) cc_final: 0.6566 (mttt) REVERT: M 256 ASP cc_start: 0.6737 (m-30) cc_final: 0.6310 (p0) REVERT: M 283 ARG cc_start: 0.7600 (mtm-85) cc_final: 0.7339 (mtm110) REVERT: M 312 ILE cc_start: 0.7714 (mt) cc_final: 0.7305 (mp) REVERT: M 337 GLU cc_start: 0.7743 (mp0) cc_final: 0.6814 (mp0) REVERT: M 383 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: N 299 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6846 (tp) REVERT: N 337 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7351 (mm-30) REVERT: N 392 GLU cc_start: 0.7186 (mp0) cc_final: 0.6521 (mp0) REVERT: O 253 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.5761 (tm-30) REVERT: O 257 LYS cc_start: 0.7923 (ptpt) cc_final: 0.7506 (pptt) REVERT: O 337 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7487 (mm-30) REVERT: O 346 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7250 (mm) REVERT: P 253 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: P 279 LYS cc_start: 0.7785 (pttp) cc_final: 0.7066 (mptp) REVERT: P 299 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7293 (tm) REVERT: P 301 GLU cc_start: 0.7467 (tp30) cc_final: 0.7142 (tp30) REVERT: Q 234 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: Q 253 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7106 (tt0) REVERT: Q 279 LYS cc_start: 0.7771 (pttp) cc_final: 0.7079 (tptt) REVERT: Q 301 GLU cc_start: 0.7407 (tp30) cc_final: 0.7174 (tp30) REVERT: R 312 ILE cc_start: 0.7888 (mt) cc_final: 0.7478 (mp) REVERT: R 327 LYS cc_start: 0.7310 (ttpt) cc_final: 0.6775 (tttt) outliers start: 249 outliers final: 134 residues processed: 771 average time/residue: 1.2965 time to fit residues: 1244.0641 Evaluate side-chains 783 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 591 time to evaluate : 4.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 145 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 338 SER 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 440 TYR 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 81 VAL Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 274 ILE 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 409 ILE Chi-restraints excluded: chain B residue 418 ASP 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 92 SER 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 348 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 407 LYS 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 504 VAL 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 5 ASN 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 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 389 SER 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 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 99 LYS Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 174 GLU 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 390 ILE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 412 LYS 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 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 366 ILE Chi-restraints excluded: chain F residue 390 ILE 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 466 GLN Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 279 LYS 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 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 379 GLN Chi-restraints excluded: chain K residue 153 PHE 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 279 LYS Chi-restraints excluded: chain K residue 325 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 337 GLU 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 244 SER 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 243 THR Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 286 SER Chi-restraints excluded: chain M residue 289 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 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 379 GLN 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 279 LYS 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 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 380 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 234 GLU 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 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 510 optimal weight: 6.9990 chunk 537 optimal weight: 0.9980 chunk 490 optimal weight: 4.9990 chunk 522 optimal weight: 0.8980 chunk 314 optimal weight: 7.9990 chunk 227 optimal weight: 0.6980 chunk 410 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 472 optimal weight: 2.9990 chunk 494 optimal weight: 5.9990 chunk 520 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 466 GLN D 234 GLN D 466 GLN E 67 GLN E 232 HIS ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 ASN E 308 HIS F 232 HIS ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 HIS ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 GLN L 383 GLN M 255 GLN M 364 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 49284 Z= 0.228 Angle : 0.507 12.307 66498 Z= 0.268 Chirality : 0.044 0.197 7248 Planarity : 0.004 0.061 8610 Dihedral : 4.431 33.057 6343 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.95 % Allowed : 27.92 % Favored : 68.13 % 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: -0.26 (0.11), residues: 5850 helix: 0.59 (0.11), residues: 2230 sheet: -1.19 (0.17), residues: 890 loop : -0.31 (0.12), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 556 HIS 0.009 0.001 HIS F 232 PHE 0.029 0.001 PHE H 184 TYR 0.028 0.001 TYR G 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 826 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 610 time to evaluate : 4.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.7864 (m110) cc_final: 0.7270 (m110) REVERT: A 20 LYS cc_start: 0.7680 (mtpp) cc_final: 0.6681 (mppt) REVERT: A 30 LYS cc_start: 0.6934 (mppt) cc_final: 0.6528 (mptp) REVERT: A 85 LYS cc_start: 0.6782 (ttmm) cc_final: 0.5811 (tttp) REVERT: A 145 LYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6320 (mtpt) REVERT: A 152 SER cc_start: 0.7406 (m) cc_final: 0.7141 (p) REVERT: A 174 GLU cc_start: 0.7227 (tp30) cc_final: 0.6212 (mt-10) REVERT: A 218 ASP cc_start: 0.7064 (m-30) cc_final: 0.6765 (m-30) REVERT: A 308 HIS cc_start: 0.7781 (p90) cc_final: 0.7535 (p90) REVERT: A 351 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7389 (mm-30) REVERT: A 408 LYS cc_start: 0.6805 (OUTLIER) cc_final: 0.6464 (mtpp) REVERT: A 412 LYS cc_start: 0.6637 (OUTLIER) cc_final: 0.5904 (pptt) REVERT: A 441 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.5917 (ttp80) REVERT: A 445 GLU cc_start: 0.6580 (pt0) cc_final: 0.5875 (mm-30) REVERT: A 467 ARG cc_start: 0.7222 (ttm-80) cc_final: 0.6997 (ttp-110) REVERT: A 560 GLU cc_start: 0.7516 (tt0) cc_final: 0.6814 (tt0) REVERT: B 20 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.6942 (mppt) REVERT: B 27 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6865 (mm-30) REVERT: B 30 LYS cc_start: 0.6617 (mptp) cc_final: 0.6205 (mptp) REVERT: B 85 LYS cc_start: 0.6867 (ttmm) cc_final: 0.5848 (tttp) REVERT: B 141 ARG cc_start: 0.7376 (mtm-85) cc_final: 0.7164 (mtm-85) REVERT: B 152 SER cc_start: 0.7365 (m) cc_final: 0.7070 (p) REVERT: B 192 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: B 207 THR cc_start: 0.8194 (m) cc_final: 0.7972 (p) REVERT: B 351 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7333 (mm-30) REVERT: B 408 LYS cc_start: 0.6602 (pttm) cc_final: 0.6369 (pttp) REVERT: B 445 GLU cc_start: 0.6583 (pt0) cc_final: 0.5838 (mm-30) REVERT: B 449 ARG cc_start: 0.6849 (ttt90) cc_final: 0.6254 (ttt-90) REVERT: B 467 ARG cc_start: 0.6769 (ttt90) cc_final: 0.5953 (ttp-110) REVERT: B 470 GLU cc_start: 0.7869 (mp0) cc_final: 0.7141 (mt-10) REVERT: C 5 ASN cc_start: 0.5597 (t0) cc_final: 0.5255 (t160) REVERT: C 6 ASP cc_start: 0.7010 (p0) cc_final: 0.5827 (m-30) REVERT: C 15 SER cc_start: 0.8014 (OUTLIER) cc_final: 0.7798 (t) REVERT: C 18 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.6769 (ttpp) REVERT: C 30 LYS cc_start: 0.7085 (ttmm) cc_final: 0.6131 (mptp) REVERT: C 65 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6598 (mp0) REVERT: C 67 GLN cc_start: 0.6583 (mm-40) cc_final: 0.6192 (mm-40) REVERT: C 88 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.6503 (ttm110) REVERT: C 104 LYS cc_start: 0.6369 (pttp) cc_final: 0.5945 (pttt) REVERT: C 141 ARG cc_start: 0.7484 (mtm110) cc_final: 0.6955 (mtm-85) REVERT: C 144 ASN cc_start: 0.7588 (p0) cc_final: 0.7257 (p0) REVERT: C 174 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7416 (mm-30) REVERT: C 204 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.6823 (p0) REVERT: C 305 GLU cc_start: 0.7831 (tp30) cc_final: 0.7594 (mp0) REVERT: C 386 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: C 436 ASP cc_start: 0.7897 (t0) cc_final: 0.7573 (t0) REVERT: C 445 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6118 (tt0) REVERT: C 470 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7118 (mm-30) REVERT: C 485 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.7480 (mmm) REVERT: C 536 LYS cc_start: 0.7557 (mppt) cc_final: 0.7029 (mppt) REVERT: D 5 ASN cc_start: 0.5101 (OUTLIER) cc_final: 0.4558 (m-40) REVERT: D 8 ASN cc_start: 0.7939 (m-40) cc_final: 0.7577 (m-40) REVERT: D 18 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.6702 (ttpp) REVERT: D 30 LYS cc_start: 0.7024 (ttmm) cc_final: 0.5996 (mptp) REVERT: D 65 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6116 (mp0) REVERT: D 70 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6288 (tttm) REVERT: D 82 LYS cc_start: 0.7565 (mtmm) cc_final: 0.7145 (mtpt) REVERT: D 88 ARG cc_start: 0.7900 (mmm-85) cc_final: 0.6526 (ttm110) REVERT: D 101 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7963 (mt-10) REVERT: D 104 LYS cc_start: 0.6658 (pttp) cc_final: 0.6230 (pttt) REVERT: D 141 ARG cc_start: 0.7540 (mtt90) cc_final: 0.6991 (mtm-85) REVERT: D 174 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7352 (mm-30) REVERT: D 309 ARG cc_start: 0.8085 (mtm180) cc_final: 0.7803 (mtm180) REVERT: D 377 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7798 (mm) REVERT: D 386 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: D 407 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6948 (ptpp) REVERT: D 436 ASP cc_start: 0.8025 (t0) cc_final: 0.7332 (m-30) REVERT: D 445 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.5917 (tt0) REVERT: D 485 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.7426 (mmm) REVERT: D 536 LYS cc_start: 0.7400 (mppt) cc_final: 0.6621 (mmtm) REVERT: E 27 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.5979 (mp0) REVERT: E 28 GLU cc_start: 0.7089 (tp30) cc_final: 0.6569 (tp30) REVERT: E 30 LYS cc_start: 0.7345 (mmmm) cc_final: 0.6783 (tppt) REVERT: E 74 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7438 (mt-10) REVERT: E 82 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7723 (mtmt) REVERT: E 99 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7637 (tttp) REVERT: E 101 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: E 174 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: E 235 ARG cc_start: 0.6383 (mtp85) cc_final: 0.5818 (ttt180) REVERT: E 321 SER cc_start: 0.5984 (OUTLIER) cc_final: 0.5635 (p) REVERT: E 366 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7322 (mm) REVERT: E 412 LYS cc_start: 0.5195 (OUTLIER) cc_final: 0.4773 (mmtm) REVERT: E 439 LYS cc_start: 0.6507 (OUTLIER) cc_final: 0.6198 (pttp) REVERT: E 521 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7822 (mm) REVERT: E 555 GLU cc_start: 0.7928 (pt0) cc_final: 0.7080 (tt0) REVERT: F 27 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6226 (mp0) REVERT: F 28 GLU cc_start: 0.7134 (tp30) cc_final: 0.6669 (tp30) REVERT: F 30 LYS cc_start: 0.7327 (mmmm) cc_final: 0.7055 (mmmm) REVERT: F 72 MET cc_start: 0.8589 (mmm) cc_final: 0.8379 (mmm) REVERT: F 118 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8072 (tp) REVERT: F 177 LYS cc_start: 0.7770 (pttt) cc_final: 0.7431 (pmmt) REVERT: F 321 SER cc_start: 0.5782 (OUTLIER) cc_final: 0.5514 (p) REVERT: F 366 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7388 (mm) REVERT: F 439 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6314 (pttp) REVERT: F 522 MET cc_start: 0.8541 (ptp) cc_final: 0.7979 (ptp) REVERT: G 219 PHE cc_start: 0.7717 (m-80) cc_final: 0.7392 (m-80) REVERT: G 223 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6886 (mm-30) REVERT: G 231 LYS cc_start: 0.7265 (mtpp) cc_final: 0.6986 (mtpp) REVERT: G 279 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7175 (ptpp) REVERT: G 283 ARG cc_start: 0.7267 (mtt90) cc_final: 0.6588 (mtp85) REVERT: G 286 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.7558 (p) REVERT: G 337 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7644 (mm-30) REVERT: H 176 GLU cc_start: 0.6679 (tm-30) cc_final: 0.6186 (tm-30) REVERT: H 231 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7660 (tptm) REVERT: H 253 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: H 301 GLU cc_start: 0.7753 (tp30) cc_final: 0.7473 (tp30) REVERT: H 366 TYR cc_start: 0.7936 (p90) cc_final: 0.7600 (p90) REVERT: H 386 ASP cc_start: 0.7076 (m-30) cc_final: 0.6314 (t0) REVERT: I 227 GLU cc_start: 0.7563 (tp30) cc_final: 0.7228 (tp30) REVERT: I 231 LYS cc_start: 0.7371 (pttp) cc_final: 0.6942 (pptt) REVERT: I 238 ARG cc_start: 0.7551 (ptp-110) cc_final: 0.7010 (mtm-85) REVERT: I 289 LEU cc_start: 0.8553 (mm) cc_final: 0.8238 (mt) REVERT: I 309 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7680 (mt-10) REVERT: J 155 ASP cc_start: 0.5281 (t70) cc_final: 0.5065 (p0) REVERT: J 230 ARG cc_start: 0.6572 (ttp-110) cc_final: 0.6123 (ttp-170) REVERT: J 238 ARG cc_start: 0.7728 (mtm110) cc_final: 0.7324 (mtm180) REVERT: J 289 LEU cc_start: 0.8495 (mm) cc_final: 0.8204 (mt) REVERT: K 171 GLU cc_start: 0.7084 (pm20) cc_final: 0.6558 (pm20) REVERT: K 174 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6233 (tt0) REVERT: K 223 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6697 (mt-10) REVERT: K 279 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7470 (pttm) REVERT: K 337 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7615 (mm-30) REVERT: L 165 LYS cc_start: 0.6164 (OUTLIER) cc_final: 0.5780 (tmtt) REVERT: L 220 TYR cc_start: 0.7022 (t80) cc_final: 0.6699 (t80) REVERT: L 279 LYS cc_start: 0.7465 (pttt) cc_final: 0.6517 (mttt) REVERT: L 301 GLU cc_start: 0.7805 (tp30) cc_final: 0.7594 (tp30) REVERT: M 256 ASP cc_start: 0.6787 (m-30) cc_final: 0.6311 (p0) REVERT: M 283 ARG cc_start: 0.7562 (mtm-85) cc_final: 0.7348 (mtm110) REVERT: M 312 ILE cc_start: 0.7682 (mt) cc_final: 0.7266 (mp) REVERT: M 337 GLU cc_start: 0.7667 (mp0) cc_final: 0.6710 (mp0) REVERT: M 383 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: N 299 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6837 (tp) REVERT: N 337 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7408 (mm-30) REVERT: O 253 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.5720 (tm-30) REVERT: O 257 LYS cc_start: 0.7991 (ptpt) cc_final: 0.7563 (pptt) REVERT: O 337 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7484 (mm-30) REVERT: O 346 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7285 (mm) REVERT: P 253 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7052 (tt0) REVERT: P 279 LYS cc_start: 0.7793 (pttp) cc_final: 0.7106 (mptp) REVERT: P 299 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7285 (tm) REVERT: P 301 GLU cc_start: 0.7485 (tp30) cc_final: 0.7184 (tp30) REVERT: Q 234 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: Q 253 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6973 (tt0) REVERT: Q 279 LYS cc_start: 0.7787 (pttp) cc_final: 0.7063 (mptp) REVERT: Q 301 GLU cc_start: 0.7390 (tp30) cc_final: 0.7185 (tp30) REVERT: R 312 ILE cc_start: 0.7897 (mt) cc_final: 0.7487 (mp) REVERT: R 314 THR cc_start: 0.8326 (p) cc_final: 0.8033 (t) REVERT: R 327 LYS cc_start: 0.7316 (ttpt) cc_final: 0.6772 (tttt) outliers start: 216 outliers final: 127 residues processed: 760 average time/residue: 1.2732 time to fit residues: 1209.3908 Evaluate side-chains 762 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 581 time to evaluate : 4.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 145 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 408 LYS 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 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 409 ILE 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 92 SER 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 348 ILE Chi-restraints excluded: chain C residue 386 GLU 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 504 VAL 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 27 GLU Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 92 SER 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 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 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 81 VAL Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 174 GLU 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 366 ILE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 412 LYS 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 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 366 ILE 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 500 LEU Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain G residue 181 SER 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 241 VAL Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 279 LYS 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 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 356 ILE Chi-restraints excluded: chain J residue 371 LEU 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 279 LYS Chi-restraints excluded: chain K residue 325 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 337 GLU 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 244 SER 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 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 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 279 LYS 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 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 380 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 234 GLU 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 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 343 optimal weight: 9.9990 chunk 552 optimal weight: 7.9990 chunk 337 optimal weight: 10.0000 chunk 262 optimal weight: 0.9990 chunk 384 optimal weight: 8.9990 chunk 579 optimal weight: 9.9990 chunk 533 optimal weight: 0.8980 chunk 461 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 356 optimal weight: 0.3980 chunk 283 optimal weight: 0.2980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN C 466 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 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 HIS ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 GLN L 255 GLN M 255 GLN M 364 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 49284 Z= 0.264 Angle : 0.520 12.205 66498 Z= 0.274 Chirality : 0.045 0.204 7248 Planarity : 0.004 0.066 8610 Dihedral : 4.428 33.138 6343 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.71 % Allowed : 28.34 % Favored : 67.95 % 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: -0.26 (0.11), residues: 5850 helix: 0.59 (0.11), residues: 2230 sheet: -1.22 (0.17), residues: 896 loop : -0.30 (0.12), residues: 2724 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 0.029 0.001 PHE C 300 TYR 0.030 0.001 TYR G 188 ARG 0.014 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 791 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 588 time to evaluate : 4.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.7854 (m110) cc_final: 0.7262 (m110) REVERT: A 20 LYS cc_start: 0.7709 (mtpp) cc_final: 0.6704 (mppt) REVERT: A 30 LYS cc_start: 0.6925 (mppt) cc_final: 0.6522 (mptp) REVERT: A 85 LYS cc_start: 0.6779 (ttmm) cc_final: 0.5800 (tttp) REVERT: A 145 LYS cc_start: 0.6764 (OUTLIER) cc_final: 0.6331 (mtpt) REVERT: A 152 SER cc_start: 0.7358 (m) cc_final: 0.7090 (p) REVERT: A 174 GLU cc_start: 0.7232 (tp30) cc_final: 0.6202 (mt-10) REVERT: A 218 ASP cc_start: 0.7063 (m-30) cc_final: 0.6758 (m-30) REVERT: A 308 HIS cc_start: 0.7763 (p90) cc_final: 0.7515 (p90) REVERT: A 351 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7411 (mm-30) REVERT: A 408 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6463 (mtpp) REVERT: A 412 LYS cc_start: 0.6658 (OUTLIER) cc_final: 0.5929 (pptt) REVERT: A 441 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.5895 (ttp80) REVERT: A 445 GLU cc_start: 0.6568 (pt0) cc_final: 0.5886 (mm-30) REVERT: A 466 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.6817 (pm20) REVERT: A 560 GLU cc_start: 0.7462 (tt0) cc_final: 0.6749 (tt0) REVERT: B 20 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.6935 (mppt) REVERT: B 27 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6879 (mm-30) REVERT: B 30 LYS cc_start: 0.6591 (mptp) cc_final: 0.6179 (mptp) REVERT: B 85 LYS cc_start: 0.6860 (ttmm) cc_final: 0.5841 (tttp) REVERT: B 141 ARG cc_start: 0.7467 (mtm-85) cc_final: 0.7253 (mtm-85) REVERT: B 152 SER cc_start: 0.7360 (m) cc_final: 0.7062 (p) REVERT: B 192 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: B 207 THR cc_start: 0.8198 (m) cc_final: 0.7962 (p) REVERT: B 351 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7362 (mm-30) REVERT: B 408 LYS cc_start: 0.6591 (pttm) cc_final: 0.6369 (pttp) REVERT: B 445 GLU cc_start: 0.6581 (pt0) cc_final: 0.5843 (mm-30) REVERT: B 449 ARG cc_start: 0.6847 (ttt90) cc_final: 0.6258 (ttt-90) REVERT: B 467 ARG cc_start: 0.6778 (ttt90) cc_final: 0.5956 (ttp-110) REVERT: B 470 GLU cc_start: 0.7856 (mp0) cc_final: 0.7096 (mt-10) REVERT: C 5 ASN cc_start: 0.5617 (t0) cc_final: 0.5277 (t160) REVERT: C 6 ASP cc_start: 0.7050 (p0) cc_final: 0.5931 (m-30) REVERT: C 15 SER cc_start: 0.8055 (OUTLIER) cc_final: 0.7837 (t) REVERT: C 18 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.6772 (ttpp) REVERT: C 30 LYS cc_start: 0.7094 (ttmm) cc_final: 0.6143 (mptp) REVERT: C 65 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6605 (mp0) REVERT: C 67 GLN cc_start: 0.6580 (mm-40) cc_final: 0.6182 (mm-40) REVERT: C 88 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.6588 (ttm110) REVERT: C 104 LYS cc_start: 0.6368 (pttp) cc_final: 0.5950 (pttt) REVERT: C 141 ARG cc_start: 0.7502 (mtm110) cc_final: 0.6945 (mtm-85) REVERT: C 144 ASN cc_start: 0.7660 (p0) cc_final: 0.7225 (p0) REVERT: C 174 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7409 (mm-30) REVERT: C 204 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.6826 (p0) REVERT: C 305 GLU cc_start: 0.7836 (tp30) cc_final: 0.7623 (mp0) REVERT: C 386 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: C 436 ASP cc_start: 0.7895 (t0) cc_final: 0.7573 (t0) REVERT: C 445 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6091 (tt0) REVERT: C 470 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7108 (mm-30) REVERT: C 485 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.7422 (mmm) REVERT: C 536 LYS cc_start: 0.7561 (mppt) cc_final: 0.7031 (mppt) REVERT: D 5 ASN cc_start: 0.5322 (OUTLIER) cc_final: 0.4806 (m-40) REVERT: D 8 ASN cc_start: 0.7959 (m-40) cc_final: 0.7603 (m-40) REVERT: D 30 LYS cc_start: 0.7023 (ttmm) cc_final: 0.5998 (mptp) REVERT: D 65 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6102 (mp0) REVERT: D 70 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6273 (tttm) REVERT: D 82 LYS cc_start: 0.7580 (mtmm) cc_final: 0.7151 (mtpt) REVERT: D 88 ARG cc_start: 0.7929 (mmm-85) cc_final: 0.6776 (ttp-110) REVERT: D 101 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7966 (mt-10) REVERT: D 104 LYS cc_start: 0.6654 (pttp) cc_final: 0.6227 (pttt) REVERT: D 141 ARG cc_start: 0.7524 (mtt90) cc_final: 0.7002 (mtm-85) REVERT: D 174 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7351 (mm-30) REVERT: D 309 ARG cc_start: 0.8103 (mtm180) cc_final: 0.7828 (mtm180) REVERT: D 377 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7844 (mm) REVERT: D 386 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: D 407 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6919 (ptpp) REVERT: D 436 ASP cc_start: 0.8019 (t0) cc_final: 0.7331 (m-30) REVERT: D 445 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.5933 (tt0) REVERT: D 485 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.7375 (mmm) REVERT: D 536 LYS cc_start: 0.7402 (mppt) cc_final: 0.6624 (mmtm) REVERT: E 27 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5974 (mp0) REVERT: E 28 GLU cc_start: 0.7064 (tp30) cc_final: 0.6546 (tp30) REVERT: E 30 LYS cc_start: 0.7318 (mmmm) cc_final: 0.6781 (tppt) REVERT: E 74 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7070 (mt-10) REVERT: E 82 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7744 (mtmt) REVERT: E 99 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7638 (tttp) REVERT: E 101 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7549 (pm20) REVERT: E 118 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7971 (tp) REVERT: E 174 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: E 235 ARG cc_start: 0.6374 (mtp85) cc_final: 0.5801 (ttt180) REVERT: E 412 LYS cc_start: 0.5195 (OUTLIER) cc_final: 0.4772 (mmtm) REVERT: E 439 LYS cc_start: 0.6511 (OUTLIER) cc_final: 0.6201 (pttp) REVERT: E 521 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7858 (mm) REVERT: E 555 GLU cc_start: 0.7922 (pt0) cc_final: 0.7094 (tt0) REVERT: F 27 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6260 (mp0) REVERT: F 28 GLU cc_start: 0.7153 (tp30) cc_final: 0.6700 (tp30) REVERT: F 30 LYS cc_start: 0.7318 (mmmm) cc_final: 0.7045 (mmmm) REVERT: F 118 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8076 (tp) REVERT: F 177 LYS cc_start: 0.7771 (pttt) cc_final: 0.7434 (pmmt) REVERT: F 235 ARG cc_start: 0.6464 (mtp-110) cc_final: 0.5639 (ttt180) REVERT: F 321 SER cc_start: 0.5792 (OUTLIER) cc_final: 0.5522 (p) REVERT: F 366 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7393 (mm) REVERT: F 439 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6314 (pttp) REVERT: F 522 MET cc_start: 0.8578 (ptp) cc_final: 0.8009 (ptp) REVERT: G 190 ILE cc_start: 0.5653 (tp) cc_final: 0.5444 (pp) REVERT: G 219 PHE cc_start: 0.7720 (m-80) cc_final: 0.7398 (m-80) REVERT: G 223 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6904 (mm-30) REVERT: G 231 LYS cc_start: 0.7281 (mtpp) cc_final: 0.6976 (mtpp) REVERT: G 279 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7194 (ptpp) REVERT: G 283 ARG cc_start: 0.7271 (mtt90) cc_final: 0.6585 (mtp85) REVERT: G 286 SER cc_start: 0.8213 (OUTLIER) cc_final: 0.7507 (p) REVERT: G 337 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7610 (mm-30) REVERT: H 176 GLU cc_start: 0.6709 (tm-30) cc_final: 0.6202 (tm-30) REVERT: H 230 ARG cc_start: 0.6418 (ttp80) cc_final: 0.6177 (ttp80) REVERT: H 231 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7658 (tptm) REVERT: H 253 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: H 301 GLU cc_start: 0.7732 (tp30) cc_final: 0.7456 (tp30) REVERT: H 366 TYR cc_start: 0.7921 (p90) cc_final: 0.7581 (p90) REVERT: H 386 ASP cc_start: 0.7065 (m-30) cc_final: 0.6311 (t0) REVERT: I 227 GLU cc_start: 0.7581 (tp30) cc_final: 0.7239 (tp30) REVERT: I 231 LYS cc_start: 0.7354 (pttp) cc_final: 0.6862 (pptt) REVERT: I 238 ARG cc_start: 0.7556 (ptp-110) cc_final: 0.7013 (mtm-85) REVERT: I 289 LEU cc_start: 0.8550 (mm) cc_final: 0.8232 (mt) REVERT: I 309 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7743 (mt-10) REVERT: J 155 ASP cc_start: 0.5298 (t70) cc_final: 0.5072 (p0) REVERT: J 230 ARG cc_start: 0.6580 (ttp-110) cc_final: 0.6130 (ttp-170) REVERT: J 238 ARG cc_start: 0.7724 (mtm110) cc_final: 0.7274 (mtm180) REVERT: J 289 LEU cc_start: 0.8482 (mm) cc_final: 0.8200 (mt) REVERT: K 153 PHE cc_start: 0.3724 (OUTLIER) cc_final: 0.3104 (t80) REVERT: K 171 GLU cc_start: 0.7096 (pm20) cc_final: 0.6557 (pm20) REVERT: K 174 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6224 (tt0) REVERT: K 223 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6711 (mt-10) REVERT: K 279 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7484 (pttm) REVERT: K 337 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7613 (mm-30) REVERT: L 220 TYR cc_start: 0.7059 (t80) cc_final: 0.6735 (t80) REVERT: L 279 LYS cc_start: 0.7463 (pttt) cc_final: 0.6516 (mttt) REVERT: L 301 GLU cc_start: 0.7807 (tp30) cc_final: 0.7590 (tp30) REVERT: M 256 ASP cc_start: 0.6837 (m-30) cc_final: 0.6436 (p0) REVERT: M 283 ARG cc_start: 0.7544 (mtm-85) cc_final: 0.7319 (mtm110) REVERT: M 312 ILE cc_start: 0.7690 (mt) cc_final: 0.7275 (mp) REVERT: M 337 GLU cc_start: 0.7670 (mp0) cc_final: 0.6712 (mp0) REVERT: M 383 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7266 (tm-30) REVERT: N 299 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6845 (tp) REVERT: N 337 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7441 (mm-30) REVERT: O 253 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.5717 (tm-30) REVERT: O 257 LYS cc_start: 0.8003 (ptpt) cc_final: 0.7569 (pptt) REVERT: O 337 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7487 (mm-30) REVERT: O 346 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7274 (mm) REVERT: P 253 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7070 (tt0) REVERT: P 279 LYS cc_start: 0.7786 (pttp) cc_final: 0.7152 (mptp) REVERT: P 299 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7301 (tm) REVERT: P 301 GLU cc_start: 0.7469 (tp30) cc_final: 0.7162 (tp30) REVERT: Q 234 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: Q 253 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6972 (tt0) REVERT: Q 279 LYS cc_start: 0.7817 (pttp) cc_final: 0.7102 (mptp) REVERT: Q 301 GLU cc_start: 0.7391 (tp30) cc_final: 0.7181 (tp30) REVERT: R 312 ILE cc_start: 0.7899 (mt) cc_final: 0.7487 (mp) REVERT: R 314 THR cc_start: 0.8262 (p) cc_final: 0.7974 (t) REVERT: R 327 LYS cc_start: 0.7317 (ttpt) cc_final: 0.6773 (tttt) outliers start: 203 outliers final: 124 residues processed: 729 average time/residue: 1.2996 time to fit residues: 1183.2062 Evaluate side-chains 770 residues out of total 5472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 593 time to evaluate : 4.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 145 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 408 LYS 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 20 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 409 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 92 SER 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 348 ILE Chi-restraints excluded: chain C residue 386 GLU 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 504 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 5 ASN 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 70 LYS Chi-restraints excluded: chain D residue 92 SER 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 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 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 81 VAL Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 174 GLU 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 393 SER Chi-restraints excluded: chain E residue 412 LYS 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 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 259 ILE Chi-restraints excluded: chain F residue 321 SER Chi-restraints excluded: chain F residue 366 ILE 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 181 SER Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 279 LYS 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 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 241 VAL Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain K residue 153 PHE 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 279 LYS Chi-restraints excluded: chain K residue 325 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 337 GLU 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 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 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 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 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 380 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 234 GLU 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 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 366 optimal weight: 9.9990 chunk 491 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 425 optimal weight: 0.2980 chunk 68 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 462 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 474 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 466 GLN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN C 466 GLN D 234 GLN D 466 GLN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 GLN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 GLN M 364 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116662 restraints weight = 56990.906| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.03 r_work: 0.3098 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 49284 Z= 0.294 Angle : 0.532 12.208 66498 Z= 0.279 Chirality : 0.045 0.211 7248 Planarity : 0.004 0.070 8610 Dihedral : 4.474 33.864 6343 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.78 % Allowed : 28.44 % Favored : 67.78 % 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: 2230 sheet: -1.35 (0.17), residues: 926 loop : -0.27 (0.12), residues: 2694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 274 HIS 0.010 0.001 HIS F 232 PHE 0.028 0.001 PHE C 300 TYR 0.030 0.002 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: 18562.10 seconds wall clock time: 319 minutes 18.51 seconds (19158.51 seconds total)