Starting phenix.real_space_refine on Wed Nov 19 01:11:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dmr_7965/11_2025/6dmr_7965.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dmr_7965/11_2025/6dmr_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 { model { file = "/net/cci-nas-00/data/ceres_data/6dmr_7965/11_2025/6dmr_7965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dmr_7965/11_2025/6dmr_7965.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dmr_7965/11_2025/6dmr_7965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dmr_7965/11_2025/6dmr_7965.map" } resolution = 3.9 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= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: B, C, D Time building chain proxies: 4.64, per 1000 atoms: 0.24 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: 1.72 Conformation dependent library (CDL) restraints added in 977.3 milliseconds 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: 0.59 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: 3.49 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: 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: 0.06 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.830 Find NCS groups from input model: 0.180 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.250 ------------------------------------------------------------------------------- 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= 0.234 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 : 3.65 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG A 610 TYR 0.016 0.002 TYR B 162 PHE 0.029 0.002 PHE D 508 TRP 0.039 0.003 TRP B 629 HIS 0.009 0.002 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00484 (19860) covalent geometry : angle 0.90766 (26964) hydrogen bonds : bond 0.19513 ( 865) hydrogen bonds : angle 6.92684 ( 2463) *********************** 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 : 0.709 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: 0.1512 time to fit residues: 100.8310 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 : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.0670 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 overall best weight: 1.8522 ------------------------------------------------------------------------------- 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 509 HIS A 513 GLN A 582 HIS B 37 ASN B 84 HIS B 122 HIS B 238 HIS B 509 HIS B 513 GLN B 582 HIS C 37 ASN C 84 HIS C 165 HIS C 238 HIS C 509 HIS C 513 GLN C 582 HIS D 37 ASN D 84 HIS D 122 HIS D 238 HIS D 509 HIS D 513 GLN D 582 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.086762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.071004 restraints weight = 51531.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.072980 restraints weight = 28654.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.074331 restraints weight = 19082.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.075253 restraints weight = 14375.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.075843 restraints weight = 11819.739| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19860 Z= 0.124 Angle : 0.601 10.365 26964 Z= 0.305 Chirality : 0.040 0.154 3072 Planarity : 0.004 0.040 3416 Dihedral : 4.630 15.403 2644 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.19 % Allowed : 12.74 % Favored : 85.07 % 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 are not related in a simple way. whole: -2.39 (0.15), residues: 2408 helix: -1.04 (0.13), residues: 1396 sheet: -1.41 (0.58), residues: 64 loop : -2.34 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 59 TYR 0.010 0.001 TYR D 222 PHE 0.015 0.001 PHE A 553 TRP 0.019 0.001 TRP C 629 HIS 0.004 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00271 (19860) covalent geometry : angle 0.60137 (26964) hydrogen bonds : bond 0.04298 ( 865) hydrogen bonds : angle 4.47343 ( 2463) *********************** 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 289 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 243 time to evaluate : 0.776 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: A 577 MET cc_start: 0.7719 (ttp) cc_final: 0.7479 (ttm) REVERT: C 165 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.8206 (m170) outliers start: 46 outliers final: 23 residues processed: 267 average time/residue: 0.1173 time to fit residues: 51.0975 Evaluate side-chains 211 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 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 490 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 386 LEU 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 386 LEU 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 228 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 chunk 233 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 217 optimal weight: 9.9990 chunk 110 optimal weight: 0.0270 chunk 119 optimal weight: 10.0000 chunk 145 optimal weight: 0.0010 overall best weight: 0.9248 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.087422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.071527 restraints weight = 51272.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.073605 restraints weight = 27840.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.075022 restraints weight = 18231.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.075980 restraints weight = 13538.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.076670 restraints weight = 11017.083| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19860 Z= 0.097 Angle : 0.545 8.945 26964 Z= 0.272 Chirality : 0.038 0.145 3072 Planarity : 0.003 0.029 3416 Dihedral : 4.268 15.894 2644 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.05 % Allowed : 15.22 % Favored : 81.73 % 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 are not related in a simple way. whole: -1.54 (0.16), residues: 2408 helix: -0.30 (0.14), residues: 1424 sheet: -1.09 (0.58), residues: 64 loop : -2.12 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 628 TYR 0.011 0.001 TYR A 89 PHE 0.020 0.001 PHE B 531 TRP 0.012 0.001 TRP C 629 HIS 0.016 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00203 (19860) covalent geometry : angle 0.54462 (26964) hydrogen bonds : bond 0.03573 ( 865) hydrogen bonds : angle 3.99515 ( 2463) *********************** 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 268 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 204 time to evaluate : 0.793 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: B 42 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8413 (tt0) outliers start: 64 outliers final: 28 residues processed: 249 average time/residue: 0.1103 time to fit residues: 45.8629 Evaluate side-chains 205 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU 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 496 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 290 LEU 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 496 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 330 CYS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 330 CYS 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 496 LEU Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 554 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 68 optimal weight: 0.7980 chunk 91 optimal weight: 0.0980 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 226 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 77 optimal weight: 0.0870 chunk 158 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.087680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.071881 restraints weight = 51220.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.073965 restraints weight = 27804.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.075362 restraints weight = 18143.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.076281 restraints weight = 13471.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.076905 restraints weight = 11046.781| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 19860 Z= 0.091 Angle : 0.526 9.865 26964 Z= 0.257 Chirality : 0.038 0.220 3072 Planarity : 0.003 0.027 3416 Dihedral : 3.989 15.042 2644 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.39 % Allowed : 17.13 % Favored : 80.49 % 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 are not related in a simple way. whole: -1.08 (0.17), residues: 2408 helix: 0.17 (0.14), residues: 1432 sheet: -1.01 (0.55), residues: 64 loop : -2.10 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 628 TYR 0.008 0.001 TYR D 89 PHE 0.016 0.001 PHE B 553 TRP 0.009 0.001 TRP B 629 HIS 0.003 0.000 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00195 (19860) covalent geometry : angle 0.52555 (26964) hydrogen bonds : bond 0.03042 ( 865) hydrogen bonds : angle 3.76568 ( 2463) *********************** 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 246 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 0.776 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: B 38 MET cc_start: 0.9299 (tpp) cc_final: 0.9080 (tpp) REVERT: B 42 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: C 557 ILE cc_start: 0.9449 (tt) cc_final: 0.9245 (tt) outliers start: 50 outliers final: 34 residues processed: 228 average time/residue: 0.1265 time to fit residues: 46.4521 Evaluate side-chains 210 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 386 LEU 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 37 ASN Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 330 CYS 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 496 LEU Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 330 CYS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 554 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 29 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS B 426 HIS C 426 HIS D 426 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.085069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.069226 restraints weight = 51674.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.071200 restraints weight = 28645.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.072517 restraints weight = 19001.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.073414 restraints weight = 14303.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.073994 restraints weight = 11777.209| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19860 Z= 0.112 Angle : 0.553 8.382 26964 Z= 0.272 Chirality : 0.039 0.330 3072 Planarity : 0.003 0.027 3416 Dihedral : 3.860 13.439 2644 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.20 % Allowed : 16.22 % Favored : 80.58 % 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 are not related in a simple way. whole: -0.76 (0.17), residues: 2408 helix: 0.41 (0.14), residues: 1428 sheet: -0.98 (0.56), residues: 64 loop : -1.92 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 628 TYR 0.007 0.001 TYR D 89 PHE 0.015 0.001 PHE A 531 TRP 0.009 0.001 TRP C 629 HIS 0.004 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00257 (19860) covalent geometry : angle 0.55298 (26964) hydrogen bonds : bond 0.03405 ( 865) hydrogen bonds : angle 3.74523 ( 2463) *********************** REFINEMENT MACRO_CYCLE 5 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 242 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 175 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8756 (mmm) cc_final: 0.8555 (mmm) REVERT: B 38 MET cc_start: 0.9315 (tpp) cc_final: 0.9047 (tpp) REVERT: B 42 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: D 38 MET cc_start: 0.9262 (tpp) cc_final: 0.9048 (tpp) outliers start: 67 outliers final: 45 residues processed: 225 average time/residue: 0.1118 time to fit residues: 41.6835 Evaluate side-chains 216 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 235 VAL 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 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 235 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 341 ILE 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 496 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 296 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 391 VAL 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 235 VAL 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 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 Chi-restraints excluded: chain D residue 554 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 238 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 chunk 72 optimal weight: 0.5980 chunk 207 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 128 GLN A 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.083201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.067111 restraints weight = 52421.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.069079 restraints weight = 28795.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.070408 restraints weight = 19100.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.071279 restraints weight = 14354.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.071912 restraints weight = 11862.222| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19860 Z= 0.125 Angle : 0.568 8.627 26964 Z= 0.278 Chirality : 0.039 0.340 3072 Planarity : 0.003 0.040 3416 Dihedral : 3.889 16.565 2644 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.10 % Allowed : 17.22 % Favored : 79.68 % 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 are not related in a simple way. whole: -0.59 (0.17), residues: 2408 helix: 0.55 (0.14), residues: 1432 sheet: -1.02 (0.55), residues: 64 loop : -1.87 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 414 TYR 0.007 0.001 TYR B 222 PHE 0.025 0.001 PHE A 553 TRP 0.009 0.001 TRP B 629 HIS 0.004 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00292 (19860) covalent geometry : angle 0.56828 (26964) hydrogen bonds : bond 0.03492 ( 865) hydrogen bonds : angle 3.80359 ( 2463) *********************** REFINEMENT MACRO_CYCLE 6 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 252 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 187 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8663 (mmm) cc_final: 0.8451 (mmm) REVERT: A 577 MET cc_start: 0.8018 (mtp) cc_final: 0.7735 (mtm) REVERT: B 38 MET cc_start: 0.9349 (tpp) cc_final: 0.9045 (tpp) REVERT: B 42 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: B 445 THR cc_start: 0.8675 (m) cc_final: 0.8408 (p) REVERT: D 38 MET cc_start: 0.9296 (tpp) cc_final: 0.9070 (tpp) outliers start: 65 outliers final: 40 residues processed: 239 average time/residue: 0.1216 time to fit residues: 46.8631 Evaluate side-chains 206 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASN 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 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 235 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 341 ILE 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 496 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 296 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 391 VAL 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 C residue 538 LEU Chi-restraints excluded: chain D residue 235 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 0.0980 chunk 149 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 89 optimal weight: 0.3980 chunk 190 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 201 optimal weight: 0.0050 overall best weight: 1.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.084242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.068262 restraints weight = 51644.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.070279 restraints weight = 28223.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.071641 restraints weight = 18527.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.072577 restraints weight = 13820.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.073159 restraints weight = 11284.257| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19860 Z= 0.104 Angle : 0.571 10.038 26964 Z= 0.277 Chirality : 0.038 0.291 3072 Planarity : 0.003 0.043 3416 Dihedral : 3.898 16.519 2644 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.67 % Allowed : 18.42 % Favored : 78.91 % 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 are not related in a simple way. whole: -0.28 (0.17), residues: 2408 helix: 0.77 (0.14), residues: 1396 sheet: -0.85 (0.54), residues: 64 loop : -1.59 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 302 TYR 0.006 0.001 TYR D 89 PHE 0.014 0.001 PHE D 553 TRP 0.008 0.001 TRP B 629 HIS 0.012 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00237 (19860) covalent geometry : angle 0.57076 (26964) hydrogen bonds : bond 0.03228 ( 865) hydrogen bonds : angle 3.76644 ( 2463) *********************** REFINEMENT MACRO_CYCLE 7 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 237 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 181 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.9044 (ttm) cc_final: 0.8701 (ttt) REVERT: A 491 MET cc_start: 0.6986 (mmp) cc_final: 0.6706 (mmm) REVERT: A 577 MET cc_start: 0.8010 (mtp) cc_final: 0.7754 (mtm) REVERT: B 38 MET cc_start: 0.9338 (tpp) cc_final: 0.9004 (tpp) REVERT: B 42 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: B 445 THR cc_start: 0.8724 (m) cc_final: 0.8511 (p) REVERT: B 491 MET cc_start: 0.6954 (mmp) cc_final: 0.6704 (mmm) REVERT: D 38 MET cc_start: 0.9302 (tpp) cc_final: 0.9026 (tpp) REVERT: D 442 MET cc_start: 0.9073 (ttm) cc_final: 0.8772 (ttt) outliers start: 56 outliers final: 38 residues processed: 220 average time/residue: 0.1098 time to fit residues: 40.8092 Evaluate side-chains 204 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 296 VAL Chi-restraints excluded: chain B residue 341 ILE 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 B residue 565 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 391 VAL 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 C residue 538 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 220 optimal weight: 8.9990 chunk 76 optimal weight: 0.1980 chunk 3 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 208 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 122 HIS A 165 HIS A 267 GLN B 37 ASN B 122 HIS B 267 GLN D 37 ASN D 122 HIS D 165 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.078319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.062116 restraints weight = 53648.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.063978 restraints weight = 30071.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.065243 restraints weight = 20159.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.066105 restraints weight = 15290.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.066579 restraints weight = 12645.677| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19860 Z= 0.229 Angle : 0.698 11.222 26964 Z= 0.347 Chirality : 0.043 0.227 3072 Planarity : 0.004 0.045 3416 Dihedral : 4.228 18.478 2644 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.96 % Allowed : 18.03 % Favored : 79.01 % 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 are not related in a simple way. whole: -0.76 (0.17), residues: 2408 helix: 0.44 (0.14), residues: 1440 sheet: -0.74 (0.55), residues: 64 loop : -2.02 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 302 TYR 0.011 0.001 TYR D 526 PHE 0.021 0.002 PHE A 553 TRP 0.012 0.002 TRP C 629 HIS 0.007 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00531 (19860) covalent geometry : angle 0.69775 (26964) hydrogen bonds : bond 0.04748 ( 865) hydrogen bonds : angle 4.23207 ( 2463) *********************** REFINEMENT MACRO_CYCLE 8 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 227 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 165 time to evaluate : 0.736 Fit side-chains REVERT: A 481 MET cc_start: 0.8712 (ppp) cc_final: 0.8480 (tmm) REVERT: A 577 MET cc_start: 0.7994 (mtp) cc_final: 0.7696 (mtm) REVERT: B 42 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8365 (tt0) REVERT: B 445 THR cc_start: 0.8820 (m) cc_final: 0.8585 (p) REVERT: B 481 MET cc_start: 0.8682 (ppp) cc_final: 0.8450 (tmm) REVERT: C 481 MET cc_start: 0.8717 (ppp) cc_final: 0.8481 (tmm) REVERT: D 38 MET cc_start: 0.9307 (tpp) cc_final: 0.9008 (tpp) REVERT: D 442 MET cc_start: 0.9252 (ttm) cc_final: 0.8777 (ttp) REVERT: D 481 MET cc_start: 0.8708 (ppp) cc_final: 0.8472 (tmm) outliers start: 62 outliers final: 40 residues processed: 216 average time/residue: 0.1073 time to fit residues: 39.3752 Evaluate side-chains 198 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 281 THR 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 500 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 341 ILE 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 296 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 391 VAL 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 C residue 538 LEU Chi-restraints excluded: chain D residue 220 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 194 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 187 optimal weight: 0.0000 chunk 195 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 209 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 overall best weight: 1.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN B 37 ASN C 206 GLN D 37 ASN D 446 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.081462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.065484 restraints weight = 52098.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.067434 restraints weight = 28952.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.068737 restraints weight = 19211.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.069602 restraints weight = 14436.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.070206 restraints weight = 11927.121| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19860 Z= 0.110 Angle : 0.599 12.008 26964 Z= 0.291 Chirality : 0.039 0.215 3072 Planarity : 0.003 0.040 3416 Dihedral : 4.111 21.799 2644 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.43 % Allowed : 18.75 % Favored : 78.82 % 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 are not related in a simple way. whole: -0.70 (0.17), residues: 2408 helix: 0.61 (0.14), residues: 1388 sheet: -0.62 (0.54), residues: 64 loop : -2.11 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 414 TYR 0.006 0.001 TYR C 216 PHE 0.019 0.001 PHE C 574 TRP 0.012 0.001 TRP D 593 HIS 0.007 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00252 (19860) covalent geometry : angle 0.59859 (26964) hydrogen bonds : bond 0.03513 ( 865) hydrogen bonds : angle 3.91209 ( 2463) *********************** REFINEMENT MACRO_CYCLE 9 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 220 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 169 time to evaluate : 0.686 Fit side-chains REVERT: A 37 ASN cc_start: 0.9420 (OUTLIER) cc_final: 0.9156 (t0) REVERT: A 442 MET cc_start: 0.9090 (ttm) cc_final: 0.8664 (ttt) REVERT: A 447 MET cc_start: 0.9271 (pmm) cc_final: 0.9032 (pmm) REVERT: A 577 MET cc_start: 0.7967 (mtp) cc_final: 0.7706 (mtm) REVERT: B 37 ASN cc_start: 0.9434 (OUTLIER) cc_final: 0.9116 (t0) REVERT: B 42 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: B 445 THR cc_start: 0.8724 (m) cc_final: 0.8512 (p) REVERT: C 536 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8864 (tt) REVERT: D 442 MET cc_start: 0.9120 (ttm) cc_final: 0.8759 (ttt) outliers start: 51 outliers final: 34 residues processed: 206 average time/residue: 0.1055 time to fit residues: 37.3613 Evaluate side-chains 199 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 281 THR 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 490 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain B residue 37 ASN Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 VAL 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 392 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 220 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 500 VAL Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 165 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.079422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.063362 restraints weight = 52835.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.065274 restraints weight = 29289.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.066559 restraints weight = 19454.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.067397 restraints weight = 14610.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.068022 restraints weight = 12043.944| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19860 Z= 0.184 Angle : 0.675 13.065 26964 Z= 0.333 Chirality : 0.042 0.211 3072 Planarity : 0.004 0.042 3416 Dihedral : 4.162 24.317 2644 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.91 % Allowed : 19.18 % Favored : 78.91 % 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 are not related in a simple way. whole: -0.74 (0.17), residues: 2408 helix: 0.49 (0.14), residues: 1412 sheet: -0.65 (0.54), residues: 64 loop : -2.03 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 35 TYR 0.009 0.001 TYR A 526 PHE 0.021 0.002 PHE C 553 TRP 0.011 0.001 TRP C 629 HIS 0.006 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00436 (19860) covalent geometry : angle 0.67532 (26964) hydrogen bonds : bond 0.04223 ( 865) hydrogen bonds : angle 4.05832 ( 2463) ********************** REFINEMENT MACRO_CYCLE 10 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 201 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.782 Fit side-chains REVERT: A 442 MET cc_start: 0.9187 (ttm) cc_final: 0.8713 (ttt) REVERT: A 577 MET cc_start: 0.8021 (mtp) cc_final: 0.7780 (mtm) REVERT: B 42 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: B 403 GLU cc_start: 0.8874 (pm20) cc_final: 0.8336 (pm20) REVERT: B 445 THR cc_start: 0.8789 (m) cc_final: 0.8549 (p) REVERT: B 578 MET cc_start: 0.8991 (mmt) cc_final: 0.8606 (mmp) REVERT: C 403 GLU cc_start: 0.8890 (pm20) cc_final: 0.8336 (pm20) REVERT: C 481 MET cc_start: 0.8678 (ppp) cc_final: 0.8477 (tmm) REVERT: D 403 GLU cc_start: 0.8870 (pm20) cc_final: 0.8322 (pm20) REVERT: D 481 MET cc_start: 0.8654 (ppp) cc_final: 0.8446 (tmm) outliers start: 40 outliers final: 35 residues processed: 194 average time/residue: 0.1078 time to fit residues: 35.7511 Evaluate side-chains 196 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 281 THR 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 538 LEU Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 296 VAL 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 392 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 220 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 500 VAL Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 16 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 41 optimal weight: 20.0000 chunk 185 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN B 37 ASN D 37 ASN D 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.081457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.065613 restraints weight = 52295.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.067512 restraints weight = 29083.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.068834 restraints weight = 19361.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.069682 restraints weight = 14515.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.070344 restraints weight = 11942.217| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19860 Z= 0.116 Angle : 0.614 11.896 26964 Z= 0.298 Chirality : 0.039 0.200 3072 Planarity : 0.003 0.039 3416 Dihedral : 4.081 22.207 2644 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.96 % Allowed : 18.99 % Favored : 79.06 % 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 are not related in a simple way. whole: -0.68 (0.17), residues: 2408 helix: 0.56 (0.14), residues: 1408 sheet: -0.57 (0.53), residues: 64 loop : -2.03 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 414 TYR 0.006 0.001 TYR D 216 PHE 0.020 0.001 PHE A 553 TRP 0.011 0.001 TRP C 629 HIS 0.006 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00272 (19860) covalent geometry : angle 0.61430 (26964) hydrogen bonds : bond 0.03541 ( 865) hydrogen bonds : angle 3.90352 ( 2463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2504.91 seconds wall clock time: 44 minutes 18.59 seconds (2658.59 seconds total)