Starting phenix.real_space_refine on Tue Nov 19 10:41:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmr_7965/11_2024/6dmr_7965.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmr_7965/11_2024/6dmr_7965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmr_7965/11_2024/6dmr_7965.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmr_7965/11_2024/6dmr_7965.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmr_7965/11_2024/6dmr_7965.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmr_7965/11_2024/6dmr_7965.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 140 5.16 5 C 12548 2.51 5 N 3284 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19412 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Restraints were copied for chains: C, B, D Time building chain proxies: 10.65, per 1000 atoms: 0.55 Number of scatterers: 19412 At special positions: 0 Unit cell: (133.1, 133.1, 127.6, 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 140 16.00 O 3440 8.00 N 3284 7.00 C 12548 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: 4.27 Conformation dependent library (CDL) restraints added in 2.3 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 8 sheets defined 69.3% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 3.537A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU A 42 " --> pdb=" O MET A 38 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 81 through 90 removed outlier: 3.717A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.514A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.617A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.841A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.627A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 removed outlier: 3.528A pdb=" N ARG A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 4.054A pdb=" N ASN A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.510A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 223 removed outlier: 3.784A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.934A pdb=" N LEU A 234 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 235' Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.539A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.552A pdb=" N ALA A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 307 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 349 removed outlier: 3.716A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG A 326 " --> pdb=" O LYS A 322 " (cutoff:3.500A) Proline residue: A 327 - end of helix removed outlier: 3.565A pdb=" N VAL A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER A 334 " --> pdb=" O CYS A 330 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 335 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 408 removed outlier: 3.510A pdb=" N ARG A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Proline residue: A 405 - end of helix removed outlier: 3.742A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 422 through 445 removed outlier: 3.661A pdb=" N HIS A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.560A pdb=" N LEU A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.760A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 511 removed outlier: 4.111A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N MET A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 567 removed outlier: 4.318A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA A 560 " --> pdb=" O CYS A 556 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA A 561 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 585 removed outlier: 3.537A pdb=" N ASP A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 608 removed outlier: 3.517A pdb=" N GLU A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 597 " --> pdb=" O TRP A 593 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 600 " --> pdb=" O GLN A 596 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 621 through 624 removed outlier: 3.609A pdb=" N GLY A 624 " --> pdb=" O TYR A 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 621 through 624' Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.538A pdb=" N ASN B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU B 42 " --> pdb=" O MET B 38 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'B' and resid 81 through 90 removed outlier: 3.717A pdb=" N VAL B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.514A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.616A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.841A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.626A pdb=" N VAL B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 185 removed outlier: 3.528A pdb=" N ARG B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 removed outlier: 4.054A pdb=" N ASN B 197 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.510A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 removed outlier: 3.785A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.933A pdb=" N LEU B 234 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 231 through 235' Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.539A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.553A pdb=" N ALA B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 307 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 349 removed outlier: 3.715A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 323 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG B 326 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Proline residue: B 327 - end of helix removed outlier: 3.564A pdb=" N VAL B 331 " --> pdb=" O PRO B 327 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA B 333 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER B 334 " --> pdb=" O CYS B 330 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 335 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 408 removed outlier: 3.511A pdb=" N ARG B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU B 403 " --> pdb=" O ILE B 399 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Proline residue: B 405 - end of helix removed outlier: 3.742A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 417 Processing helix chain 'B' and resid 422 through 445 removed outlier: 3.660A pdb=" N HIS B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.560A pdb=" N LEU B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 457 " --> pdb=" O PRO B 453 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.759A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 511 removed outlier: 4.112A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N MET B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE B 504 " --> pdb=" O VAL B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 567 removed outlier: 4.317A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 560 " --> pdb=" O CYS B 556 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA B 561 " --> pdb=" O ILE B 557 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 562 " --> pdb=" O THR B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 585 removed outlier: 3.537A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 608 removed outlier: 3.517A pdb=" N GLU B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 597 " --> pdb=" O TRP B 593 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 600 " --> pdb=" O GLN B 596 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 621 through 624 removed outlier: 3.609A pdb=" N GLY B 624 " --> pdb=" O TYR B 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 621 through 624' Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.537A pdb=" N ASN C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 Processing helix chain 'C' and resid 81 through 90 removed outlier: 3.717A pdb=" N VAL C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.514A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.616A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 128 removed outlier: 3.842A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.626A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 removed outlier: 3.528A pdb=" N ARG C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 removed outlier: 4.054A pdb=" N ASN C 197 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.510A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 223 removed outlier: 3.784A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.934A pdb=" N LEU C 234 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 235' Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.538A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.552A pdb=" N ALA C 304 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 349 removed outlier: 3.716A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 323 " --> pdb=" O PHE C 319 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG C 326 " --> pdb=" O LYS C 322 " (cutoff:3.500A) Proline residue: C 327 - end of helix removed outlier: 3.565A pdb=" N VAL C 331 " --> pdb=" O PRO C 327 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA C 333 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER C 334 " --> pdb=" O CYS C 330 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 408 removed outlier: 3.511A pdb=" N ARG C 385 " --> pdb=" O GLN C 381 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL C 387 " --> pdb=" O ASN C 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE C 398 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C 399 " --> pdb=" O GLY C 395 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 400 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU C 403 " --> pdb=" O ILE C 399 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Proline residue: C 405 - end of helix removed outlier: 3.742A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 417 Processing helix chain 'C' and resid 422 through 445 removed outlier: 3.661A pdb=" N HIS C 426 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.561A pdb=" N LEU C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 457 " --> pdb=" O PRO C 453 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.759A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 511 removed outlier: 4.112A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N MET C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE C 504 " --> pdb=" O VAL C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 567 removed outlier: 4.317A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA C 560 " --> pdb=" O CYS C 556 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA C 561 " --> pdb=" O ILE C 557 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE C 562 " --> pdb=" O THR C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 585 removed outlier: 3.537A pdb=" N ASP C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 608 removed outlier: 3.517A pdb=" N GLU C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 597 " --> pdb=" O TRP C 593 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 600 " --> pdb=" O GLN C 596 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 621 through 624 removed outlier: 3.609A pdb=" N GLY C 624 " --> pdb=" O TYR C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 621 through 624' Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.538A pdb=" N ASN D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 81 through 90 removed outlier: 3.717A pdb=" N VAL D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.514A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.616A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU D 108 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.842A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.626A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 185 removed outlier: 3.528A pdb=" N ARG D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 removed outlier: 4.054A pdb=" N ASN D 197 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.510A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 223 removed outlier: 3.784A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.934A pdb=" N LEU D 234 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 231 through 235' Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.539A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 301 through 309 removed outlier: 3.552A pdb=" N ALA D 304 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE D 307 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 349 removed outlier: 3.715A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS D 323 " --> pdb=" O PHE D 319 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG D 326 " --> pdb=" O LYS D 322 " (cutoff:3.500A) Proline residue: D 327 - end of helix removed outlier: 3.564A pdb=" N VAL D 331 " --> pdb=" O PRO D 327 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA D 333 " --> pdb=" O PHE D 329 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER D 334 " --> pdb=" O CYS D 330 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 335 " --> pdb=" O VAL D 331 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR D 349 " --> pdb=" O THR D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 408 removed outlier: 3.511A pdb=" N ARG D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL D 397 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE D 398 " --> pdb=" O THR D 394 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE D 399 " --> pdb=" O GLY D 395 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) Proline residue: D 405 - end of helix removed outlier: 3.742A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 422 through 445 removed outlier: 3.661A pdb=" N HIS D 426 " --> pdb=" O GLY D 422 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR D 431 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET D 440 " --> pdb=" O VAL D 436 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR D 445 " --> pdb=" O VAL D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.560A pdb=" N LEU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA D 457 " --> pdb=" O PRO D 453 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS D 463 " --> pdb=" O VAL D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.759A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE D 472 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 511 removed outlier: 4.112A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N MET D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE D 504 " --> pdb=" O VAL D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 567 removed outlier: 4.317A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA D 560 " --> pdb=" O CYS D 556 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA D 561 " --> pdb=" O ILE D 557 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE D 562 " --> pdb=" O THR D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 585 removed outlier: 3.537A pdb=" N ASP D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 608 removed outlier: 3.516A pdb=" N GLU D 591 " --> pdb=" O GLN D 587 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP D 593 " --> pdb=" O ARG D 589 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 597 " --> pdb=" O TRP D 593 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 600 " --> pdb=" O GLN D 596 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing helix chain 'D' and resid 621 through 624 removed outlier: 3.610A pdb=" N GLY D 624 " --> pdb=" O TYR D 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 621 through 624' Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.818A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.819A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.819A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.819A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 865 hydrogen bonds defined for protein. 2463 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: 5.47 Time building geometry restraints manager: 5.15 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: 6181 1.34 - 1.46: 3401 1.46 - 1.57: 10050 1.57 - 1.69: 0 1.69 - 1.81: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" C GLU A 164 " pdb=" N HIS A 165 " ideal model delta sigma weight residual 1.329 1.280 0.049 3.03e-02 1.09e+03 2.57e+00 bond pdb=" C GLU B 164 " pdb=" N HIS B 165 " ideal model delta sigma weight residual 1.329 1.280 0.048 3.03e-02 1.09e+03 2.56e+00 bond pdb=" C GLU C 164 " pdb=" N HIS C 165 " ideal model delta sigma weight residual 1.329 1.280 0.048 3.03e-02 1.09e+03 2.53e+00 bond pdb=" C GLU D 164 " pdb=" N HIS D 165 " ideal model delta sigma weight residual 1.329 1.281 0.048 3.03e-02 1.09e+03 2.51e+00 bond pdb=" C TYR C 526 " pdb=" N PRO C 527 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.23e-02 6.61e+03 1.96e+00 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 26202 2.40 - 4.81: 665 4.81 - 7.21: 72 7.21 - 9.62: 21 9.62 - 12.02: 4 Bond angle restraints: 26964 Sorted by residual: angle pdb=" C VAL C 451 " pdb=" N VAL C 452 " pdb=" CA VAL C 452 " ideal model delta sigma weight residual 120.33 123.91 -3.58 8.00e-01 1.56e+00 2.00e+01 angle pdb=" C VAL A 451 " pdb=" N VAL A 452 " pdb=" CA VAL A 452 " ideal model delta sigma weight residual 120.33 123.89 -3.56 8.00e-01 1.56e+00 1.98e+01 angle pdb=" C VAL B 451 " pdb=" N VAL B 452 " pdb=" CA VAL B 452 " ideal model delta sigma weight residual 120.33 123.88 -3.55 8.00e-01 1.56e+00 1.97e+01 angle pdb=" C VAL D 451 " pdb=" N VAL D 452 " pdb=" CA VAL D 452 " ideal model delta sigma weight residual 120.33 123.83 -3.50 8.00e-01 1.56e+00 1.91e+01 angle pdb=" CA VAL D 452 " pdb=" C VAL D 452 " pdb=" N PRO D 453 " ideal model delta sigma weight residual 120.83 123.02 -2.19 6.10e-01 2.69e+00 1.29e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.11: 10976 14.11 - 28.21: 588 28.21 - 42.32: 232 42.32 - 56.43: 4 56.43 - 70.53: 12 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA GLY A 79 " pdb=" C GLY A 79 " pdb=" N GLU A 80 " pdb=" CA GLU A 80 " ideal model delta harmonic sigma weight residual -180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA GLY D 79 " pdb=" C GLY D 79 " pdb=" N GLU D 80 " pdb=" CA GLU D 80 " ideal model delta harmonic sigma weight residual -180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA GLY B 79 " pdb=" C GLY B 79 " pdb=" N GLU B 80 " pdb=" CA GLU B 80 " ideal model delta harmonic sigma weight residual -180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2031 0.046 - 0.092: 791 0.092 - 0.138: 190 0.138 - 0.184: 40 0.184 - 0.230: 20 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CA THR B 311 " pdb=" N THR B 311 " pdb=" C THR B 311 " pdb=" CB THR B 311 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA THR C 311 " pdb=" N THR C 311 " pdb=" C THR C 311 " pdb=" CB THR C 311 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 629 " -0.020 2.00e-02 2.50e+03 1.66e-02 6.88e+00 pdb=" CG TRP B 629 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B 629 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 629 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP B 629 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 629 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 629 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 629 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 629 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 629 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 629 " -0.020 2.00e-02 2.50e+03 1.65e-02 6.82e+00 pdb=" CG TRP D 629 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP D 629 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 629 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP D 629 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 629 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 629 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 629 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 629 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP D 629 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 629 " -0.020 2.00e-02 2.50e+03 1.65e-02 6.81e+00 pdb=" CG TRP C 629 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 629 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 629 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP C 629 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 629 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 629 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 629 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 629 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP C 629 " -0.009 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5362 2.80 - 3.33: 18205 3.33 - 3.85: 30715 3.85 - 4.38: 33969 4.38 - 4.90: 56086 Nonbonded interactions: 144337 Sorted by model distance: nonbonded pdb=" O GLU A 93 " pdb=" OG1 THR A 96 " model vdw 2.280 3.040 nonbonded pdb=" O GLU C 93 " pdb=" OG1 THR C 96 " model vdw 2.281 3.040 nonbonded pdb=" O GLU D 93 " pdb=" OG1 THR D 96 " model vdw 2.281 3.040 nonbonded pdb=" O GLU B 93 " pdb=" OG1 THR B 96 " model vdw 2.282 3.040 nonbonded pdb=" O HIS A 165 " pdb=" OG SER A 168 " model vdw 2.327 3.040 ... (remaining 144332 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.420 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: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 40.300 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 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 0.054 19860 Z= 0.315 Angle : 0.908 12.024 26964 Z= 0.489 Chirality : 0.053 0.230 3072 Planarity : 0.006 0.050 3416 Dihedral : 10.340 70.532 7236 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.13), residues: 2408 helix: -2.76 (0.10), residues: 1384 sheet: -2.98 (0.44), residues: 56 loop : -2.62 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 629 HIS 0.009 0.002 HIS C 185 PHE 0.029 0.002 PHE D 508 TYR 0.016 0.002 TYR B 162 ARG 0.007 0.001 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7198 (tt0) REVERT: A 315 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8261 (mp0) REVERT: A 447 MET cc_start: 0.6483 (tpt) cc_final: 0.5807 (mtt) REVERT: A 474 MET cc_start: 0.8266 (ptt) cc_final: 0.7944 (ptt) REVERT: A 483 GLN cc_start: 0.7983 (tt0) cc_final: 0.7764 (tm-30) REVERT: B 257 GLN cc_start: 0.8597 (pt0) cc_final: 0.8359 (pp30) REVERT: B 303 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7251 (tt0) REVERT: B 447 MET cc_start: 0.6668 (tpt) cc_final: 0.5975 (mtt) REVERT: B 474 MET cc_start: 0.8286 (ptt) cc_final: 0.7938 (ptt) REVERT: B 483 GLN cc_start: 0.7941 (tt0) cc_final: 0.7709 (tm-30) REVERT: C 257 GLN cc_start: 0.8623 (pt0) cc_final: 0.8406 (pp30) REVERT: C 303 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7210 (tt0) REVERT: C 315 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8267 (mp0) REVERT: C 447 MET cc_start: 0.6549 (tpt) cc_final: 0.5879 (mtt) REVERT: C 474 MET cc_start: 0.8256 (ptt) cc_final: 0.7918 (ptt) REVERT: C 483 GLN cc_start: 0.7947 (tt0) cc_final: 0.7736 (tm-30) REVERT: D 257 GLN cc_start: 0.8577 (pt0) cc_final: 0.8368 (pp30) REVERT: D 303 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7216 (tt0) REVERT: D 315 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8228 (mp0) REVERT: D 447 MET cc_start: 0.6613 (tpt) cc_final: 0.5921 (mtt) REVERT: D 474 MET cc_start: 0.8263 (ptt) cc_final: 0.7942 (ptt) REVERT: D 483 GLN cc_start: 0.7961 (tt0) cc_final: 0.7733 (tm-30) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.3542 time to fit residues: 234.3995 Evaluate side-chains 213 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 217 optimal weight: 7.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 84 HIS A 122 HIS A 238 HIS A 426 HIS A 509 HIS A 513 GLN A 582 HIS B 37 ASN B 84 HIS B 122 HIS B 238 HIS B 426 HIS B 509 HIS B 513 GLN B 582 HIS C 37 ASN C 84 HIS C 165 HIS C 238 HIS C 426 HIS C 509 HIS C 513 GLN C 582 HIS D 37 ASN D 84 HIS D 122 HIS D 238 HIS D 426 HIS D 509 HIS D 513 GLN D 582 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19860 Z= 0.251 Angle : 0.641 9.688 26964 Z= 0.330 Chirality : 0.041 0.155 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.653 15.874 2644 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.96 % Allowed : 12.69 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.16), residues: 2408 helix: -1.00 (0.13), residues: 1424 sheet: -1.44 (0.57), residues: 64 loop : -2.26 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 629 HIS 0.006 0.001 HIS C 426 PHE 0.017 0.002 PHE A 553 TYR 0.009 0.001 TYR B 162 ARG 0.007 0.001 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7115 (tt0) REVERT: A 315 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8410 (mp0) REVERT: A 442 MET cc_start: 0.8121 (ttp) cc_final: 0.7886 (ttm) REVERT: A 474 MET cc_start: 0.8284 (ptt) cc_final: 0.8047 (ptt) REVERT: A 483 GLN cc_start: 0.7973 (tt0) cc_final: 0.7736 (tm-30) REVERT: A 608 MET cc_start: 0.7314 (mtm) cc_final: 0.7065 (mtm) REVERT: B 257 GLN cc_start: 0.8611 (pt0) cc_final: 0.8352 (pp30) REVERT: B 303 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7108 (tt0) REVERT: B 403 GLU cc_start: 0.8119 (pm20) cc_final: 0.7878 (pm20) REVERT: B 442 MET cc_start: 0.7950 (ttp) cc_final: 0.7462 (ttm) REVERT: B 474 MET cc_start: 0.8236 (ptt) cc_final: 0.8006 (ptt) REVERT: B 483 GLN cc_start: 0.7969 (tt0) cc_final: 0.7749 (tm-30) REVERT: C 303 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7132 (tt0) REVERT: C 315 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8394 (mp0) REVERT: C 442 MET cc_start: 0.8124 (ttp) cc_final: 0.7777 (ttm) REVERT: C 447 MET cc_start: 0.6428 (tpt) cc_final: 0.6164 (mtt) REVERT: C 474 MET cc_start: 0.8176 (ptt) cc_final: 0.7952 (ptt) REVERT: C 483 GLN cc_start: 0.7953 (tt0) cc_final: 0.7737 (tm-30) REVERT: D 303 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7138 (tt0) REVERT: D 315 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8391 (mp0) REVERT: D 442 MET cc_start: 0.8095 (ttt) cc_final: 0.7653 (ttm) REVERT: D 474 MET cc_start: 0.8230 (ptt) cc_final: 0.8023 (ptt) REVERT: D 483 GLN cc_start: 0.7949 (tt0) cc_final: 0.7707 (tm-30) outliers start: 62 outliers final: 30 residues processed: 260 average time/residue: 0.2756 time to fit residues: 117.6425 Evaluate side-chains 213 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 330 CYS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 434 SER Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 510 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 7.9990 chunk 67 optimal weight: 0.0470 chunk 181 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 0.4980 chunk 235 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 overall best weight: 1.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19860 Z= 0.165 Angle : 0.551 8.495 26964 Z= 0.279 Chirality : 0.039 0.165 3072 Planarity : 0.003 0.028 3416 Dihedral : 4.323 15.552 2644 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.48 % Allowed : 14.07 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.16), residues: 2408 helix: -0.26 (0.14), residues: 1424 sheet: -1.21 (0.55), residues: 64 loop : -2.09 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 629 HIS 0.004 0.001 HIS A 426 PHE 0.021 0.001 PHE C 531 TYR 0.008 0.001 TYR C 162 ARG 0.003 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 201 time to evaluate : 3.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.7543 (mtp-110) cc_final: 0.7325 (mtp-110) REVERT: A 303 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7181 (tt0) REVERT: A 315 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8387 (mp0) REVERT: A 474 MET cc_start: 0.8191 (ptt) cc_final: 0.7951 (ptt) REVERT: A 483 GLN cc_start: 0.7943 (tt0) cc_final: 0.7658 (tm-30) REVERT: B 42 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: B 302 ARG cc_start: 0.7581 (mtp-110) cc_final: 0.7360 (mtp-110) REVERT: B 303 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7189 (tt0) REVERT: B 474 MET cc_start: 0.8140 (ptt) cc_final: 0.7904 (ptt) REVERT: C 302 ARG cc_start: 0.7572 (mtp-110) cc_final: 0.7351 (mtp-110) REVERT: C 303 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7184 (tt0) REVERT: C 315 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8405 (mp0) REVERT: C 442 MET cc_start: 0.8315 (ttp) cc_final: 0.7965 (ttm) REVERT: C 447 MET cc_start: 0.6336 (tpt) cc_final: 0.6076 (mtt) REVERT: C 474 MET cc_start: 0.8070 (ptt) cc_final: 0.7834 (ptt) REVERT: C 483 GLN cc_start: 0.7951 (tt0) cc_final: 0.7662 (tm-30) REVERT: D 303 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7169 (tt0) REVERT: D 315 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8403 (mp0) REVERT: D 474 MET cc_start: 0.8199 (ptt) cc_final: 0.7959 (ptt) REVERT: D 483 GLN cc_start: 0.7963 (tt0) cc_final: 0.7663 (tm-30) outliers start: 73 outliers final: 45 residues processed: 253 average time/residue: 0.2813 time to fit residues: 115.3454 Evaluate side-chains 229 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 10.0000 chunk 164 optimal weight: 0.0020 chunk 113 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19860 Z= 0.175 Angle : 0.558 9.227 26964 Z= 0.278 Chirality : 0.039 0.257 3072 Planarity : 0.003 0.028 3416 Dihedral : 4.137 14.967 2644 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.01 % Allowed : 15.65 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.17), residues: 2408 helix: 0.11 (0.14), residues: 1428 sheet: -1.14 (0.54), residues: 64 loop : -1.97 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 629 HIS 0.008 0.001 HIS C 165 PHE 0.021 0.001 PHE B 531 TYR 0.006 0.001 TYR D 162 ARG 0.005 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 196 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7175 (tt0) REVERT: A 315 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8400 (mp0) REVERT: A 474 MET cc_start: 0.8311 (ptt) cc_final: 0.8055 (ptt) REVERT: A 483 GLN cc_start: 0.7922 (tt0) cc_final: 0.7722 (tm-30) REVERT: A 608 MET cc_start: 0.7585 (mtp) cc_final: 0.7259 (mtm) REVERT: B 42 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: B 303 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7181 (tt0) REVERT: B 474 MET cc_start: 0.8099 (ptt) cc_final: 0.7861 (ptt) REVERT: C 303 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7179 (tt0) REVERT: C 315 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8430 (mp0) REVERT: C 442 MET cc_start: 0.8484 (ttp) cc_final: 0.8126 (ttm) REVERT: C 474 MET cc_start: 0.8069 (ptt) cc_final: 0.7821 (ptt) REVERT: D 303 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7170 (tt0) REVERT: D 315 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8428 (mp0) REVERT: D 474 MET cc_start: 0.8075 (ptt) cc_final: 0.7842 (ptt) REVERT: D 483 GLN cc_start: 0.7946 (tt0) cc_final: 0.7722 (tm-30) outliers start: 63 outliers final: 48 residues processed: 241 average time/residue: 0.3063 time to fit residues: 118.2153 Evaluate side-chains 222 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 208 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS A 165 HIS B 122 HIS C 165 HIS D 122 HIS D 165 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.4123 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: