Starting phenix.real_space_refine on Mon Aug 25 07:54:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xau_38203/08_2025/8xau_38203.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xau_38203/08_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_38203/08_2025/8xau_38203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xau_38203/08_2025/8xau_38203.map" model { file = "/net/cci-nas-00/data/ceres_data/8xau_38203/08_2025/8xau_38203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xau_38203/08_2025/8xau_38203.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.44, per 1000 atoms: 0.24 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: 1.74 Conformation dependent library (CDL) restraints added in 814.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.06 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: 5.35 Time building geometry restraints manager: 2.32 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: 0.920 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.320 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.740 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.016 0.001 ARG D 141 TYR 0.034 0.002 TYR F 368 PHE 0.044 0.002 PHE F 250 TRP 0.033 0.002 TRP A 556 HIS 0.009 0.001 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00519 (27144) covalent geometry : angle 0.80619 (36673) hydrogen bonds : bond 0.27453 ( 868) hydrogen bonds : angle 9.89477 ( 2391) *********************** 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 : 1.170 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: 0.8026 (m-80) outliers start: 13 outliers final: 11 residues processed: 321 average time/residue: 0.1816 time to fit residues: 92.7655 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 : 1.063 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN A 331 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 58 ASN E 17 ASN E 183 HIS E 263 HIS E 478 GLN F 234 GLN F 245 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.181897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.137726 restraints weight = 30871.066| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.87 r_work: 0.3120 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27144 Z= 0.187 Angle : 0.576 9.588 36673 Z= 0.305 Chirality : 0.046 0.164 4115 Planarity : 0.005 0.062 4749 Dihedral : 5.075 82.624 3566 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.50 % Allowed : 22.46 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.14), residues: 3313 helix: -0.77 (0.15), residues: 1084 sheet: -1.41 (0.22), residues: 503 loop : -0.56 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 239 TYR 0.014 0.001 TYR C 267 PHE 0.017 0.001 PHE A 400 TRP 0.014 0.002 TRP A 556 HIS 0.005 0.001 HIS F 159 Details of bonding type rmsd covalent geometry : bond 0.00442 (27144) covalent geometry : angle 0.57617 (36673) hydrogen bonds : bond 0.04410 ( 868) hydrogen bonds : angle 6.09148 ( 2391) *********************** 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 409 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 303 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8088 (mttm) REVERT: A 441 ARG cc_start: 0.7652 (ttp80) cc_final: 0.6796 (tpp80) REVERT: A 548 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.6566 (t80) REVERT: B 404 TYR cc_start: 0.8972 (t80) cc_final: 0.8719 (t80) REVERT: C 34 GLU cc_start: 0.7168 (pt0) cc_final: 0.6962 (pt0) REVERT: C 106 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7453 (p0) REVERT: C 199 ASN cc_start: 0.7871 (t0) cc_final: 0.7671 (t0) REVERT: C 234 GLN cc_start: 0.7755 (mt0) cc_final: 0.7547 (mt0) REVERT: C 267 TYR cc_start: 0.8263 (t80) cc_final: 0.8032 (t80) REVERT: C 291 HIS cc_start: 0.7596 (m-70) cc_final: 0.7370 (m170) REVERT: C 502 ASP cc_start: 0.8740 (p0) cc_final: 0.8403 (p0) REVERT: C 524 ASP cc_start: 0.8601 (t0) cc_final: 0.8395 (m-30) REVERT: D 62 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: D 120 ASP cc_start: 0.7985 (t0) cc_final: 0.7764 (t0) REVERT: D 251 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7756 (mm-40) REVERT: D 341 PHE cc_start: 0.8478 (m-80) cc_final: 0.8116 (m-80) REVERT: D 553 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7633 (mtt90) REVERT: E 337 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8385 (mm-40) REVERT: E 448 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8437 (mt-10) REVERT: E 478 GLN cc_start: 0.8147 (tp40) cc_final: 0.7933 (tp-100) outliers start: 106 outliers final: 56 residues processed: 383 average time/residue: 0.1544 time to fit residues: 96.3611 Evaluate side-chains 337 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 275 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 225 LEU 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 549 LEU 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 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 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 106 ASP Chi-restraints excluded: chain D residue 131 THR 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 D residue 553 ARG 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 481 THR Chi-restraints excluded: chain F residue 521 ILE 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 83 optimal weight: 9.9990 chunk 230 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 254 optimal weight: 10.0000 chunk 222 optimal weight: 0.0770 chunk 280 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 225 optimal weight: 7.9990 chunk 231 optimal weight: 20.0000 chunk 248 optimal weight: 0.0980 chunk 140 optimal weight: 9.9990 overall best weight: 1.8342 ------------------------------------------------------------------------------- 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 C 232 HIS D 166 GLN D 281 ASN E 183 HIS E 331 ASN F 230 ASN F 234 GLN F 337 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.181837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137473 restraints weight = 30781.589| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.97 r_work: 0.3245 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27144 Z= 0.153 Angle : 0.535 8.677 36673 Z= 0.281 Chirality : 0.045 0.176 4115 Planarity : 0.004 0.056 4749 Dihedral : 4.678 80.506 3559 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.17 % Allowed : 22.83 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.14), residues: 3313 helix: -0.08 (0.16), residues: 1088 sheet: -1.47 (0.22), residues: 502 loop : -0.44 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 235 TYR 0.014 0.001 TYR A 276 PHE 0.022 0.001 PHE A 561 TRP 0.011 0.001 TRP A 556 HIS 0.014 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00362 (27144) covalent geometry : angle 0.53490 (36673) hydrogen bonds : bond 0.03634 ( 868) hydrogen bonds : angle 5.60806 ( 2391) *********************** 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 408 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 312 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8527 (m) REVERT: A 195 ASN cc_start: 0.8186 (t0) cc_final: 0.7790 (t0) REVERT: A 408 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8163 (mttm) REVERT: A 441 ARG cc_start: 0.7485 (ttp80) cc_final: 0.6808 (tpp80) REVERT: A 548 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.6656 (t80) REVERT: A 555 GLU cc_start: 0.7381 (tm-30) cc_final: 0.7071 (tm-30) REVERT: B 305 GLU cc_start: 0.8566 (tp30) cc_final: 0.8340 (tp30) REVERT: B 404 TYR cc_start: 0.8884 (t80) cc_final: 0.8593 (t80) REVERT: B 445 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7940 (tm-30) REVERT: C 199 ASN cc_start: 0.7632 (t0) cc_final: 0.7383 (t0) REVERT: C 427 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8199 (mm-30) REVERT: C 502 ASP cc_start: 0.8513 (p0) cc_final: 0.8237 (p0) REVERT: D 120 ASP cc_start: 0.8015 (t0) cc_final: 0.7725 (t0) REVERT: D 251 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7677 (mm-40) REVERT: D 341 PHE cc_start: 0.8431 (m-80) cc_final: 0.8146 (m-80) REVERT: D 439 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8259 (ptmt) REVERT: D 441 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7954 (ttp80) REVERT: D 553 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7539 (mtt90) outliers start: 96 outliers final: 67 residues processed: 385 average time/residue: 0.1611 time to fit residues: 100.5228 Evaluate side-chains 353 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 281 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 160 THR 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 549 LEU 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 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 111 ILE 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 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 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 103 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 198 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 304 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 274 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 A 493 GLN ** D 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 478 GLN F 234 GLN 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 = 0.181568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.137432 restraints weight = 30801.720| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.79 r_work: 0.3155 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27144 Z= 0.157 Angle : 0.528 7.960 36673 Z= 0.275 Chirality : 0.045 0.176 4115 Planarity : 0.004 0.051 4749 Dihedral : 4.568 79.085 3559 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 4.20 % Allowed : 22.50 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.15), residues: 3313 helix: 0.09 (0.16), residues: 1136 sheet: -1.52 (0.22), residues: 487 loop : -0.42 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 235 TYR 0.012 0.001 TYR A 276 PHE 0.022 0.001 PHE A 561 TRP 0.010 0.001 TRP A 556 HIS 0.003 0.001 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00373 (27144) covalent geometry : angle 0.52804 (36673) hydrogen bonds : bond 0.03293 ( 868) hydrogen bonds : angle 5.39192 ( 2391) *********************** 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 437 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 310 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 144 ASN cc_start: 0.8668 (p0) cc_final: 0.8360 (p0) REVERT: A 150 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8537 (m) REVERT: A 195 ASN cc_start: 0.8194 (t0) cc_final: 0.7809 (t0) REVERT: A 408 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7890 (mttm) REVERT: A 441 ARG cc_start: 0.7451 (ttp80) cc_final: 0.6781 (tpp80) REVERT: A 548 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.6471 (t80) REVERT: A 555 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7034 (tm-30) REVERT: B 305 GLU cc_start: 0.8578 (tp30) cc_final: 0.8364 (tp30) REVERT: B 445 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7926 (tm-30) REVERT: C 21 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7790 (pt) REVERT: C 69 GLN cc_start: 0.7716 (tt0) cc_final: 0.7506 (tt0) REVERT: C 199 ASN cc_start: 0.7701 (t0) cc_final: 0.7450 (t0) REVERT: C 427 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8286 (mm-30) REVERT: D 62 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: D 120 ASP cc_start: 0.8133 (t0) cc_final: 0.7839 (t0) REVERT: D 251 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7716 (mm-40) REVERT: D 278 ASN cc_start: 0.7516 (t0) cc_final: 0.7048 (t0) REVERT: D 341 PHE cc_start: 0.8413 (m-80) cc_final: 0.8191 (m-80) REVERT: D 439 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8271 (ptmt) REVERT: D 441 ARG cc_start: 0.8201 (ttp80) cc_final: 0.7996 (ttp80) REVERT: D 553 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7843 (mtt180) outliers start: 127 outliers final: 86 residues processed: 411 average time/residue: 0.1673 time to fit residues: 111.4050 Evaluate side-chains 377 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 284 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 133 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 264 SER 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 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 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 524 ASP Chi-restraints excluded: chain B residue 549 LEU 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 240 GLN Chi-restraints excluded: chain C residue 248 ILE 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 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 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 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 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 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 392 VAL 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 150 VAL 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 329 LEU Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 356 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 225 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 325 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** 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 478 GLN E 493 GLN ** F 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.179497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.134702 restraints weight = 30766.374| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.80 r_work: 0.3236 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27144 Z= 0.169 Angle : 0.538 8.984 36673 Z= 0.279 Chirality : 0.045 0.186 4115 Planarity : 0.004 0.050 4749 Dihedral : 4.506 78.734 3557 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 4.36 % Allowed : 22.83 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.15), residues: 3313 helix: 0.33 (0.16), residues: 1118 sheet: -1.57 (0.22), residues: 487 loop : -0.41 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 455 TYR 0.015 0.001 TYR A 276 PHE 0.023 0.001 PHE A 561 TRP 0.011 0.001 TRP A 556 HIS 0.002 0.001 HIS E 308 Details of bonding type rmsd covalent geometry : bond 0.00404 (27144) covalent geometry : angle 0.53820 (36673) hydrogen bonds : bond 0.03203 ( 868) hydrogen bonds : angle 5.31251 ( 2391) *********************** 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 428 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 296 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 441 ARG cc_start: 0.7515 (ttp80) cc_final: 0.6813 (tpp80) REVERT: A 548 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.6506 (t80) REVERT: A 555 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7007 (tm-30) REVERT: B 305 GLU cc_start: 0.8506 (tp30) cc_final: 0.8296 (tp30) REVERT: B 404 TYR cc_start: 0.8939 (t80) cc_final: 0.8533 (t80) REVERT: B 445 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7927 (tm-30) REVERT: C 21 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7837 (pt) REVERT: C 335 ARG cc_start: 0.7388 (ttt-90) cc_final: 0.7163 (ttt-90) REVERT: C 427 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8063 (mm-30) REVERT: D 62 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: D 72 MET cc_start: 0.7671 (mtt) cc_final: 0.7320 (ttm) REVERT: D 120 ASP cc_start: 0.8170 (t0) cc_final: 0.7866 (t0) REVERT: D 341 PHE cc_start: 0.8473 (m-80) cc_final: 0.8210 (m-80) REVERT: D 439 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8271 (ptmt) REVERT: D 553 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7905 (mtt180) REVERT: E 318 ASP cc_start: 0.4445 (p0) cc_final: 0.4199 (p0) outliers start: 132 outliers final: 100 residues processed: 400 average time/residue: 0.1450 time to fit residues: 95.3100 Evaluate side-chains 381 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 276 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 127 LEU Chi-restraints excluded: chain A residue 129 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 264 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 364 THR 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 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 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 524 ASP Chi-restraints excluded: chain B residue 549 LEU 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 248 ILE 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 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 538 THR 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 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 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 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 392 VAL 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 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 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 521 ILE 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 156 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 254 optimal weight: 20.0000 chunk 46 optimal weight: 0.2980 chunk 184 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 324 optimal weight: 1.9990 chunk 309 optimal weight: 30.0000 chunk 232 optimal weight: 7.9990 chunk 284 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 A 331 ASN ** D 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 249 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.183194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.136508 restraints weight = 30842.216| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.83 r_work: 0.3248 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27144 Z= 0.143 Angle : 0.524 8.373 36673 Z= 0.272 Chirality : 0.045 0.182 4115 Planarity : 0.004 0.046 4749 Dihedral : 4.382 79.091 3555 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.53 % Favored : 96.38 % Rotamer: Outliers : 4.20 % Allowed : 22.99 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.15), residues: 3313 helix: 0.48 (0.16), residues: 1112 sheet: -1.54 (0.22), residues: 511 loop : -0.42 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 239 TYR 0.016 0.001 TYR B 495 PHE 0.014 0.001 PHE A 400 TRP 0.010 0.001 TRP A 556 HIS 0.002 0.000 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00341 (27144) covalent geometry : angle 0.52424 (36673) hydrogen bonds : bond 0.03026 ( 868) hydrogen bonds : angle 5.20637 ( 2391) *********************** 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 423 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 296 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 144 ASN cc_start: 0.8684 (p0) cc_final: 0.8476 (p0) REVERT: A 150 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8583 (m) REVERT: A 441 ARG cc_start: 0.7496 (ttp80) cc_final: 0.6804 (tpp80) REVERT: A 548 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.6291 (t80) REVERT: A 552 TRP cc_start: 0.6392 (OUTLIER) cc_final: 0.4974 (m100) REVERT: B 445 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7866 (tm-30) REVERT: B 515 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8106 (mttm) REVERT: C 551 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7821 (mm-30) REVERT: D 62 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: D 72 MET cc_start: 0.7662 (mtt) cc_final: 0.7299 (ttm) REVERT: D 120 ASP cc_start: 0.8145 (t0) cc_final: 0.7829 (t0) REVERT: D 341 PHE cc_start: 0.8433 (m-80) cc_final: 0.8182 (m-80) REVERT: D 439 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8214 (ptmt) REVERT: D 553 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7836 (mtt90) REVERT: E 318 ASP cc_start: 0.4522 (p0) cc_final: 0.4273 (p0) outliers start: 127 outliers final: 102 residues processed: 396 average time/residue: 0.1544 time to fit residues: 99.2343 Evaluate side-chains 384 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 275 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 114 ASP 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 160 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 364 THR 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 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 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 524 ASP Chi-restraints excluded: chain B residue 549 LEU 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 160 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 248 ILE 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 356 VAL Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 496 VAL 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 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 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 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 392 VAL Chi-restraints excluded: chain E residue 478 GLN 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 204 ASN 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 173 optimal weight: 8.9990 chunk 196 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 302 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 213 optimal weight: 4.9990 chunk 307 optimal weight: 4.9990 chunk 329 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 303 optimal weight: 2.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN A 331 ASN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 ASN E 183 HIS E 240 GLN E 478 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 = 0.4014 r_free = 0.4014 target = 0.177399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.132634 restraints weight = 30772.527| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.85 r_work: 0.3166 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 27144 Z= 0.258 Angle : 0.609 9.415 36673 Z= 0.314 Chirality : 0.048 0.232 4115 Planarity : 0.004 0.047 4749 Dihedral : 4.699 80.243 3555 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.38 % Favored : 95.50 % Rotamer: Outliers : 4.76 % Allowed : 22.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.15), residues: 3313 helix: 0.27 (0.16), residues: 1122 sheet: -1.68 (0.22), residues: 511 loop : -0.47 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 455 TYR 0.024 0.002 TYR F 368 PHE 0.026 0.002 PHE A 561 TRP 0.013 0.002 TRP A 213 HIS 0.003 0.001 HIS F 183 Details of bonding type rmsd covalent geometry : bond 0.00624 (27144) covalent geometry : angle 0.60938 (36673) hydrogen bonds : bond 0.03458 ( 868) hydrogen bonds : angle 5.45730 ( 2391) *********************** 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 421 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 277 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 426 GLU cc_start: 0.7953 (tp30) cc_final: 0.7469 (tp30) REVERT: A 427 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8420 (mm-30) REVERT: A 441 ARG cc_start: 0.7522 (ttp80) cc_final: 0.6857 (tpp80) REVERT: A 548 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.6482 (t80) REVERT: B 445 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 515 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8240 (mttm) REVERT: C 21 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7990 (pt) REVERT: D 62 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: D 72 MET cc_start: 0.7696 (mtt) cc_final: 0.7108 (ttm) REVERT: D 120 ASP cc_start: 0.8180 (t0) cc_final: 0.7828 (t0) REVERT: D 341 PHE cc_start: 0.8520 (m-80) cc_final: 0.8256 (m-80) REVERT: D 439 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8320 (ptmt) REVERT: D 553 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7991 (mtt90) REVERT: E 318 ASP cc_start: 0.4609 (p0) cc_final: 0.4319 (p0) REVERT: E 375 ILE cc_start: 0.8782 (mt) cc_final: 0.8479 (mm) REVERT: F 26 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6553 (pp) REVERT: F 234 GLN cc_start: 0.6061 (OUTLIER) cc_final: 0.5522 (pm20) outliers start: 144 outliers final: 111 residues processed: 395 average time/residue: 0.1589 time to fit residues: 102.5048 Evaluate side-chains 385 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 266 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 114 ASP 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 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 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 530 SER 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 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 316 THR 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 427 GLU 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 549 LEU 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 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 248 ILE Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 300 PHE 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 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 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 510 LEU 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 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 392 VAL 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 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 26 LEU 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 242 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 272 optimal weight: 0.0670 chunk 326 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 231 optimal weight: 20.0000 chunk 87 optimal weight: 40.0000 chunk 26 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 331 ASN B 233 ASN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 263 HIS F 234 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.176517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.131786 restraints weight = 30862.929| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.91 r_work: 0.3150 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2292 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 : 0.585 10.042 36673 Z= 0.301 Chirality : 0.047 0.220 4115 Planarity : 0.004 0.047 4749 Dihedral : 4.671 79.870 3555 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.95 % Favored : 95.93 % Rotamer: Outliers : 4.82 % Allowed : 22.70 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.15), residues: 3313 helix: 0.35 (0.16), residues: 1092 sheet: -1.77 (0.22), residues: 503 loop : -0.42 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 235 TYR 0.024 0.002 TYR F 368 PHE 0.028 0.002 PHE A 561 TRP 0.012 0.002 TRP B 556 HIS 0.003 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00548 (27144) covalent geometry : angle 0.58487 (36673) hydrogen bonds : bond 0.03299 ( 868) hydrogen bonds : angle 5.40264 ( 2391) *********************** 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 428 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 282 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 426 GLU cc_start: 0.7922 (tp30) cc_final: 0.7448 (tp30) REVERT: A 441 ARG cc_start: 0.7569 (ttp80) cc_final: 0.6946 (tpp80) REVERT: A 548 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.6506 (t80) REVERT: B 445 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7932 (tm-30) REVERT: B 515 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8228 (mttm) REVERT: C 21 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7970 (pt) REVERT: C 199 ASN cc_start: 0.7673 (t0) cc_final: 0.7396 (t0) REVERT: D 62 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: D 72 MET cc_start: 0.7778 (mtt) cc_final: 0.7180 (ttm) REVERT: D 120 ASP cc_start: 0.8185 (t0) cc_final: 0.7860 (t0) REVERT: D 278 ASN cc_start: 0.7618 (t0) cc_final: 0.7072 (t0) REVERT: D 341 PHE cc_start: 0.8475 (m-80) cc_final: 0.8237 (m-80) REVERT: D 439 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8275 (ptmt) REVERT: D 553 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7977 (mtt90) REVERT: E 303 ASP cc_start: 0.7749 (p0) cc_final: 0.7545 (p0) REVERT: E 318 ASP cc_start: 0.4528 (p0) cc_final: 0.4224 (p0) REVERT: F 234 GLN cc_start: 0.6106 (OUTLIER) cc_final: 0.5553 (pm20) outliers start: 146 outliers final: 117 residues processed: 399 average time/residue: 0.1681 time to fit residues: 109.1295 Evaluate side-chains 396 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 272 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 114 ASP 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 150 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 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 530 SER 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 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 316 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 356 VAL 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 515 LYS Chi-restraints excluded: chain B residue 549 LEU 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 50 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 160 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 300 PHE 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 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 510 LEU Chi-restraints excluded: chain D residue 552 TRP Chi-restraints excluded: chain D residue 553 ARG Chi-restraints excluded: chain E residue 12 VAL 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 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 392 VAL Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 509 ASN Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 539 ILE 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 242 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 147 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 284 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 171 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN C 17 ASN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 263 HIS F 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.180929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135844 restraints weight = 30699.827| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.84 r_work: 0.3219 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27144 Z= 0.139 Angle : 0.546 11.733 36673 Z= 0.280 Chirality : 0.045 0.205 4115 Planarity : 0.004 0.046 4749 Dihedral : 4.478 79.343 3555 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.53 % Favored : 96.35 % Rotamer: Outliers : 3.83 % Allowed : 23.95 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.15), residues: 3313 helix: 0.64 (0.16), residues: 1090 sheet: -1.69 (0.22), residues: 503 loop : -0.41 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 441 TYR 0.019 0.001 TYR C 267 PHE 0.030 0.001 PHE A 561 TRP 0.011 0.001 TRP B 556 HIS 0.005 0.000 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00335 (27144) covalent geometry : angle 0.54636 (36673) hydrogen bonds : bond 0.02985 ( 868) hydrogen bonds : angle 5.19127 ( 2391) *********************** 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 414 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 298 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8561 (m) REVERT: A 192 GLU cc_start: 0.8249 (tt0) cc_final: 0.8006 (tt0) REVERT: A 441 ARG cc_start: 0.7526 (ttp80) cc_final: 0.6898 (tpp80) REVERT: A 548 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.6451 (t80) REVERT: A 552 TRP cc_start: 0.6679 (OUTLIER) cc_final: 0.5158 (m100) REVERT: B 445 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 515 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8169 (mttm) REVERT: C 21 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7833 (pt) REVERT: C 116 ILE cc_start: 0.8342 (mp) cc_final: 0.8104 (mp) REVERT: C 199 ASN cc_start: 0.7591 (t0) cc_final: 0.7304 (t0) REVERT: D 62 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: D 72 MET cc_start: 0.7738 (mtt) cc_final: 0.7174 (ttm) REVERT: D 120 ASP cc_start: 0.8133 (t0) cc_final: 0.7868 (t0) REVERT: D 439 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8243 (ptmt) REVERT: D 553 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7842 (mtt90) REVERT: E 318 ASP cc_start: 0.4671 (p0) cc_final: 0.4333 (p0) REVERT: E 375 ILE cc_start: 0.8715 (mt) cc_final: 0.8451 (mm) REVERT: F 234 GLN cc_start: 0.6213 (OUTLIER) cc_final: 0.5569 (pm20) outliers start: 116 outliers final: 97 residues processed: 391 average time/residue: 0.1578 time to fit residues: 100.4017 Evaluate side-chains 386 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 280 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 114 ASP 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 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 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 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 356 VAL Chi-restraints excluded: chain B residue 386 GLU 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 549 LEU 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 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 248 ILE 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 496 VAL Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 537 CYS 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 12 VAL 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 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 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 E residue 539 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 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 242 ILE 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 158 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 206 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 264 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 304 ASN A 331 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.183318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.136683 restraints weight = 30631.904| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.87 r_work: 0.3196 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27144 Z= 0.129 Angle : 0.544 10.953 36673 Z= 0.279 Chirality : 0.045 0.219 4115 Planarity : 0.004 0.046 4749 Dihedral : 4.396 79.097 3555 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.44 % Favored : 96.44 % Rotamer: Outliers : 3.67 % Allowed : 24.41 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.15), residues: 3313 helix: 0.74 (0.16), residues: 1096 sheet: -1.62 (0.22), residues: 503 loop : -0.39 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 235 TYR 0.018 0.001 TYR F 368 PHE 0.030 0.001 PHE A 561 TRP 0.010 0.001 TRP B 556 HIS 0.002 0.000 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00309 (27144) covalent geometry : angle 0.54396 (36673) hydrogen bonds : bond 0.02897 ( 868) hydrogen bonds : angle 5.11266 ( 2391) ********************** 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 401 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 290 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8387 (tt0) cc_final: 0.8130 (tt0) REVERT: A 195 ASN cc_start: 0.8410 (t0) cc_final: 0.8065 (t0) REVERT: A 441 ARG cc_start: 0.7688 (ttp80) cc_final: 0.6920 (tpp80) REVERT: A 548 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.6553 (t80) REVERT: A 552 TRP cc_start: 0.6726 (OUTLIER) cc_final: 0.5221 (m100) REVERT: A 555 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6950 (tm-30) REVERT: B 445 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8118 (tm-30) REVERT: B 515 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8175 (mttm) REVERT: C 21 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7856 (pt) REVERT: C 28 GLU cc_start: 0.8273 (tt0) cc_final: 0.7730 (tm-30) REVERT: C 199 ASN cc_start: 0.7860 (t0) cc_final: 0.7576 (t0) REVERT: C 267 TYR cc_start: 0.8314 (t80) cc_final: 0.8073 (t80) REVERT: D 62 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: D 72 MET cc_start: 0.7943 (mtt) cc_final: 0.7313 (ttm) REVERT: D 120 ASP cc_start: 0.8310 (t0) cc_final: 0.7748 (t0) REVERT: D 439 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8317 (ptmt) REVERT: D 553 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7925 (mtt90) REVERT: E 219 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7534 (mt-10) REVERT: E 318 ASP cc_start: 0.4849 (p0) cc_final: 0.4622 (p0) REVERT: E 375 ILE cc_start: 0.8702 (mt) cc_final: 0.8416 (mm) REVERT: F 234 GLN cc_start: 0.6072 (OUTLIER) cc_final: 0.5394 (pm20) outliers start: 111 outliers final: 92 residues processed: 381 average time/residue: 0.1604 time to fit residues: 99.2987 Evaluate side-chains 377 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 277 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 114 ASP Chi-restraints excluded: chain A residue 127 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 474 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 524 ASP 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 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 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 543 SER Chi-restraints excluded: chain B residue 549 LEU 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 50 VAL 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 248 ILE 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 496 VAL Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 537 CYS 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 552 TRP Chi-restraints excluded: chain D residue 553 ARG Chi-restraints excluded: chain E residue 12 VAL 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 434 LYS Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 509 ASN Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 539 ILE 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 242 ILE 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 188 optimal weight: 4.9990 chunk 161 optimal weight: 0.4980 chunk 233 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 321 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 266 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS E 279 ASN F 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.181374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137296 restraints weight = 30519.500| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.80 r_work: 0.3250 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 27144 Z= 0.120 Angle : 0.539 10.785 36673 Z= 0.276 Chirality : 0.044 0.220 4115 Planarity : 0.004 0.047 4749 Dihedral : 4.312 79.186 3555 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.14 % Favored : 96.71 % Rotamer: Outliers : 3.34 % Allowed : 24.71 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.15), residues: 3313 helix: 0.80 (0.16), residues: 1095 sheet: -1.56 (0.22), residues: 503 loop : -0.34 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 441 TYR 0.018 0.001 TYR A 276 PHE 0.029 0.001 PHE A 561 TRP 0.010 0.001 TRP B 556 HIS 0.002 0.000 HIS E 291 Details of bonding type rmsd covalent geometry : bond 0.00289 (27144) covalent geometry : angle 0.53862 (36673) hydrogen bonds : bond 0.02803 ( 868) hydrogen bonds : angle 5.02819 ( 2391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5946.55 seconds wall clock time: 103 minutes 13.87 seconds (6193.87 seconds total)