Starting phenix.real_space_refine on Sun Jun 22 20:15:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xau_38203/06_2025/8xau_38203.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xau_38203/06_2025/8xau_38203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xau_38203/06_2025/8xau_38203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xau_38203/06_2025/8xau_38203.map" model { file = "/net/cci-nas-00/data/ceres_data/8xau_38203/06_2025/8xau_38203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xau_38203/06_2025/8xau_38203.cif" } resolution = 3.14 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= 0.002 sd= 0.058 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 36 5.16 5 C 16931 2.51 5 N 4472 2.21 5 O 5201 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26640 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4508 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 21, 'TRANS': 541} Chain: "B" Number of atoms: 4508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4508 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 21, 'TRANS': 541} Chain: "C" Number of atoms: 4508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4508 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 21, 'TRANS': 541} Chain: "D" Number of atoms: 4508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4508 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 21, 'TRANS': 541} Chain: "E" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4411 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 21, 'TRANS': 529} Chain breaks: 2 Chain: "F" Number of atoms: 4197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4197 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 21, 'TRANS': 506} Chain breaks: 1 Time building chain proxies: 15.47, per 1000 atoms: 0.58 Number of scatterers: 26640 At special positions: 0 Unit cell: (122.55, 124.45, 152.95, 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 36 16.00 O 5201 8.00 N 4472 7.00 C 16931 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: 6.32 Conformation dependent library (CDL) restraints added in 3.5 seconds 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6326 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 21 sheets defined 42.0% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.988A pdb=" N ILE A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 4.041A pdb=" N TYR A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.572A pdb=" N PHE A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 Processing helix chain 'A' and resid 211 through 215 removed outlier: 4.004A pdb=" N LEU A 214 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 removed outlier: 3.529A pdb=" N GLU A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 249 removed outlier: 3.742A pdb=" N LYS A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.919A pdb=" N GLU A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 280 Processing helix chain 'A' and resid 303 through 312 removed outlier: 3.718A pdb=" N ALA A 307 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N HIS A 308 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG A 309 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 312 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.776A pdb=" N ASP A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) 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 350 through 356 removed outlier: 3.751A pdb=" N LYS A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 366 removed outlier: 3.575A pdb=" N THR A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 414 removed outlier: 4.657A pdb=" N SER A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 409 " --> pdb=" O HIS A 405 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 4.271A pdb=" N TYR A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'A' and resid 467 through 471 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 489 through 500 Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 547 through 553 Processing helix chain 'A' and resid 559 through 569 removed outlier: 4.027A pdb=" N LYS A 563 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A 566 " --> pdb=" O ASP A 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 removed outlier: 3.709A pdb=" N PHE B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 25 through 30' Processing helix chain 'B' and resid 104 through 114 removed outlier: 3.746A pdb=" N TYR B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 114 " --> pdb=" O SER B 110 " (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: 3.871A pdb=" N LYS B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 171 removed outlier: 3.581A pdb=" N THR B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 removed outlier: 3.694A pdb=" N LEU B 214 " --> pdb=" O PRO B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 223 removed outlier: 3.607A pdb=" N GLU B 221 " --> pdb=" O GLY B 217 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 222 " --> pdb=" O ASP B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 249 removed outlier: 3.671A pdb=" N PHE B 238 " --> pdb=" O GLN B 234 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 removed outlier: 3.667A pdb=" N LYS B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 258' Processing helix chain 'B' and resid 269 through 280 Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.771A pdb=" N ARG B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.838A pdb=" N LYS B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 366 removed outlier: 3.652A pdb=" N ILE B 366 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 414 removed outlier: 3.510A pdb=" N SER B 393 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS B 408 " --> pdb=" O TYR B 404 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE B 409 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 412 " --> pdb=" O LYS B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 removed outlier: 4.012A pdb=" N TYR B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 454 Processing helix chain 'B' and resid 467 through 471 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 489 through 500 Processing helix chain 'B' and resid 510 through 514 removed outlier: 3.519A pdb=" N LEU B 514 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 Processing helix chain 'B' and resid 558 through 569 removed outlier: 4.373A pdb=" N ASP B 562 " --> pdb=" O ASP B 558 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS B 563 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 565 " --> pdb=" O PHE B 561 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 566 " --> pdb=" O ASP B 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 31 removed outlier: 3.870A pdb=" N ILE C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.747A pdb=" N TYR C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 145 removed outlier: 3.520A pdb=" N PHE C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.813A 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 211 through 215 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 231 through 249 removed outlier: 3.802A pdb=" N ARG C 235 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 237 " --> pdb=" O ASN C 233 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 238 " --> pdb=" O GLN C 234 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 244 " --> pdb=" O GLN C 240 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 247 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 removed outlier: 3.607A pdb=" N GLU C 258 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.625A pdb=" N ASN C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 310 removed outlier: 3.717A pdb=" N ALA C 307 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N HIS C 308 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG C 309 " --> pdb=" O ASN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 341 removed outlier: 3.780A pdb=" N ASP C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C 335 " --> pdb=" O ASN C 331 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 3.892A 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: 3.832A pdb=" N LYS C 354 " --> pdb=" O GLY C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 366 removed outlier: 3.508A pdb=" N THR C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 362 " --> pdb=" O PHE C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 414 removed outlier: 3.616A pdb=" N SER C 393 " --> pdb=" O SER C 389 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE C 409 " --> pdb=" O HIS C 405 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 432 removed outlier: 4.229A pdb=" N TYR C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 440 through 454 Processing helix chain 'C' and resid 467 through 471 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 removed outlier: 3.639A pdb=" N LEU C 511 " --> pdb=" O THR C 508 " (cutoff:3.500A) 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: 4.181A pdb=" N ASP C 562 " --> pdb=" O ASP C 558 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS C 563 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 565 " --> pdb=" O PHE C 561 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 566 " --> pdb=" O ASP C 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 31 removed outlier: 3.571A pdb=" N ILE D 31 " --> pdb=" O GLU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 113 removed outlier: 3.687A pdb=" N SER D 110 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.598A pdb=" N PHE D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 3.960A 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 211 through 215 removed outlier: 3.588A pdb=" N LEU D 214 " --> pdb=" O PRO D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 225 Processing helix chain 'D' and resid 231 through 249 removed outlier: 3.882A pdb=" N ARG D 235 " --> pdb=" O ASP D 231 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL D 237 " --> pdb=" O ASN D 233 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE D 238 " --> pdb=" O GLN D 234 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS D 247 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.816A pdb=" N GLU D 258 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 281 Processing helix chain 'D' and resid 306 through 312 removed outlier: 3.744A pdb=" N PHE D 311 " --> pdb=" O HIS D 308 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS D 312 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 341 removed outlier: 4.239A pdb=" N SER D 338 " --> pdb=" O ASP D 334 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 3.581A 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: 3.743A pdb=" N LYS D 354 " --> pdb=" O GLY D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 366 removed outlier: 3.622A pdb=" N ILE D 366 " --> pdb=" O LEU D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 405 Processing helix chain 'D' and resid 405 through 414 removed outlier: 3.902A pdb=" N ILE D 409 " --> pdb=" O HIS D 405 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG D 411 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 412 " --> pdb=" O LYS D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 432 removed outlier: 4.115A pdb=" N TYR D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 454 Processing helix chain 'D' and resid 467 through 471 Processing helix chain 'D' and resid 472 through 477 Processing helix chain 'D' and resid 489 through 500 Processing helix chain 'D' and resid 507 through 511 Processing helix chain 'D' and resid 547 through 553 Processing helix chain 'D' and resid 558 through 569 removed outlier: 4.049A pdb=" N ASP D 562 " --> pdb=" O ASP D 558 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS D 563 " --> pdb=" O SER D 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 104 through 114 removed outlier: 3.874A pdb=" N TYR E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 144 Processing helix chain 'E' and resid 156 through 171 Processing helix chain 'E' and resid 211 through 215 removed outlier: 3.594A pdb=" N LEU E 214 " --> pdb=" O PRO E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 225 removed outlier: 3.777A pdb=" N GLU E 222 " --> pdb=" O ASP E 218 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 250 removed outlier: 3.918A pdb=" N VAL E 237 " --> pdb=" O ASN E 233 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE E 238 " --> pdb=" O GLN E 234 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS E 247 " --> pdb=" O THR E 243 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE E 248 " --> pdb=" O LEU E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 260 Processing helix chain 'E' and resid 269 through 282 removed outlier: 3.508A pdb=" N VAL E 273 " --> pdb=" O ASP E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 311 removed outlier: 3.919A pdb=" N ALA E 307 " --> pdb=" O ASN E 304 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HIS E 308 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG E 309 " --> pdb=" O ASN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 341 removed outlier: 3.619A pdb=" N LYS E 339 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE E 341 " --> pdb=" O GLN E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 344 No H-bonds generated for 'chain 'E' and resid 342 through 344' Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 350 through 356 removed outlier: 3.631A pdb=" N LYS E 354 " --> pdb=" O GLY E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 366 removed outlier: 3.609A pdb=" N LEU E 365 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 411 removed outlier: 4.560A pdb=" N SER E 389 " --> pdb=" O PHE E 385 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE E 390 " --> pdb=" O GLU E 386 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER E 393 " --> pdb=" O SER E 389 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER E 396 " --> pdb=" O VAL E 392 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS E 408 " --> pdb=" O TYR E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 432 removed outlier: 4.102A 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 453 removed outlier: 3.554A pdb=" N GLU E 445 " --> pdb=" O ARG E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 471 Processing helix chain 'E' and resid 472 through 479 removed outlier: 3.713A pdb=" N GLN E 478 " --> pdb=" O THR E 474 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N CYS E 479 " --> pdb=" O ILE E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 499 Processing helix chain 'E' and resid 510 through 514 Processing helix chain 'E' and resid 547 through 554 removed outlier: 3.730A pdb=" N LYS E 554 " --> pdb=" O ASP E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 569 removed outlier: 4.403A pdb=" N ASP E 562 " --> pdb=" O ASP E 558 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS E 563 " --> pdb=" O SER E 559 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE E 565 " --> pdb=" O PHE E 561 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU E 566 " --> pdb=" O ASP E 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 113 removed outlier: 4.346A pdb=" N TYR F 112 " --> pdb=" O ILE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 144 removed outlier: 3.814A pdb=" N ASN F 144 " --> pdb=" O ASN F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 171 removed outlier: 3.593A pdb=" N ILE F 164 " --> pdb=" O THR F 160 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU F 165 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 225 removed outlier: 3.679A pdb=" N GLU F 222 " --> pdb=" O ASP F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 230 removed outlier: 3.839A pdb=" N ASN F 230 " --> pdb=" O THR F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 249 removed outlier: 3.506A pdb=" N VAL F 237 " --> pdb=" O ASN F 233 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE F 248 " --> pdb=" O LEU F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 257 Processing helix chain 'F' and resid 270 through 281 Processing helix chain 'F' and resid 303 through 311 removed outlier: 5.249A pdb=" N HIS F 308 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE F 311 " --> pdb=" O HIS F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 341 removed outlier: 4.205A pdb=" N ARG F 335 " --> pdb=" O ASN F 331 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F 336 " --> pdb=" O PHE F 332 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE F 341 " --> pdb=" O GLN F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 344 No H-bonds generated for 'chain 'F' and resid 342 through 344' Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 350 through 356 removed outlier: 3.775A pdb=" N LYS F 354 " --> pdb=" O GLY F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 366 removed outlier: 3.789A pdb=" N LEU F 362 " --> pdb=" O PHE F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 387 through 414 removed outlier: 3.542A pdb=" N PHE F 402 " --> pdb=" O LEU F 398 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS F 408 " --> pdb=" O TYR F 404 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG F 411 " --> pdb=" O LYS F 407 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS F 412 " --> pdb=" O LYS F 408 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER F 413 " --> pdb=" O ILE F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 432 removed outlier: 3.927A 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 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 sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.567A pdb=" N LYS A 20 " --> pdb=" O VAL A 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 19 through 23 current: chain 'A' and resid 50 through 62 removed outlier: 6.631A pdb=" N ALA A 51 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU A 80 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 53 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU A 74 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE A 59 " --> pdb=" O MET A 72 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N MET A 72 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE A 61 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS A 70 " --> pdb=" O ILE A 61 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 85 through 88 current: chain 'B' and resid 19 through 23 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 19 through 23 current: chain 'B' and resid 50 through 62 removed outlier: 6.743A pdb=" N ALA B 51 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU B 80 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 53 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU B 74 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N PHE B 59 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET B 72 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE B 61 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LYS B 70 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 138 removed outlier: 7.778A pdb=" N VAL A 135 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE A 124 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 147 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N SER A 465 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE A 149 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE A 185 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU A 426 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N PHE A 187 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE A 184 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU A 378 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 186 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 301 Processing sheet with id=AA5, first strand: chain 'B' and resid 134 through 138 removed outlier: 4.611A pdb=" N SER B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL B 137 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N THR B 123 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE B 147 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N SER B 465 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE B 149 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N HIS B 183 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL B 424 " --> pdb=" O HIS B 183 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE B 185 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU B 426 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N PHE B 187 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE B 184 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU B 378 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE B 186 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASN B 201 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASP B 379 " --> pdb=" O ASN B 201 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU B 203 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AA7, first strand: chain 'B' and resid 299 through 301 Processing sheet with id=AA8, first strand: chain 'C' and resid 9 through 14 removed outlier: 6.612A pdb=" N LYS C 20 " --> pdb=" O VAL C 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 19 through 23 current: chain 'C' and resid 50 through 59 removed outlier: 6.057A pdb=" N ILE C 55 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ASP C 57 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA C 75 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE C 59 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE C 73 " --> pdb=" O PHE C 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 85 through 88 current: chain 'D' and resid 19 through 23 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: 7.229A pdb=" N ALA D 51 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU D 80 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU D 53 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU D 74 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE D 59 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N MET D 72 " --> pdb=" O PHE D 59 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE D 61 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS D 70 " --> pdb=" O ILE D 61 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 85 through 88 current: chain 'E' and resid 19 through 23 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 19 through 23 current: chain 'E' and resid 50 through 62 removed outlier: 6.721A pdb=" N ALA E 51 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU E 80 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU E 53 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU E 74 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE E 59 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET E 72 " --> pdb=" O PHE E 59 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE E 61 " --> pdb=" O LYS E 70 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS E 70 " --> pdb=" O ILE E 61 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 134 through 138 removed outlier: 7.812A pdb=" N VAL C 135 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE C 124 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 201 through 202 removed outlier: 6.430A pdb=" N ASN C 201 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE C 185 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU C 426 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.601A pdb=" N SER C 321 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 299 through 301 Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 138 removed outlier: 7.758A pdb=" N VAL D 135 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE D 124 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE D 147 " --> pdb=" O LEU D 463 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N SER D 465 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE D 149 " --> pdb=" O SER D 465 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS D 183 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL D 424 " --> pdb=" O HIS D 183 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE D 185 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLU D 426 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE D 187 " --> pdb=" O GLU D 426 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE D 184 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU D 378 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE D 186 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASN D 201 " --> pdb=" O ILE D 377 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP D 379 " --> pdb=" O ASN D 201 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU D 203 " --> pdb=" O ASP D 379 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 284 through 285 Processing sheet with id=AB6, first strand: chain 'D' and resid 299 through 301 removed outlier: 3.962A pdb=" N ILE D 292 " --> pdb=" O ASP D 318 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 134 through 138 removed outlier: 7.935A pdb=" N VAL E 135 " --> pdb=" O PHE E 124 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE E 124 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER E 530 " --> pdb=" O ILE E 521 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE E 521 " --> pdb=" O SER E 530 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 147 " --> pdb=" O LEU E 461 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N HIS E 183 " --> pdb=" O LEU E 422 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL E 424 " --> pdb=" O HIS E 183 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE E 185 " --> pdb=" O VAL E 424 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLU E 426 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE E 187 " --> pdb=" O GLU E 426 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE E 184 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU E 378 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE E 186 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 284 through 285 Processing sheet with id=AB9, first strand: chain 'E' and resid 292 through 294 Processing sheet with id=AC1, first strand: chain 'F' and resid 10 through 14 removed outlier: 4.324A pdb=" N GLU F 10 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER F 22 " --> pdb=" O GLU F 10 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS F 20 " --> pdb=" O VAL F 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 19 through 23 current: chain 'F' and resid 51 through 61 removed outlier: 6.868A pdb=" N ALA F 51 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU F 80 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU F 53 " --> pdb=" O ILE F 78 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU F 74 " --> pdb=" O ASP F 57 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N PHE F 59 " --> pdb=" O MET F 72 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N MET F 72 " --> pdb=" O PHE F 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 134 through 138 removed outlier: 3.620A pdb=" N VAL F 135 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N SER F 125 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL F 137 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N THR F 123 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER F 530 " --> pdb=" O ILE F 521 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N HIS F 146 " --> pdb=" O ASN F 480 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N PHE F 482 " --> pdb=" O HIS F 146 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA F 148 " --> pdb=" O PHE F 482 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER F 484 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL F 150 " --> pdb=" O SER F 484 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE F 147 " --> pdb=" O LEU F 463 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N SER F 465 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE F 149 " --> pdb=" O SER F 465 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE F 421 " --> pdb=" O THR F 460 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU F 462 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE F 423 " --> pdb=" O LEU F 462 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA F 464 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR F 425 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE F 184 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU F 378 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE F 186 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASN F 201 " --> pdb=" O ILE F 377 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 293 through 294 removed outlier: 4.690A pdb=" N TRP F 293 " --> pdb=" O PHE F 300 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE F 300 " --> pdb=" O TRP F 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 868 hydrogen bonds defined for protein. 2391 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: 9.06 Time building geometry restraints manager: 7.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8751 1.34 - 1.46: 5271 1.46 - 1.58: 13067 1.58 - 1.70: 1 1.70 - 1.82: 54 Bond restraints: 27144 Sorted by residual: bond pdb=" CB PRO A 265 " pdb=" CG PRO A 265 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.71e+00 bond pdb=" CA VAL D 557 " pdb=" CB VAL D 557 " ideal model delta sigma weight residual 1.530 1.553 -0.023 1.05e-02 9.07e+03 4.75e+00 bond pdb=" CB GLU B 305 " pdb=" CG GLU B 305 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.52e+00 bond pdb=" CB GLU B 28 " pdb=" CG GLU B 28 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.36e+00 bond pdb=" CB GLU B 445 " pdb=" CG GLU B 445 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 3.04e+00 ... (remaining 27139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 36131 2.80 - 5.61: 435 5.61 - 8.41: 82 8.41 - 11.22: 22 11.22 - 14.02: 3 Bond angle restraints: 36673 Sorted by residual: angle pdb=" CA PRO A 265 " pdb=" N PRO A 265 " pdb=" CD PRO A 265 " ideal model delta sigma weight residual 112.00 99.24 12.76 1.40e+00 5.10e-01 8.31e+01 angle pdb=" CA GLN E 478 " pdb=" CB GLN E 478 " pdb=" CG GLN E 478 " ideal model delta sigma weight residual 114.10 124.88 -10.78 2.00e+00 2.50e-01 2.91e+01 angle pdb=" CA GLU B 28 " pdb=" CB GLU B 28 " pdb=" CG GLU B 28 " ideal model delta sigma weight residual 114.10 123.93 -9.83 2.00e+00 2.50e-01 2.41e+01 angle pdb=" C GLN B 48 " pdb=" N ASP B 49 " pdb=" CA ASP B 49 " ideal model delta sigma weight residual 121.54 130.37 -8.83 1.91e+00 2.74e-01 2.14e+01 angle pdb=" CA TRP D 552 " pdb=" CB TRP D 552 " pdb=" CG TRP D 552 " ideal model delta sigma weight residual 113.60 122.34 -8.74 1.90e+00 2.77e-01 2.12e+01 ... (remaining 36668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14201 17.95 - 35.90: 1824 35.90 - 53.84: 451 53.84 - 71.79: 78 71.79 - 89.74: 25 Dihedral angle restraints: 16579 sinusoidal: 6824 harmonic: 9755 Sorted by residual: dihedral pdb=" CA LEU F 93 " pdb=" C LEU F 93 " pdb=" N ALA F 94 " pdb=" CA ALA F 94 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ALA F 94 " pdb=" C ALA F 94 " pdb=" N LEU F 95 " pdb=" CA LEU F 95 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ILE D 73 " pdb=" C ILE D 73 " pdb=" N GLU D 74 " pdb=" CA GLU D 74 " ideal model delta harmonic sigma weight residual 180.00 161.37 18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 16576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3437 0.069 - 0.138: 613 0.138 - 0.207: 55 0.207 - 0.275: 7 0.275 - 0.344: 3 Chirality restraints: 4115 Sorted by residual: chirality pdb=" CB ILE D 340 " pdb=" CA ILE D 340 " pdb=" CG1 ILE D 340 " pdb=" CG2 ILE D 340 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB ILE A 544 " pdb=" CA ILE A 544 " pdb=" CG1 ILE A 544 " pdb=" CG2 ILE A 544 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB ILE B 31 " pdb=" CA ILE B 31 " pdb=" CG1 ILE B 31 " pdb=" CG2 ILE B 31 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 4112 not shown) Planarity restraints: 4749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 316 " 0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO C 317 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 317 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 317 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 264 " -0.062 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO A 265 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 558 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" CG ASP A 558 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASP A 558 " 0.021 2.00e-02 2.50e+03 pdb=" OD2 ASP A 558 " 0.020 2.00e-02 2.50e+03 ... (remaining 4746 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3859 2.76 - 3.29: 25671 3.29 - 3.83: 45126 3.83 - 4.36: 55576 4.36 - 4.90: 95710 Nonbonded interactions: 225942 Sorted by model distance: nonbonded pdb=" OD1 ASP B 524 " pdb=" OG1 THR C 153 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR A 193 " pdb=" OE1 GLU A 426 " model vdw 2.256 3.040 nonbonded pdb=" O ILE C 189 " pdb=" OG SER C 381 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR A 368 " pdb=" O VAL B 557 " model vdw 2.258 3.040 nonbonded pdb=" O GLU C 473 " pdb=" OG SER C 477 " model vdw 2.262 3.040 ... (remaining 225937 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 7 through 28 or resid 36 through 411 or resid 419 through \ 541)) selection = (chain 'B' and (resid 7 through 28 or resid 36 through 411 or resid 419 through \ 541)) selection = (chain 'C' and (resid 7 through 28 or resid 36 through 411 or resid 419 through \ 541)) selection = (chain 'D' and (resid 7 through 28 or resid 36 through 411 or resid 419 through \ 541)) selection = (chain 'E' and (resid 7 through 28 or resid 36 through 541)) selection = (chain 'F' and (resid 7 through 411 or resid 419 through 541)) } 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.250 Set scattering table: 0.250 Process input model: 59.040 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 : 0.005 0.156 27144 Z= 0.212 Angle : 0.806 14.025 36673 Z= 0.423 Chirality : 0.053 0.344 4115 Planarity : 0.006 0.088 4749 Dihedral : 16.895 89.740 10253 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.43 % Allowed : 25.07 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.40 (0.13), residues: 3313 helix: -2.69 (0.11), residues: 1079 sheet: -1.28 (0.24), residues: 428 loop : -0.83 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 556 HIS 0.009 0.001 HIS C 429 PHE 0.044 0.002 PHE F 250 TYR 0.034 0.002 TYR F 368 ARG 0.016 0.001 ARG D 141 Details of bonding type rmsd hydrogen bonds : bond 0.27453 ( 868) hydrogen bonds : angle 9.89477 ( 2391) covalent geometry : bond 0.00519 (27144) covalent geometry : angle 0.80619 (36673) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 313 time to evaluate : 3.116 Fit side-chains revert: symmetry clash REVERT: A 548 TYR cc_start: 0.8219 (m-80) cc_final: 0.6609 (t80) REVERT: B 47 ASN cc_start: 0.6021 (p0) cc_final: 0.4559 (m-40) REVERT: E 548 TYR cc_start: 0.8794 (m-80) cc_final: 0.8027 (m-80) outliers start: 13 outliers final: 11 residues processed: 321 average time/residue: 0.4001 time to fit residues: 205.4187 Evaluate side-chains 297 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 286 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 552 TRP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain F residue 385 PHE Chi-restraints excluded: chain F residue 522 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 279 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 169 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 259 optimal weight: 20.0000 chunk 100 optimal weight: 0.2980 chunk 157 optimal weight: 3.9990 chunk 193 optimal weight: 0.5980 chunk 300 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 245 ASN A 304 ASN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN C 199 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 ASN E 183 HIS E 478 GLN F 245 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.183364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139907 restraints weight = 30592.393| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.67 r_work: 0.3303 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27144 Z= 0.150 Angle : 0.550 8.966 36673 Z= 0.292 Chirality : 0.045 0.164 4115 Planarity : 0.005 0.061 4749 Dihedral : 5.011 88.918 3566 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.14 % Allowed : 22.40 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.20 (0.14), residues: 3313 helix: -0.69 (0.15), residues: 1080 sheet: -1.37 (0.22), residues: 503 loop : -0.54 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 556 HIS 0.003 0.001 HIS C 429 PHE 0.017 0.001 PHE E 341 TYR 0.015 0.001 TYR C 267 ARG 0.006 0.000 ARG B 239 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 868) hydrogen bonds : angle 6.01465 ( 2391) covalent geometry : bond 0.00351 (27144) covalent geometry : angle 0.55048 (36673) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 318 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 TYR cc_start: 0.7191 (t80) cc_final: 0.6949 (t80) REVERT: A 408 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8074 (mmtt) REVERT: A 441 ARG cc_start: 0.7693 (ttp80) cc_final: 0.6908 (tpp80) REVERT: A 548 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.6696 (t80) REVERT: B 404 TYR cc_start: 0.8954 (t80) cc_final: 0.8727 (t80) REVERT: B 445 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8190 (tm-30) REVERT: C 34 GLU cc_start: 0.7201 (pt0) cc_final: 0.6934 (pt0) REVERT: C 106 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7473 (p0) REVERT: C 199 ASN cc_start: 0.7831 (t0) cc_final: 0.7625 (t0) REVERT: C 248 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8206 (pt) REVERT: C 267 TYR cc_start: 0.8116 (t80) cc_final: 0.7891 (t80) REVERT: C 291 HIS cc_start: 0.7666 (m-70) cc_final: 0.7457 (m170) REVERT: C 502 ASP cc_start: 0.8652 (p0) cc_final: 0.8358 (p0) REVERT: D 120 ASP cc_start: 0.8029 (t0) cc_final: 0.7817 (t0) REVERT: D 251 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7752 (mm-40) REVERT: D 341 PHE cc_start: 0.8394 (m-80) cc_final: 0.8014 (m-80) REVERT: E 309 ARG cc_start: 0.8323 (mtp180) cc_final: 0.8092 (ptm160) REVERT: E 337 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8315 (mm-40) REVERT: E 448 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8424 (mt-10) REVERT: F 411 ARG cc_start: 0.6638 (mpt-90) cc_final: 0.6390 (mmm160) outliers start: 95 outliers final: 54 residues processed: 392 average time/residue: 0.3604 time to fit residues: 229.9875 Evaluate side-chains 341 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 282 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 552 TRP Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 448 GLU Chi-restraints excluded: chain E residue 560 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 528 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 257 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 290 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 255 optimal weight: 8.9990 chunk 288 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 285 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 234 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN C 232 HIS C 234 GLN D 166 GLN ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 263 HIS E 331 ASN F 234 GLN F 337 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.179331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.134596 restraints weight = 30704.315| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.90 r_work: 0.3224 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 27144 Z= 0.190 Angle : 0.559 8.608 36673 Z= 0.293 Chirality : 0.046 0.191 4115 Planarity : 0.004 0.055 4749 Dihedral : 4.737 79.253 3559 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 3.20 % Allowed : 22.99 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.14), residues: 3313 helix: -0.17 (0.16), residues: 1111 sheet: -1.45 (0.22), residues: 492 loop : -0.50 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 556 HIS 0.017 0.001 HIS C 232 PHE 0.022 0.001 PHE A 561 TYR 0.015 0.001 TYR C 404 ARG 0.004 0.000 ARG E 239 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 868) hydrogen bonds : angle 5.64456 ( 2391) covalent geometry : bond 0.00453 (27144) covalent geometry : angle 0.55916 (36673) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 296 time to evaluate : 3.277 Fit side-chains revert: symmetry clash REVERT: A 408 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8216 (mttm) REVERT: A 441 ARG cc_start: 0.7521 (ttp80) cc_final: 0.6807 (tpp80) REVERT: A 548 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.6644 (t80) REVERT: A 555 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7090 (tm-30) REVERT: B 305 GLU cc_start: 0.8570 (tp30) cc_final: 0.8354 (tp30) REVERT: B 445 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7944 (tm-30) REVERT: C 199 ASN cc_start: 0.7683 (t0) cc_final: 0.7439 (t0) REVERT: C 502 ASP cc_start: 0.8523 (p0) cc_final: 0.8269 (p0) REVERT: D 62 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: D 120 ASP cc_start: 0.8015 (t0) cc_final: 0.7705 (t0) REVERT: D 251 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7691 (mm-40) REVERT: D 341 PHE cc_start: 0.8465 (m-80) cc_final: 0.8221 (m-80) REVERT: D 439 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8270 (ptmt) REVERT: D 553 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7664 (mtt90) outliers start: 97 outliers final: 69 residues processed: 369 average time/residue: 0.3856 time to fit residues: 228.1737 Evaluate side-chains 349 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 275 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 552 TRP Chi-restraints excluded: chain D residue 553 ARG Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 385 PHE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 528 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 135 optimal weight: 0.8980 chunk 321 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 266 optimal weight: 8.9990 chunk 213 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 124 optimal weight: 0.0070 chunk 17 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 234 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN A 331 ASN A 493 GLN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN ** D 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 478 GLN F 230 ASN F 234 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.185760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.139044 restraints weight = 30914.616| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.79 r_work: 0.3284 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27144 Z= 0.109 Angle : 0.497 7.859 36673 Z= 0.260 Chirality : 0.044 0.175 4115 Planarity : 0.004 0.056 4749 Dihedral : 4.425 79.508 3559 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 3.14 % Allowed : 23.16 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.57 (0.15), residues: 3313 helix: 0.25 (0.16), residues: 1124 sheet: -1.41 (0.22), residues: 490 loop : -0.36 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 556 HIS 0.002 0.000 HIS C 429 PHE 0.022 0.001 PHE A 561 TYR 0.011 0.001 TYR C 404 ARG 0.004 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 868) hydrogen bonds : angle 5.23223 ( 2391) covalent geometry : bond 0.00255 (27144) covalent geometry : angle 0.49729 (36673) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 320 time to evaluate : 3.266 Fit side-chains revert: symmetry clash REVERT: A 144 ASN cc_start: 0.8756 (p0) cc_final: 0.8489 (p0) REVERT: A 195 ASN cc_start: 0.8309 (t0) cc_final: 0.7958 (t0) REVERT: A 441 ARG cc_start: 0.7711 (ttp80) cc_final: 0.6867 (tpp80) REVERT: A 548 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.6620 (t80) REVERT: A 555 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7061 (tm-30) REVERT: B 305 GLU cc_start: 0.8659 (tp30) cc_final: 0.8441 (tp30) REVERT: B 404 TYR cc_start: 0.8995 (t80) cc_final: 0.8632 (t80) REVERT: B 445 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8130 (tm-30) REVERT: C 34 GLU cc_start: 0.7182 (pt0) cc_final: 0.6889 (pt0) REVERT: C 199 ASN cc_start: 0.7906 (t0) cc_final: 0.7670 (t0) REVERT: C 427 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8452 (mm-30) REVERT: C 502 ASP cc_start: 0.8563 (p0) cc_final: 0.8306 (p0) REVERT: D 62 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: D 120 ASP cc_start: 0.8283 (t0) cc_final: 0.7934 (t0) REVERT: D 341 PHE cc_start: 0.8409 (m-80) cc_final: 0.8157 (m-80) REVERT: D 439 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8238 (ptmt) REVERT: D 553 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7560 (mtt90) REVERT: F 234 GLN cc_start: 0.5737 (OUTLIER) cc_final: 0.5508 (pp30) outliers start: 95 outliers final: 58 residues processed: 396 average time/residue: 0.3635 time to fit residues: 234.6484 Evaluate side-chains 350 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 287 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 552 TRP Chi-restraints excluded: chain D residue 553 ARG Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 560 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 234 GLN Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 481 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 119 optimal weight: 0.6980 chunk 326 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.0470 chunk 84 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN A 331 ASN B 279 ASN D 281 ASN ** D 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 279 ASN E 478 GLN F 234 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.183466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136675 restraints weight = 30825.675| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.89 r_work: 0.3190 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27144 Z= 0.156 Angle : 0.527 8.668 36673 Z= 0.273 Chirality : 0.045 0.185 4115 Planarity : 0.004 0.049 4749 Dihedral : 4.339 79.076 3555 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 3.87 % Allowed : 22.96 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.15), residues: 3313 helix: 0.43 (0.16), residues: 1113 sheet: -1.44 (0.23), residues: 487 loop : -0.39 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 213 HIS 0.002 0.001 HIS F 146 PHE 0.024 0.001 PHE A 561 TYR 0.012 0.001 TYR C 267 ARG 0.005 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03111 ( 868) hydrogen bonds : angle 5.20009 ( 2391) covalent geometry : bond 0.00371 (27144) covalent geometry : angle 0.52721 (36673) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 291 time to evaluate : 3.558 Fit side-chains revert: symmetry clash REVERT: A 195 ASN cc_start: 0.8305 (t0) cc_final: 0.7897 (t0) REVERT: A 441 ARG cc_start: 0.7705 (ttp80) cc_final: 0.6830 (tpp80) REVERT: A 548 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.6347 (t80) REVERT: A 555 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7105 (tm-30) REVERT: B 305 GLU cc_start: 0.8613 (tp30) cc_final: 0.8386 (tp30) REVERT: B 445 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8143 (tm-30) REVERT: C 21 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7883 (pt) REVERT: C 34 GLU cc_start: 0.7129 (pt0) cc_final: 0.6840 (pt0) REVERT: C 199 ASN cc_start: 0.7906 (t0) cc_final: 0.7654 (t0) REVERT: C 427 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8433 (mm-30) REVERT: C 502 ASP cc_start: 0.8648 (p0) cc_final: 0.8373 (p0) REVERT: C 524 ASP cc_start: 0.8579 (t0) cc_final: 0.8363 (m-30) REVERT: D 35 LYS cc_start: 0.7029 (mmmt) cc_final: 0.6802 (mtmt) REVERT: D 62 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: D 72 MET cc_start: 0.7959 (mtt) cc_final: 0.7629 (ttm) REVERT: D 120 ASP cc_start: 0.8308 (t0) cc_final: 0.7744 (t0) REVERT: D 341 PHE cc_start: 0.8458 (m-80) cc_final: 0.8180 (m-80) REVERT: D 439 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8285 (ptmt) REVERT: D 553 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7689 (mtt90) REVERT: E 318 ASP cc_start: 0.4669 (p0) cc_final: 0.4458 (p0) REVERT: F 234 GLN cc_start: 0.5965 (OUTLIER) cc_final: 0.5467 (pm20) outliers start: 117 outliers final: 87 residues processed: 382 average time/residue: 0.4859 time to fit residues: 300.8417 Evaluate side-chains 366 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 273 time to evaluate : 4.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 552 TRP Chi-restraints excluded: chain D residue 553 ARG Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 560 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 234 GLN Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 385 PHE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 528 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 254 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 240 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 315 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 312 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 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 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 245 ASN E 249 HIS E 478 GLN E 493 GLN F 234 GLN F 236 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.178589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.133787 restraints weight = 30782.289| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.84 r_work: 0.3165 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 27144 Z= 0.227 Angle : 0.578 8.942 36673 Z= 0.298 Chirality : 0.047 0.212 4115 Planarity : 0.004 0.047 4749 Dihedral : 4.555 79.779 3555 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.83 % Favored : 96.08 % Rotamer: Outliers : 4.33 % Allowed : 22.73 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 3313 helix: 0.36 (0.16), residues: 1118 sheet: -1.56 (0.22), residues: 511 loop : -0.46 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 552 HIS 0.003 0.001 HIS D 405 PHE 0.023 0.001 PHE A 561 TYR 0.015 0.001 TYR F 368 ARG 0.007 0.000 ARG A 455 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 868) hydrogen bonds : angle 5.35278 ( 2391) covalent geometry : bond 0.00549 (27144) covalent geometry : angle 0.57782 (36673) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 295 time to evaluate : 3.417 Fit side-chains revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7185 (m-30) REVERT: A 408 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8148 (mttm) REVERT: A 441 ARG cc_start: 0.7566 (ttp80) cc_final: 0.6904 (tpp80) REVERT: A 548 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.6571 (t80) REVERT: B 445 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7891 (tm-30) REVERT: C 21 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7962 (pt) REVERT: C 427 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8132 (mm-30) REVERT: C 502 ASP cc_start: 0.8566 (p0) cc_final: 0.8307 (p0) REVERT: D 62 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: D 72 MET cc_start: 0.7740 (mtt) cc_final: 0.7222 (ttm) REVERT: D 120 ASP cc_start: 0.8205 (t0) cc_final: 0.7878 (t0) REVERT: D 278 ASN cc_start: 0.7629 (t0) cc_final: 0.7102 (t0) REVERT: D 341 PHE cc_start: 0.8496 (m-80) cc_final: 0.8255 (m-80) REVERT: D 439 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8309 (ptmt) REVERT: D 553 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7893 (mtt90) REVERT: E 165 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8627 (mp) REVERT: E 318 ASP cc_start: 0.4479 (p0) cc_final: 0.4197 (p0) REVERT: E 375 ILE cc_start: 0.8740 (mt) cc_final: 0.8456 (mm) REVERT: F 234 GLN cc_start: 0.6058 (OUTLIER) cc_final: 0.5621 (pm20) outliers start: 131 outliers final: 98 residues processed: 400 average time/residue: 0.3595 time to fit residues: 235.1967 Evaluate side-chains 379 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 272 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 552 TRP Chi-restraints excluded: chain D residue 553 ARG Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 521 ILE Chi-restraints excluded: chain E residue 560 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 234 GLN Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 385 PHE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 528 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 75 optimal weight: 4.9990 chunk 28 optimal weight: 40.0000 chunk 223 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 188 optimal weight: 0.0470 chunk 24 optimal weight: 0.7980 chunk 235 optimal weight: 20.0000 chunk 249 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 311 optimal weight: 30.0000 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN C 17 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN E 183 HIS E 263 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.183694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.140763 restraints weight = 30720.552| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.74 r_work: 0.3285 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27144 Z= 0.104 Angle : 0.508 8.582 36673 Z= 0.263 Chirality : 0.044 0.196 4115 Planarity : 0.004 0.049 4749 Dihedral : 4.275 79.904 3555 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.08 % Favored : 96.80 % Rotamer: Outliers : 3.47 % Allowed : 23.69 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.15), residues: 3313 helix: 0.72 (0.16), residues: 1098 sheet: -1.49 (0.22), residues: 511 loop : -0.36 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 556 HIS 0.003 0.000 HIS A 429 PHE 0.017 0.001 PHE A 561 TYR 0.013 0.001 TYR F 368 ARG 0.009 0.000 ARG F 235 Details of bonding type rmsd hydrogen bonds : bond 0.02825 ( 868) hydrogen bonds : angle 5.03858 ( 2391) covalent geometry : bond 0.00244 (27144) covalent geometry : angle 0.50762 (36673) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 309 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8164 (tt0) cc_final: 0.7904 (tt0) REVERT: A 195 ASN cc_start: 0.8186 (t0) cc_final: 0.7920 (t0) REVERT: A 441 ARG cc_start: 0.7547 (ttp80) cc_final: 0.6841 (tpp80) REVERT: A 466 GLN cc_start: 0.8291 (mt0) cc_final: 0.7974 (mp10) REVERT: A 548 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.6806 (t80) REVERT: B 404 TYR cc_start: 0.8874 (t80) cc_final: 0.8565 (t80) REVERT: B 445 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7850 (tm-30) REVERT: C 427 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8228 (mm-30) REVERT: C 524 ASP cc_start: 0.8240 (t0) cc_final: 0.8020 (m-30) REVERT: D 72 MET cc_start: 0.7617 (mtt) cc_final: 0.7094 (ttm) REVERT: D 120 ASP cc_start: 0.8138 (t0) cc_final: 0.7722 (t0) REVERT: D 341 PHE cc_start: 0.8307 (m-80) cc_final: 0.8106 (m-80) REVERT: D 439 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8282 (ptmt) REVERT: D 522 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7958 (ptp) REVERT: D 553 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7625 (mtt90) REVERT: E 165 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8572 (mp) REVERT: E 318 ASP cc_start: 0.4538 (p0) cc_final: 0.4229 (p0) REVERT: E 375 ILE cc_start: 0.8645 (mt) cc_final: 0.8390 (mm) REVERT: E 397 ARG cc_start: 0.7698 (ttp80) cc_final: 0.7443 (ttp80) outliers start: 105 outliers final: 73 residues processed: 393 average time/residue: 0.3722 time to fit residues: 238.3185 Evaluate side-chains 362 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 284 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain D residue 552 TRP Chi-restraints excluded: chain D residue 553 ARG Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 385 PHE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 528 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 286 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 324 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 291 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 249 HIS F 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.180433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135698 restraints weight = 30715.567| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.85 r_work: 0.3208 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27144 Z= 0.176 Angle : 0.557 9.634 36673 Z= 0.286 Chirality : 0.046 0.215 4115 Planarity : 0.004 0.044 4749 Dihedral : 4.395 79.617 3555 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 3.73 % Allowed : 23.62 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.15), residues: 3313 helix: 0.69 (0.16), residues: 1103 sheet: -1.52 (0.22), residues: 511 loop : -0.38 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 213 HIS 0.002 0.001 HIS A 429 PHE 0.029 0.001 PHE A 561 TYR 0.020 0.001 TYR C 267 ARG 0.009 0.000 ARG C 455 Details of bonding type rmsd hydrogen bonds : bond 0.03047 ( 868) hydrogen bonds : angle 5.13118 ( 2391) covalent geometry : bond 0.00425 (27144) covalent geometry : angle 0.55713 (36673) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 288 time to evaluate : 3.340 Fit side-chains revert: symmetry clash REVERT: A 441 ARG cc_start: 0.7552 (ttp80) cc_final: 0.6836 (tpp80) REVERT: A 548 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.6397 (t80) REVERT: A 552 TRP cc_start: 0.6593 (OUTLIER) cc_final: 0.5043 (m100) REVERT: A 555 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6946 (tm-30) REVERT: B 404 TYR cc_start: 0.8960 (t80) cc_final: 0.8640 (t80) REVERT: B 445 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7868 (tm-30) REVERT: B 515 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8119 (mttm) REVERT: C 28 GLU cc_start: 0.8132 (tt0) cc_final: 0.7713 (tm-30) REVERT: C 427 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8037 (mm-30) REVERT: D 62 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6715 (mp0) REVERT: D 72 MET cc_start: 0.7671 (mtt) cc_final: 0.7107 (ttm) REVERT: D 120 ASP cc_start: 0.8168 (t0) cc_final: 0.7717 (t0) REVERT: D 341 PHE cc_start: 0.8390 (m-80) cc_final: 0.8190 (m-80) REVERT: D 439 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8370 (ptmt) REVERT: D 522 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.8057 (ptp) REVERT: D 553 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7772 (mtt90) REVERT: E 165 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8493 (mp) REVERT: E 318 ASP cc_start: 0.4530 (p0) cc_final: 0.4185 (p0) REVERT: E 375 ILE cc_start: 0.8690 (mt) cc_final: 0.8395 (mm) REVERT: F 234 GLN cc_start: 0.6018 (OUTLIER) cc_final: 0.5502 (pm20) outliers start: 113 outliers final: 84 residues processed: 379 average time/residue: 0.3684 time to fit residues: 227.8240 Evaluate side-chains 371 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 278 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain D residue 552 TRP Chi-restraints excluded: chain D residue 553 ARG Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 509 ASN Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 234 GLN Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 385 PHE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 528 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 258 optimal weight: 9.9990 chunk 131 optimal weight: 0.6980 chunk 262 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 267 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 199 optimal weight: 0.5980 chunk 268 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN E 183 HIS ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS E 279 ASN E 478 GLN ** F 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.181669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.138110 restraints weight = 30839.583| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.73 r_work: 0.3258 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27144 Z= 0.140 Angle : 0.538 9.486 36673 Z= 0.276 Chirality : 0.045 0.217 4115 Planarity : 0.004 0.047 4749 Dihedral : 4.346 80.051 3555 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 3.47 % Allowed : 23.89 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.15), residues: 3313 helix: 0.73 (0.16), residues: 1107 sheet: -1.52 (0.22), residues: 503 loop : -0.36 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 556 HIS 0.002 0.000 HIS E 291 PHE 0.031 0.001 PHE A 561 TYR 0.015 0.001 TYR F 368 ARG 0.008 0.000 ARG C 455 Details of bonding type rmsd hydrogen bonds : bond 0.02907 ( 868) hydrogen bonds : angle 5.05982 ( 2391) covalent geometry : bond 0.00337 (27144) covalent geometry : angle 0.53843 (36673) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 292 time to evaluate : 3.205 Fit side-chains revert: symmetry clash REVERT: A 195 ASN cc_start: 0.8273 (t0) cc_final: 0.7919 (t0) REVERT: A 441 ARG cc_start: 0.7498 (ttp80) cc_final: 0.6858 (tpp80) REVERT: A 548 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.6556 (t80) REVERT: A 552 TRP cc_start: 0.6660 (OUTLIER) cc_final: 0.5227 (m100) REVERT: B 445 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7877 (tm-30) REVERT: B 515 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8108 (mttm) REVERT: C 28 GLU cc_start: 0.8111 (tt0) cc_final: 0.7730 (tm-30) REVERT: C 427 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8039 (mm-30) REVERT: D 62 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6725 (mp0) REVERT: D 72 MET cc_start: 0.7725 (mtt) cc_final: 0.7151 (ttm) REVERT: D 120 ASP cc_start: 0.8163 (t0) cc_final: 0.7737 (t0) REVERT: D 341 PHE cc_start: 0.8335 (m-80) cc_final: 0.8113 (m-80) REVERT: D 439 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8355 (ptmt) REVERT: D 522 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.8030 (ptp) REVERT: D 553 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7730 (mtt90) REVERT: E 165 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8561 (mp) REVERT: E 318 ASP cc_start: 0.4548 (p0) cc_final: 0.4222 (p0) REVERT: E 375 ILE cc_start: 0.8680 (mt) cc_final: 0.8395 (mm) REVERT: E 397 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7518 (ttp80) REVERT: E 478 GLN cc_start: 0.8034 (tp-100) cc_final: 0.7683 (tp-100) REVERT: F 208 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7637 (pp) outliers start: 105 outliers final: 84 residues processed: 377 average time/residue: 0.3660 time to fit residues: 225.1136 Evaluate side-chains 376 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 283 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain D residue 552 TRP Chi-restraints excluded: chain D residue 553 ARG Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 509 ASN Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 385 PHE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 528 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 255 optimal weight: 30.0000 chunk 275 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 304 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN E 183 HIS ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 GLN F 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.182137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138851 restraints weight = 30722.688| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.83 r_work: 0.3252 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27144 Z= 0.131 Angle : 0.535 10.250 36673 Z= 0.275 Chirality : 0.045 0.225 4115 Planarity : 0.004 0.045 4749 Dihedral : 4.312 79.923 3555 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.29 % Favored : 96.56 % Rotamer: Outliers : 3.20 % Allowed : 24.15 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.15), residues: 3313 helix: 0.77 (0.16), residues: 1107 sheet: -1.49 (0.22), residues: 503 loop : -0.34 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 556 HIS 0.002 0.000 HIS E 291 PHE 0.031 0.001 PHE A 561 TYR 0.024 0.001 TYR C 267 ARG 0.007 0.000 ARG C 455 Details of bonding type rmsd hydrogen bonds : bond 0.02857 ( 868) hydrogen bonds : angle 5.01089 ( 2391) covalent geometry : bond 0.00317 (27144) covalent geometry : angle 0.53536 (36673) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 288 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.8275 (t0) cc_final: 0.7922 (t0) REVERT: A 441 ARG cc_start: 0.7441 (ttp80) cc_final: 0.6824 (tpp80) REVERT: A 548 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.6578 (t80) REVERT: A 552 TRP cc_start: 0.6583 (OUTLIER) cc_final: 0.5144 (m100) REVERT: B 445 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7858 (tm-30) REVERT: B 515 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8097 (mttm) REVERT: C 28 GLU cc_start: 0.8121 (tt0) cc_final: 0.7720 (tm-30) REVERT: C 427 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8022 (mm-30) REVERT: C 524 ASP cc_start: 0.8356 (t0) cc_final: 0.8104 (m-30) REVERT: D 62 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: D 72 MET cc_start: 0.7663 (mtt) cc_final: 0.7070 (ttm) REVERT: D 120 ASP cc_start: 0.8157 (t0) cc_final: 0.7723 (t0) REVERT: D 439 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8346 (ptmt) REVERT: D 553 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7641 (mtt90) REVERT: E 165 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8511 (mp) REVERT: E 318 ASP cc_start: 0.4604 (p0) cc_final: 0.4287 (p0) REVERT: E 375 ILE cc_start: 0.8672 (mt) cc_final: 0.8382 (mm) REVERT: E 397 ARG cc_start: 0.7692 (ttp80) cc_final: 0.7471 (ttp80) REVERT: F 234 GLN cc_start: 0.6079 (OUTLIER) cc_final: 0.5641 (pm20) outliers start: 97 outliers final: 84 residues processed: 366 average time/residue: 0.3716 time to fit residues: 221.4688 Evaluate side-chains 376 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 284 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 552 TRP Chi-restraints excluded: chain D residue 553 ARG Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 234 GLN Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 385 PHE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 528 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 267 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 269 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 205 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 291 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 329 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN E 183 HIS ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS ** F 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.180647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137459 restraints weight = 30876.145| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.74 r_work: 0.3237 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27144 Z= 0.169 Angle : 0.560 10.706 36673 Z= 0.287 Chirality : 0.045 0.224 4115 Planarity : 0.004 0.045 4749 Dihedral : 4.386 79.998 3555 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.53 % Favored : 96.32 % Rotamer: Outliers : 3.53 % Allowed : 23.85 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.15), residues: 3313 helix: 0.73 (0.16), residues: 1107 sheet: -1.51 (0.22), residues: 503 loop : -0.35 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 213 HIS 0.002 0.001 HIS D 190 PHE 0.031 0.001 PHE A 561 TYR 0.016 0.001 TYR F 368 ARG 0.008 0.000 ARG B 239 Details of bonding type rmsd hydrogen bonds : bond 0.02969 ( 868) hydrogen bonds : angle 5.07067 ( 2391) covalent geometry : bond 0.00409 (27144) covalent geometry : angle 0.55966 (36673) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14552.82 seconds wall clock time: 254 minutes 29.21 seconds (15269.21 seconds total)