Starting phenix.real_space_refine on Mon Oct 26 00:02:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6t8g_10400/10_2026/6t8g_10400.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t8g_10400/10_2026/6t8g_10400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6t8g_10400/10_2026/6t8g_10400.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6t8g_10400/10_2026/6t8g_10400.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t8g_10400/10_2026/6t8g_10400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t8g_10400/10_2026/6t8g_10400.map" model { file = "/net/cci-nas-00/data/ceres_data/6t8g_10400/10_2026/6t8g_10400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t8g_10400/10_2026/6t8g_10400.cif" } resolution = 4.34 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 44 5.49 5 S 90 5.16 5 C 11870 2.51 5 N 3262 2.21 5 O 3609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18875 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3028 Classifications: {'peptide': 397} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 368} Chain breaks: 1 Chain: "B" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2976 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 363} Chain breaks: 1 Chain: "C" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3013 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 368} Chain breaks: 1 Chain: "D" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2991 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 365} Chain breaks: 1 Chain: "E" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3028 Classifications: {'peptide': 397} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 368} Chain breaks: 1 Chain: "F" Number of atoms: 3021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3021 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 368} Chain breaks: 1 Chain: "G" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "H" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.58, per 1000 atoms: 0.30 Number of scatterers: 18875 At special positions: 0 Unit cell: (139.384, 104.8, 135.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 44 15.00 O 3609 8.00 N 3262 7.00 C 11870 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: 1.59 Conformation dependent library (CDL) restraints added in 890.0 milliseconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4410 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 20 sheets defined 40.7% alpha, 12.8% beta 16 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 317 through 321 removed outlier: 4.486A pdb=" N LEU A 320 " --> pdb=" O PRO A 317 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 321 " --> pdb=" O LEU A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 317 through 321' Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.849A pdb=" N MET A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'A' and resid 422 through 428 removed outlier: 3.595A pdb=" N VAL A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 434 removed outlier: 4.021A pdb=" N ASP A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 485 removed outlier: 3.579A pdb=" N PHE A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.575A pdb=" N ILE A 506 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR A 507 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 546 removed outlier: 4.835A pdb=" N ASN A 526 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 removed outlier: 3.820A pdb=" N LYS A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 605 removed outlier: 4.006A pdb=" N MET A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 617 removed outlier: 3.566A pdb=" N ALA A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 removed outlier: 3.898A pdb=" N ALA A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 Processing helix chain 'A' and resid 668 through 672 removed outlier: 3.781A pdb=" N LEU A 672 " --> pdb=" O ALA A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 711 Processing helix chain 'B' and resid 328 through 332 removed outlier: 4.282A pdb=" N TYR B 331 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 332 " --> pdb=" O LYS B 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 328 through 332' Processing helix chain 'B' and resid 335 through 350 removed outlier: 3.697A pdb=" N MET B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 384 through 392 Processing helix chain 'B' and resid 422 through 428 Processing helix chain 'B' and resid 429 through 434 Processing helix chain 'B' and resid 471 through 485 Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 521 through 545 removed outlier: 3.609A pdb=" N ARG B 529 " --> pdb=" O ALA B 525 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 530 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 543 " --> pdb=" O TYR B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 562 Processing helix chain 'B' and resid 597 through 604 Processing helix chain 'B' and resid 606 through 613 Processing helix chain 'B' and resid 619 through 623 removed outlier: 4.109A pdb=" N GLY B 623 " --> pdb=" O ARG B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 644 Processing helix chain 'B' and resid 658 through 663 removed outlier: 4.462A pdb=" N ILE B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 711 removed outlier: 3.763A pdb=" N ARG B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 349 removed outlier: 3.526A pdb=" N LEU C 336 " --> pdb=" O SER C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 383 Processing helix chain 'C' and resid 384 through 390 Processing helix chain 'C' and resid 422 through 428 Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 520 through 544 removed outlier: 4.183A pdb=" N ASN C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 561 Processing helix chain 'C' and resid 596 through 604 removed outlier: 3.580A pdb=" N MET C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 619 Processing helix chain 'C' and resid 656 through 664 removed outlier: 3.513A pdb=" N LEU C 664 " --> pdb=" O SER C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 709 removed outlier: 4.250A pdb=" N GLU C 706 " --> pdb=" O HIS C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 712 No H-bonds generated for 'chain 'C' and resid 710 through 712' Processing helix chain 'C' and resid 717 through 721 removed outlier: 3.649A pdb=" N LEU C 721 " --> pdb=" O GLU C 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.590A pdb=" N LEU D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 321 " --> pdb=" O LEU D 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 317 through 321' Processing helix chain 'D' and resid 332 through 350 Processing helix chain 'D' and resid 378 through 383 Processing helix chain 'D' and resid 384 through 393 Processing helix chain 'D' and resid 422 through 427 Processing helix chain 'D' and resid 429 through 434 Processing helix chain 'D' and resid 471 through 485 Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.615A pdb=" N ILE D 506 " --> pdb=" O GLU D 503 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR D 507 " --> pdb=" O LEU D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 546 Processing helix chain 'D' and resid 549 through 564 removed outlier: 3.546A pdb=" N PHE D 553 " --> pdb=" O ASN D 549 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA D 563 " --> pdb=" O ASP D 559 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 604 removed outlier: 4.107A pdb=" N MET D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 604 " --> pdb=" O MET D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 618 removed outlier: 4.090A pdb=" N GLU D 609 " --> pdb=" O GLY D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 646 removed outlier: 4.498A pdb=" N ASN D 645 " --> pdb=" O LEU D 641 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE D 646 " --> pdb=" O ILE D 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 641 through 646' Processing helix chain 'D' and resid 656 through 664 Processing helix chain 'D' and resid 668 through 672 removed outlier: 4.215A pdb=" N LEU D 672 " --> pdb=" O ALA D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 712 removed outlier: 3.787A pdb=" N VAL D 701 " --> pdb=" O SER D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 721 removed outlier: 3.912A pdb=" N ILE D 720 " --> pdb=" O ILE D 717 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU D 721 " --> pdb=" O GLU D 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 717 through 721' Processing helix chain 'E' and resid 317 through 321 removed outlier: 4.138A pdb=" N LEU E 320 " --> pdb=" O PRO E 317 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 321 " --> pdb=" O LEU E 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 317 through 321' Processing helix chain 'E' and resid 332 through 349 Processing helix chain 'E' and resid 378 through 383 Processing helix chain 'E' and resid 384 through 392 Processing helix chain 'E' and resid 422 through 428 Processing helix chain 'E' and resid 429 through 434 removed outlier: 3.715A pdb=" N ASP E 433 " --> pdb=" O SER E 429 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 434 " --> pdb=" O PRO E 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 429 through 434' Processing helix chain 'E' and resid 471 through 484 Processing helix chain 'E' and resid 503 through 508 removed outlier: 3.827A pdb=" N ILE E 506 " --> pdb=" O GLU E 503 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 508 " --> pdb=" O SER E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 546 removed outlier: 3.520A pdb=" N ASN E 526 " --> pdb=" O LYS E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 564 removed outlier: 3.943A pdb=" N ALA E 563 " --> pdb=" O ASP E 559 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY E 564 " --> pdb=" O ALA E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 603 Processing helix chain 'E' and resid 605 through 618 removed outlier: 4.322A pdb=" N GLU E 609 " --> pdb=" O GLY E 605 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS E 618 " --> pdb=" O ARG E 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 664 Processing helix chain 'E' and resid 697 through 711 removed outlier: 3.625A pdb=" N VAL E 701 " --> pdb=" O SER E 697 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG E 711 " --> pdb=" O ALA E 707 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 321 removed outlier: 3.630A pdb=" N LEU F 320 " --> pdb=" O PRO F 317 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU F 321 " --> pdb=" O LEU F 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 317 through 321' Processing helix chain 'F' and resid 332 through 349 Processing helix chain 'F' and resid 377 through 383 Processing helix chain 'F' and resid 384 through 392 Processing helix chain 'F' and resid 423 through 428 Processing helix chain 'F' and resid 429 through 434 removed outlier: 3.895A pdb=" N ASP F 433 " --> pdb=" O SER F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 485 Processing helix chain 'F' and resid 521 through 546 Processing helix chain 'F' and resid 549 through 563 removed outlier: 3.565A pdb=" N PHE F 553 " --> pdb=" O ASN F 549 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG F 555 " --> pdb=" O ALA F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 596 through 603 removed outlier: 3.776A pdb=" N MET F 600 " --> pdb=" O GLU F 596 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 619 Processing helix chain 'F' and resid 639 through 645 removed outlier: 3.675A pdb=" N ASN F 645 " --> pdb=" O LEU F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 664 removed outlier: 3.667A pdb=" N SER F 660 " --> pdb=" O SER F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 697 through 710 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 360 removed outlier: 6.631A pdb=" N GLU A 369 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL A 359 " --> pdb=" O ARG A 367 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARG A 367 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 398 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 440 through 445 removed outlier: 5.349A pdb=" N ALA A 442 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR A 454 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY A 444 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 492 through 497 removed outlier: 6.756A pdb=" N ILE A 590 " --> pdb=" O HIS A 625 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE A 627 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A 592 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ALA A 629 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 594 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE A 650 " --> pdb=" O HIS A 461 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU A 463 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 360 removed outlier: 4.175A pdb=" N GLU B 369 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL B 359 " --> pdb=" O ARG B 367 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ARG B 367 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 411 " --> pdb=" O PHE B 368 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B 398 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 440 through 441 Processing sheet with id=AA6, first strand: chain 'B' and resid 444 through 445 Processing sheet with id=AA7, first strand: chain 'B' and resid 627 through 629 removed outlier: 5.575A pdb=" N LEU B 463 " --> pdb=" O ILE B 650 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 494 through 495 Processing sheet with id=AA9, first strand: chain 'C' and resid 354 through 361 removed outlier: 4.801A pdb=" N VAL C 356 " --> pdb=" O GLN C 371 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLN C 371 " --> pdb=" O VAL C 356 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER C 358 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 411 " --> pdb=" O PHE C 368 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 451 through 455 removed outlier: 3.643A pdb=" N GLY C 444 " --> pdb=" O ILE C 452 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR C 454 " --> pdb=" O ALA C 442 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ALA C 442 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU C 463 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE C 652 " --> pdb=" O LEU C 463 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 494 through 497 removed outlier: 6.753A pdb=" N VAL C 592 " --> pdb=" O ILE C 627 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 356 through 361 removed outlier: 4.102A pdb=" N SER D 358 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 440 through 445 removed outlier: 5.229A pdb=" N ALA D 442 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR D 454 " --> pdb=" O ALA D 442 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY D 444 " --> pdb=" O ILE D 452 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 492 through 497 removed outlier: 6.106A pdb=" N ARG D 493 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL D 593 " --> pdb=" O ARG D 493 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE D 495 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 627 " --> pdb=" O VAL D 592 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N HIS D 461 " --> pdb=" O THR D 648 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE D 650 " --> pdb=" O HIS D 461 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU D 463 " --> pdb=" O ILE D 650 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 354 through 361 removed outlier: 5.365A pdb=" N VAL E 356 " --> pdb=" O GLN E 371 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLN E 371 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE E 370 " --> pdb=" O VAL E 409 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 440 through 445 removed outlier: 3.810A pdb=" N LEU E 443 " --> pdb=" O ILE E 452 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE E 452 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 492 through 497 removed outlier: 6.501A pdb=" N ILE E 590 " --> pdb=" O HIS E 625 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE E 627 " --> pdb=" O ILE E 590 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL E 592 " --> pdb=" O ILE E 627 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA E 629 " --> pdb=" O VAL E 592 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL E 594 " --> pdb=" O ALA E 629 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG E 649 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 356 through 361 removed outlier: 3.599A pdb=" N ILE F 413 " --> pdb=" O THR F 366 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY F 410 " --> pdb=" O VAL F 400 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 440 through 445 removed outlier: 3.880A pdb=" N LEU F 443 " --> pdb=" O ILE F 452 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE F 452 " --> pdb=" O LEU F 443 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 492 through 497 removed outlier: 6.885A pdb=" N ARG F 493 " --> pdb=" O VAL F 591 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL F 593 " --> pdb=" O ARG F 493 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE F 495 " --> pdb=" O VAL F 593 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 590 " --> pdb=" O HIS F 625 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE F 627 " --> pdb=" O ILE F 590 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL F 592 " --> pdb=" O ILE F 627 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA F 629 " --> pdb=" O VAL F 592 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL F 594 " --> pdb=" O ALA F 629 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU F 462 " --> pdb=" O LEU F 628 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N THR F 630 " --> pdb=" O LEU F 462 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL F 464 " --> pdb=" O THR F 630 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE F 650 " --> pdb=" O HIS F 461 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU F 463 " --> pdb=" O ILE F 650 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 2004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5269 1.33 - 1.45: 2768 1.45 - 1.57: 10985 1.57 - 1.69: 80 1.69 - 1.81: 174 Bond restraints: 19276 Sorted by residual: bond pdb=" C3' DT H 16 " pdb=" C2' DT H 16 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.48e+00 bond pdb=" C3' DA H 9 " pdb=" C2' DA H 9 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.47e+00 bond pdb=" C3' DT G 8 " pdb=" C2' DT G 8 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.14e+00 bond pdb=" C5' DT G 2 " pdb=" C4' DT G 2 " ideal model delta sigma weight residual 1.512 1.529 -0.017 7.00e-03 2.04e+04 5.90e+00 bond pdb=" C3' DA H 11 " pdb=" O3' DA H 11 " ideal model delta sigma weight residual 1.435 1.404 0.031 1.30e-02 5.92e+03 5.62e+00 ... (remaining 19271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 25691 3.07 - 6.14: 539 6.14 - 9.20: 62 9.20 - 12.27: 13 12.27 - 15.34: 8 Bond angle restraints: 26313 Sorted by residual: angle pdb=" N ILE B 615 " pdb=" CA ILE B 615 " pdb=" C ILE B 615 " ideal model delta sigma weight residual 112.17 105.43 6.74 9.50e-01 1.11e+00 5.03e+01 angle pdb=" C MET F 459 " pdb=" N PRO F 460 " pdb=" CD PRO F 460 " ideal model delta sigma weight residual 120.60 105.26 15.34 2.20e+00 2.07e-01 4.86e+01 angle pdb=" C MET F 459 " pdb=" N PRO F 460 " pdb=" CA PRO F 460 " ideal model delta sigma weight residual 127.00 142.34 -15.34 2.40e+00 1.74e-01 4.08e+01 angle pdb=" C MET B 459 " pdb=" N PRO B 460 " pdb=" CD PRO B 460 " ideal model delta sigma weight residual 120.60 106.99 13.61 2.20e+00 2.07e-01 3.83e+01 angle pdb=" C MET D 459 " pdb=" N PRO D 460 " pdb=" CD PRO D 460 " ideal model delta sigma weight residual 120.60 108.38 12.22 2.20e+00 2.07e-01 3.08e+01 ... (remaining 26308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 11635 35.89 - 71.78: 218 71.78 - 107.66: 4 107.66 - 143.55: 4 143.55 - 179.44: 3 Dihedral angle restraints: 11864 sinusoidal: 5063 harmonic: 6801 Sorted by residual: dihedral pdb=" O2A ADP D 801 " pdb=" O3A ADP D 801 " pdb=" PA ADP D 801 " pdb=" PB ADP D 801 " ideal model delta sinusoidal sigma weight residual 300.00 120.56 179.44 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PA ADP F 801 " pdb=" PB ADP F 801 " ideal model delta sinusoidal sigma weight residual -60.00 96.97 -156.97 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C5' ADP D 801 " pdb=" O5' ADP D 801 " pdb=" PA ADP D 801 " pdb=" O2A ADP D 801 " ideal model delta sinusoidal sigma weight residual -60.00 83.57 -143.56 1 2.00e+01 2.50e-03 4.33e+01 ... (remaining 11861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2539 0.075 - 0.150: 547 0.150 - 0.226: 41 0.226 - 0.301: 9 0.301 - 0.376: 4 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CG LEU B 550 " pdb=" CB LEU B 550 " pdb=" CD1 LEU B 550 " pdb=" CD2 LEU B 550 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB ILE B 452 " pdb=" CA ILE B 452 " pdb=" CG1 ILE B 452 " pdb=" CG2 ILE B 452 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB ILE D 638 " pdb=" CA ILE D 638 " pdb=" CG1 ILE D 638 " pdb=" CG2 ILE D 638 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 3137 not shown) Planarity restraints: 3226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 459 " -0.047 5.00e-02 4.00e+02 6.99e-02 7.81e+00 pdb=" N PRO B 460 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 460 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 460 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 569 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.65e+00 pdb=" N PRO B 570 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 570 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 570 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 632 " -0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO C 633 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 633 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 633 " -0.034 5.00e-02 4.00e+02 ... (remaining 3223 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3151 2.76 - 3.30: 17618 3.30 - 3.83: 31836 3.83 - 4.37: 35378 4.37 - 4.90: 59190 Nonbonded interactions: 147173 Sorted by model distance: nonbonded pdb=" OG SER F 660 " pdb=" O GLN F 666 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR F 539 " pdb=" O LYS F 618 " model vdw 2.241 3.040 nonbonded pdb=" OG SER F 355 " pdb=" O GLN F 371 " model vdw 2.270 3.040 nonbonded pdb=" O ILE D 483 " pdb=" OG SER D 487 " model vdw 2.295 3.040 nonbonded pdb=" OG SER C 355 " pdb=" O GLN C 371 " model vdw 2.304 3.040 ... (remaining 147168 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 315 through 570 or resid 587 through 720 or resid 801)) selection = chain 'B' selection = (chain 'C' and (resid 315 through 570 or resid 587 through 720 or resid 801)) selection = (chain 'D' and (resid 315 through 570 or resid 587 through 720 or resid 801)) selection = (chain 'E' and (resid 315 through 570 or resid 587 through 720 or resid 801)) selection = (chain 'F' and (resid 315 through 570 or resid 587 through 720 or resid 801)) } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.360 Find NCS groups from input model: 0.570 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: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.008 0.069 19276 Z= 0.371 Angle : 1.132 15.339 26313 Z= 0.605 Chirality : 0.061 0.376 3140 Planarity : 0.008 0.070 3226 Dihedral : 13.329 179.437 7454 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 0.15 % Allowed : 5.70 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -4.29 (0.14), residues: 2343 helix: -2.63 (0.13), residues: 873 sheet: -2.12 (0.25), residues: 394 loop : -3.29 (0.15), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 711 TYR 0.030 0.003 TYR D 507 PHE 0.025 0.003 PHE E 597 TRP 0.036 0.005 TRP A 530 HIS 0.013 0.002 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00772 / 0.37 (19276) covalent geometry : angle 1.13171 / 0.60 (26313) hydrogen bonds : bond 0.17131 / 11.35 ( 729) hydrogen bonds : angle 7.58101 / 5.14 ( 2068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 635 time to evaluate : 0.725 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: symmetry clash revert: symmetry clash REVERT: A 435 HIS cc_start: 0.9094 (t-90) cc_final: 0.8235 (t-90) REVERT: A 513 LEU cc_start: 0.8782 (tt) cc_final: 0.8400 (tt) REVERT: A 517 VAL cc_start: 0.8890 (t) cc_final: 0.8368 (m) REVERT: A 521 MET cc_start: 0.7301 (pp-130) cc_final: 0.5550 (pp-130) REVERT: A 535 MET cc_start: 0.8756 (ttm) cc_final: 0.8187 (ttp) REVERT: A 602 MET cc_start: 0.9019 (mtp) cc_final: 0.8735 (mtm) REVERT: A 609 GLU cc_start: 0.8245 (tp30) cc_final: 0.7885 (tp30) REVERT: A 614 ARG cc_start: 0.8518 (tmt-80) cc_final: 0.8253 (ttp-170) REVERT: A 632 ARG cc_start: 0.8112 (ppt-90) cc_final: 0.6618 (ptt-90) REVERT: A 650 ILE cc_start: 0.9368 (mt) cc_final: 0.9099 (tt) REVERT: A 678 MET cc_start: 0.7114 (pp-130) cc_final: 0.6558 (pp-130) REVERT: A 679 LEU cc_start: 0.8642 (mm) cc_final: 0.8278 (mm) REVERT: A 695 PHE cc_start: 0.8741 (t80) cc_final: 0.8446 (t80) REVERT: A 699 ASP cc_start: 0.9214 (m-30) cc_final: 0.8903 (t70) REVERT: B 445 HIS cc_start: 0.8335 (m90) cc_final: 0.8005 (m-70) REVERT: B 519 THR cc_start: 0.8761 (m) cc_final: 0.8528 (p) REVERT: B 542 MET cc_start: 0.9140 (ttp) cc_final: 0.8726 (ttp) REVERT: B 556 LYS cc_start: 0.9404 (mmpt) cc_final: 0.8950 (ptmm) REVERT: B 600 MET cc_start: 0.8213 (mtp) cc_final: 0.7787 (mtp) REVERT: B 614 ARG cc_start: 0.7583 (mpp80) cc_final: 0.6956 (mmm-85) REVERT: B 632 ARG cc_start: 0.5756 (tmm160) cc_final: 0.5548 (tmm160) REVERT: B 699 ASP cc_start: 0.8901 (m-30) cc_final: 0.8583 (t70) REVERT: B 716 TYR cc_start: 0.8375 (m-80) cc_final: 0.8174 (m-80) REVERT: C 425 GLU cc_start: 0.9199 (tt0) cc_final: 0.8555 (tm-30) REVERT: C 507 TYR cc_start: 0.8676 (m-80) cc_final: 0.8222 (m-80) REVERT: C 631 GLN cc_start: 0.8859 (tt0) cc_final: 0.7665 (tt0) REVERT: D 318 LEU cc_start: 0.9232 (tp) cc_final: 0.8980 (mp) REVERT: D 406 LYS cc_start: 0.8984 (mttt) cc_final: 0.8642 (mtpm) REVERT: D 441 LEU cc_start: 0.9092 (mt) cc_final: 0.8827 (mt) REVERT: D 468 THR cc_start: 0.8502 (p) cc_final: 0.7816 (m) REVERT: D 479 MET cc_start: 0.9340 (mtt) cc_final: 0.8873 (mtm) REVERT: D 595 ASP cc_start: 0.8269 (t0) cc_final: 0.8042 (t0) REVERT: D 632 ARG cc_start: 0.8534 (ptt180) cc_final: 0.7892 (tpp-160) REVERT: D 641 LEU cc_start: 0.9086 (tp) cc_final: 0.8595 (mp) REVERT: D 708 TRP cc_start: 0.8608 (m100) cc_final: 0.7962 (m100) REVERT: E 459 MET cc_start: 0.9150 (mtp) cc_final: 0.8375 (mtp) REVERT: E 540 ARG cc_start: 0.8542 (mtt180) cc_final: 0.7811 (mtm-85) REVERT: E 591 VAL cc_start: 0.9615 (t) cc_final: 0.9350 (m) REVERT: E 600 MET cc_start: 0.8778 (mtt) cc_final: 0.8545 (mtt) REVERT: E 675 HIS cc_start: 0.8044 (m170) cc_final: 0.7642 (m-70) REVERT: E 678 MET cc_start: 0.8659 (mtm) cc_final: 0.8418 (mtm) REVERT: E 702 HIS cc_start: 0.8719 (m90) cc_final: 0.8155 (m90) REVERT: F 339 MET cc_start: 0.9423 (tpp) cc_final: 0.9154 (tpp) REVERT: F 368 PHE cc_start: 0.9449 (m-80) cc_final: 0.9107 (m-10) REVERT: F 371 GLN cc_start: 0.9063 (tt0) cc_final: 0.8540 (tm-30) REVERT: F 431 GLU cc_start: 0.8745 (pm20) cc_final: 0.8232 (pm20) REVERT: F 601 MET cc_start: 0.7814 (tmt) cc_final: 0.6844 (tmm) REVERT: F 633 PRO cc_start: 0.8593 (Cg_exo) cc_final: 0.7504 (Cg_endo) REVERT: F 659 ASP cc_start: 0.7478 (m-30) cc_final: 0.7120 (m-30) outliers start: 3 outliers final: 0 residues processed: 636 average time/residue: 0.1499 time to fit residues: 141.7221 Evaluate side-chains 376 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.0050 chunk 235 optimal weight: 30.0000 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 512 HIS ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 435 HIS B 445 HIS ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN D 554 ASN D 617 GLN F 435 HIS ** F 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 675 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.091138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.073697 restraints weight = 54892.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.075545 restraints weight = 34731.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.076862 restraints weight = 24827.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.077783 restraints weight = 19320.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.078390 restraints weight = 16078.194| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19276 Z= 0.171 Angle : 0.822 9.492 26313 Z= 0.403 Chirality : 0.050 0.316 3140 Planarity : 0.007 0.072 3226 Dihedral : 15.252 157.165 2973 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.25 % Allowed : 4.00 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.04 (0.16), residues: 2343 helix: -1.23 (0.16), residues: 883 sheet: -1.63 (0.26), residues: 383 loop : -2.84 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 537 TYR 0.041 0.002 TYR E 432 PHE 0.023 0.002 PHE A 553 TRP 0.023 0.002 TRP C 530 HIS 0.010 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (19276) covalent geometry : angle 0.82198 / 0.40 (26313) hydrogen bonds : bond 0.04901 / 3.28 ( 729) hydrogen bonds : angle 5.87455 / 4.03 ( 2068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 511 time to evaluate : 0.681 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: A 435 HIS cc_start: 0.8710 (t-90) cc_final: 0.8433 (t-90) REVERT: A 481 LEU cc_start: 0.9679 (mm) cc_final: 0.9455 (mm) REVERT: A 595 ASP cc_start: 0.6928 (t70) cc_final: 0.6584 (t70) REVERT: A 626 LEU cc_start: 0.9684 (tp) cc_final: 0.9452 (tp) REVERT: A 675 HIS cc_start: 0.7746 (m170) cc_final: 0.7544 (m170) REVERT: B 398 ARG cc_start: 0.7512 (ptm-80) cc_final: 0.6960 (mtm110) REVERT: B 441 LEU cc_start: 0.8020 (mt) cc_final: 0.7543 (mt) REVERT: B 445 HIS cc_start: 0.8346 (m-70) cc_final: 0.7669 (m-70) REVERT: B 447 ILE cc_start: 0.8062 (mm) cc_final: 0.7752 (mm) REVERT: B 529 ARG cc_start: 0.8638 (mpp-170) cc_final: 0.8083 (mtt-85) REVERT: B 535 MET cc_start: 0.9223 (tmm) cc_final: 0.8918 (tmm) REVERT: B 542 MET cc_start: 0.9183 (ttp) cc_final: 0.8734 (ttp) REVERT: B 556 LYS cc_start: 0.9320 (mmpt) cc_final: 0.8867 (ptmm) REVERT: B 664 LEU cc_start: 0.6898 (tp) cc_final: 0.6372 (tp) REVERT: B 665 ASP cc_start: 0.6698 (m-30) cc_final: 0.6423 (m-30) REVERT: C 420 MET cc_start: 0.7699 (tmm) cc_final: 0.7473 (tmm) REVERT: C 425 GLU cc_start: 0.9220 (tt0) cc_final: 0.8689 (tm-30) REVERT: C 468 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7449 (m) REVERT: C 507 TYR cc_start: 0.8520 (m-80) cc_final: 0.8302 (m-80) REVERT: C 518 VAL cc_start: 0.7774 (t) cc_final: 0.7545 (t) REVERT: C 521 MET cc_start: 0.7251 (mmm) cc_final: 0.5599 (mmt) REVERT: D 369 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6784 (tt0) REVERT: D 406 LYS cc_start: 0.8877 (mttt) cc_final: 0.8317 (mtpt) REVERT: D 425 GLU cc_start: 0.8288 (tt0) cc_final: 0.7454 (tp30) REVERT: D 447 ILE cc_start: 0.9459 (pt) cc_final: 0.9163 (mp) REVERT: D 496 MET cc_start: 0.8243 (mtp) cc_final: 0.8032 (mtp) REVERT: D 595 ASP cc_start: 0.8142 (t0) cc_final: 0.7755 (t0) REVERT: D 602 MET cc_start: 0.8278 (tpt) cc_final: 0.8007 (tpp) REVERT: D 632 ARG cc_start: 0.8057 (ptt180) cc_final: 0.7737 (tpm170) REVERT: D 671 GLN cc_start: 0.8879 (mp10) cc_final: 0.8661 (mp10) REVERT: E 329 LYS cc_start: 0.8445 (mmpt) cc_final: 0.6876 (tptt) REVERT: E 369 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7624 (mt-10) REVERT: E 456 LEU cc_start: 0.9375 (tp) cc_final: 0.9080 (tp) REVERT: E 459 MET cc_start: 0.9066 (mtp) cc_final: 0.8393 (mtp) REVERT: E 538 ARG cc_start: 0.8875 (mtt-85) cc_final: 0.8629 (mtt180) REVERT: E 540 ARG cc_start: 0.8488 (mtt180) cc_final: 0.7860 (mtm-85) REVERT: E 600 MET cc_start: 0.8427 (mtt) cc_final: 0.8199 (mtt) REVERT: E 618 LYS cc_start: 0.7911 (ttmt) cc_final: 0.6667 (ttmt) REVERT: E 650 ILE cc_start: 0.8741 (tp) cc_final: 0.8326 (tp) REVERT: E 678 MET cc_start: 0.8489 (mtm) cc_final: 0.8270 (mtm) REVERT: F 367 ARG cc_start: 0.8827 (ttm170) cc_final: 0.8289 (ttm-80) REVERT: F 368 PHE cc_start: 0.9381 (m-80) cc_final: 0.9062 (m-10) REVERT: F 371 GLN cc_start: 0.8796 (tt0) cc_final: 0.8453 (tm-30) REVERT: F 464 VAL cc_start: 0.9114 (t) cc_final: 0.8867 (m) REVERT: F 496 MET cc_start: 0.8745 (mmm) cc_final: 0.8419 (mmm) REVERT: F 529 ARG cc_start: 0.9016 (mpt-90) cc_final: 0.8637 (mtm-85) REVERT: F 633 PRO cc_start: 0.8262 (Cg_exo) cc_final: 0.7038 (Cg_endo) REVERT: F 659 ASP cc_start: 0.7411 (m-30) cc_final: 0.6924 (m-30) outliers start: 5 outliers final: 0 residues processed: 515 average time/residue: 0.1446 time to fit residues: 111.9445 Evaluate side-chains 379 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 378 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [84, 57, 117, 200, 23, 160, 115, 31, 141, 85, 233] chunk 84 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 233 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 675 HIS F 435 HIS F 675 HIS F 702 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.072377 restraints weight = 56483.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.074222 restraints weight = 35837.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.075494 restraints weight = 25537.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.076384 restraints weight = 19997.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.076964 restraints weight = 16711.488| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19276 Z= 0.186 Angle : 0.783 11.835 26313 Z= 0.380 Chirality : 0.049 0.235 3140 Planarity : 0.005 0.055 3226 Dihedral : 14.908 154.174 2973 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.05 % Allowed : 4.60 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.53 (0.16), residues: 2343 helix: -0.70 (0.17), residues: 890 sheet: -1.47 (0.26), residues: 382 loop : -2.62 (0.17), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 537 TYR 0.039 0.002 TYR E 432 PHE 0.015 0.002 PHE C 423 TRP 0.018 0.002 TRP A 530 HIS 0.010 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (19276) covalent geometry : angle 0.78267 / 0.38 (26313) hydrogen bonds : bond 0.04422 / 2.94 ( 729) hydrogen bonds : angle 5.52780 / 3.82 ( 2068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 458 time to evaluate : 0.732 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 435 HIS cc_start: 0.8956 (t-90) cc_final: 0.8347 (t-90) REVERT: A 521 MET cc_start: 0.7539 (ptp) cc_final: 0.7026 (pmm) REVERT: A 542 MET cc_start: 0.8150 (mmt) cc_final: 0.7886 (mmt) REVERT: A 626 LEU cc_start: 0.9689 (tp) cc_final: 0.9452 (tp) REVERT: B 398 ARG cc_start: 0.7633 (ptm-80) cc_final: 0.7150 (mtm110) REVERT: B 445 HIS cc_start: 0.8359 (m-70) cc_final: 0.7767 (m-70) REVERT: B 447 ILE cc_start: 0.8212 (mm) cc_final: 0.7865 (mm) REVERT: B 500 LYS cc_start: 0.6361 (mttt) cc_final: 0.6108 (mttt) REVERT: B 535 MET cc_start: 0.9271 (tmm) cc_final: 0.9038 (tmm) REVERT: B 538 ARG cc_start: 0.6945 (ptp-170) cc_final: 0.6572 (mtm180) REVERT: B 542 MET cc_start: 0.9246 (ttp) cc_final: 0.8735 (ttp) REVERT: B 556 LYS cc_start: 0.9293 (mmpt) cc_final: 0.8886 (ptmm) REVERT: C 420 MET cc_start: 0.7792 (tmm) cc_final: 0.7530 (tmm) REVERT: C 425 GLU cc_start: 0.9257 (tt0) cc_final: 0.8813 (tm-30) REVERT: C 426 VAL cc_start: 0.9004 (t) cc_final: 0.8741 (t) REVERT: C 441 LEU cc_start: 0.8412 (mt) cc_final: 0.8035 (mp) REVERT: C 479 MET cc_start: 0.8914 (mtp) cc_final: 0.8703 (mtp) REVERT: C 541 LEU cc_start: 0.9254 (tp) cc_final: 0.8901 (tp) REVERT: D 369 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6351 (tt0) REVERT: D 406 LYS cc_start: 0.8943 (mttt) cc_final: 0.8349 (mtpt) REVERT: D 425 GLU cc_start: 0.8313 (tt0) cc_final: 0.7480 (tp30) REVERT: D 447 ILE cc_start: 0.9531 (pt) cc_final: 0.9131 (mp) REVERT: D 496 MET cc_start: 0.8265 (mtp) cc_final: 0.8036 (mtp) REVERT: D 521 MET cc_start: 0.8488 (mpp) cc_final: 0.7927 (mtt) REVERT: D 595 ASP cc_start: 0.8142 (t0) cc_final: 0.7888 (t0) REVERT: D 603 ILE cc_start: 0.8134 (mm) cc_final: 0.7672 (mm) REVERT: D 614 ARG cc_start: 0.8499 (mtt180) cc_final: 0.8290 (mmt90) REVERT: D 617 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8304 (tm-30) REVERT: D 632 ARG cc_start: 0.8181 (ptt180) cc_final: 0.7636 (tpm170) REVERT: D 671 GLN cc_start: 0.8868 (mp10) cc_final: 0.8627 (mp10) REVERT: E 369 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7661 (mt-10) REVERT: E 456 LEU cc_start: 0.9335 (tp) cc_final: 0.8754 (tp) REVERT: E 459 MET cc_start: 0.9103 (mtp) cc_final: 0.8195 (mtp) REVERT: E 521 MET cc_start: 0.7363 (tmm) cc_final: 0.7130 (tmm) REVERT: E 540 ARG cc_start: 0.8522 (mtt180) cc_final: 0.7955 (mtm-85) REVERT: E 618 LYS cc_start: 0.8032 (ttmt) cc_final: 0.6798 (ttmt) REVERT: E 650 ILE cc_start: 0.8993 (tp) cc_final: 0.8441 (tp) REVERT: E 675 HIS cc_start: 0.7850 (m-70) cc_final: 0.7439 (m90) REVERT: E 678 MET cc_start: 0.8451 (mtm) cc_final: 0.8241 (mtm) REVERT: F 367 ARG cc_start: 0.8885 (ttm170) cc_final: 0.8649 (ttm-80) REVERT: F 371 GLN cc_start: 0.8710 (tt0) cc_final: 0.8366 (tm-30) REVERT: F 441 LEU cc_start: 0.9016 (mt) cc_final: 0.8781 (mt) REVERT: F 479 MET cc_start: 0.9079 (mtm) cc_final: 0.8736 (mtm) REVERT: F 496 MET cc_start: 0.8706 (mmm) cc_final: 0.8399 (mmm) REVERT: F 500 LYS cc_start: 0.7710 (pttt) cc_final: 0.7026 (pttt) REVERT: F 601 MET cc_start: 0.7500 (tmm) cc_final: 0.6848 (tmm) outliers start: 1 outliers final: 0 residues processed: 459 average time/residue: 0.1421 time to fit residues: 98.7263 Evaluate side-chains 351 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [31, 86, 217, 78, 44, 160, 193, 22, 205, 2, 206] chunk 31 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 205 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 HIS ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 ASN C 415 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 ASN E 477 ASN F 435 HIS F 645 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.089892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.072709 restraints weight = 56030.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.074555 restraints weight = 35406.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.075859 restraints weight = 25173.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.076754 restraints weight = 19547.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.077383 restraints weight = 16285.896| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19276 Z= 0.178 Angle : 0.780 10.860 26313 Z= 0.376 Chirality : 0.048 0.255 3140 Planarity : 0.005 0.060 3226 Dihedral : 14.724 154.707 2973 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -2.27 (0.17), residues: 2343 helix: -0.48 (0.17), residues: 896 sheet: -1.27 (0.25), residues: 402 loop : -2.53 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 529 TYR 0.023 0.002 TYR D 432 PHE 0.017 0.001 PHE A 553 TRP 0.015 0.002 TRP B 530 HIS 0.010 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (19276) covalent geometry : angle 0.78024 / 0.38 (26313) hydrogen bonds : bond 0.04210 / 2.81 ( 729) hydrogen bonds : angle 5.43385 / 3.74 ( 2068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 448 time to evaluate : 0.716 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: A 435 HIS cc_start: 0.8819 (t-90) cc_final: 0.8303 (t-90) REVERT: A 542 MET cc_start: 0.8071 (mmt) cc_final: 0.7815 (mmt) REVERT: A 620 ARG cc_start: 0.8638 (tpt90) cc_final: 0.8329 (ttt180) REVERT: A 626 LEU cc_start: 0.9666 (tp) cc_final: 0.9455 (tp) REVERT: B 398 ARG cc_start: 0.7684 (ptm-80) cc_final: 0.7175 (mtm110) REVERT: B 419 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7516 (tm-30) REVERT: B 445 HIS cc_start: 0.8378 (m-70) cc_final: 0.7708 (m-70) REVERT: B 447 ILE cc_start: 0.8254 (mm) cc_final: 0.7908 (mm) REVERT: B 519 THR cc_start: 0.8391 (p) cc_final: 0.8186 (p) REVERT: B 529 ARG cc_start: 0.8707 (mpp-170) cc_final: 0.8408 (mtt-85) REVERT: B 535 MET cc_start: 0.9200 (tmm) cc_final: 0.8935 (tmm) REVERT: B 542 MET cc_start: 0.9205 (ttp) cc_final: 0.8094 (ttp) REVERT: B 553 PHE cc_start: 0.8108 (t80) cc_final: 0.6806 (t80) REVERT: B 556 LYS cc_start: 0.9295 (mmpt) cc_final: 0.8861 (ptmm) REVERT: C 420 MET cc_start: 0.7882 (tmm) cc_final: 0.7518 (tmm) REVERT: C 425 GLU cc_start: 0.9235 (tt0) cc_final: 0.8822 (tm-30) REVERT: C 426 VAL cc_start: 0.8993 (t) cc_final: 0.8719 (t) REVERT: C 481 LEU cc_start: 0.8844 (mp) cc_final: 0.8426 (mp) REVERT: C 541 LEU cc_start: 0.9142 (tp) cc_final: 0.8819 (tp) REVERT: C 617 GLN cc_start: 0.8304 (tp-100) cc_final: 0.7960 (tp40) REVERT: D 369 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6350 (tt0) REVERT: D 406 LYS cc_start: 0.8940 (mttt) cc_final: 0.8348 (mtpt) REVERT: D 425 GLU cc_start: 0.8248 (tt0) cc_final: 0.7415 (tp30) REVERT: D 447 ILE cc_start: 0.9529 (pt) cc_final: 0.9107 (mp) REVERT: D 496 MET cc_start: 0.8249 (mtp) cc_final: 0.7999 (mtp) REVERT: D 521 MET cc_start: 0.8444 (mpp) cc_final: 0.8051 (mtt) REVERT: D 595 ASP cc_start: 0.8203 (t0) cc_final: 0.7934 (t0) REVERT: D 599 ASP cc_start: 0.8237 (m-30) cc_final: 0.7980 (m-30) REVERT: D 602 MET cc_start: 0.8322 (tmm) cc_final: 0.8095 (tpp) REVERT: D 632 ARG cc_start: 0.8183 (ptt180) cc_final: 0.7585 (tpm170) REVERT: D 671 GLN cc_start: 0.8925 (mp10) cc_final: 0.8629 (mp10) REVERT: E 369 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7453 (mt-10) REVERT: E 422 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7874 (mmm-85) REVERT: E 459 MET cc_start: 0.9085 (mtp) cc_final: 0.8399 (mtp) REVERT: E 540 ARG cc_start: 0.8484 (mtt180) cc_final: 0.7919 (mtm-85) REVERT: E 601 MET cc_start: 0.8517 (tpp) cc_final: 0.8288 (mmm) REVERT: E 618 LYS cc_start: 0.8097 (ttmt) cc_final: 0.6781 (ttmt) REVERT: E 650 ILE cc_start: 0.8936 (tp) cc_final: 0.8628 (tp) REVERT: E 675 HIS cc_start: 0.7794 (m-70) cc_final: 0.7433 (m90) REVERT: F 371 GLN cc_start: 0.8703 (tt0) cc_final: 0.8219 (tm-30) REVERT: F 418 ARG cc_start: 0.8235 (ttp-170) cc_final: 0.7752 (ttp-170) REVERT: F 441 LEU cc_start: 0.8983 (mt) cc_final: 0.8775 (mt) REVERT: F 479 MET cc_start: 0.9088 (mtm) cc_final: 0.8729 (mtm) REVERT: F 496 MET cc_start: 0.8693 (mmm) cc_final: 0.8396 (mmm) REVERT: F 500 LYS cc_start: 0.7860 (pttt) cc_final: 0.7341 (pttt) REVERT: F 659 ASP cc_start: 0.7365 (m-30) cc_final: 0.7135 (m-30) outliers start: 1 outliers final: 0 residues processed: 448 average time/residue: 0.1333 time to fit residues: 92.0471 Evaluate side-chains 343 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [207, 227, 82, 130, 208, 105, 133, 88, 120, 111, 115] chunk 207 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN F 435 HIS F 666 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.088095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.071098 restraints weight = 56506.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.072879 restraints weight = 35759.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.074139 restraints weight = 25573.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.075009 restraints weight = 19906.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.075601 restraints weight = 16610.876| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 19276 Z= 0.256 Angle : 0.827 11.118 26313 Z= 0.401 Chirality : 0.050 0.245 3140 Planarity : 0.006 0.058 3226 Dihedral : 14.670 158.353 2973 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -2.12 (0.17), residues: 2343 helix: -0.38 (0.17), residues: 904 sheet: -1.20 (0.25), residues: 400 loop : -2.42 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 529 TYR 0.034 0.003 TYR C 507 PHE 0.017 0.002 PHE A 553 TRP 0.014 0.002 TRP B 530 HIS 0.008 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.26 (19276) covalent geometry : angle 0.82695 / 0.40 (26313) hydrogen bonds : bond 0.04394 / 2.92 ( 729) hydrogen bonds : angle 5.53713 / 3.81 ( 2068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 HIS cc_start: 0.9006 (t-90) cc_final: 0.8588 (t-90) REVERT: A 500 LYS cc_start: 0.8450 (ttpt) cc_final: 0.8101 (mtmt) REVERT: A 521 MET cc_start: 0.8010 (ptp) cc_final: 0.6335 (pmm) REVERT: A 542 MET cc_start: 0.8089 (mmt) cc_final: 0.7885 (mmt) REVERT: A 595 ASP cc_start: 0.6793 (t70) cc_final: 0.6438 (t70) REVERT: A 601 MET cc_start: 0.7530 (tmm) cc_final: 0.7175 (tmm) REVERT: A 626 LEU cc_start: 0.9669 (tp) cc_final: 0.9423 (tp) REVERT: B 398 ARG cc_start: 0.7743 (ptm-80) cc_final: 0.7427 (mtm110) REVERT: B 419 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7747 (tm-30) REVERT: B 445 HIS cc_start: 0.8449 (m-70) cc_final: 0.7815 (m-70) REVERT: B 447 ILE cc_start: 0.8376 (mm) cc_final: 0.8007 (mm) REVERT: B 529 ARG cc_start: 0.8763 (mpp-170) cc_final: 0.8484 (mtt-85) REVERT: B 535 MET cc_start: 0.9237 (tmm) cc_final: 0.8956 (tmm) REVERT: B 542 MET cc_start: 0.9188 (ttp) cc_final: 0.7803 (ttp) REVERT: B 553 PHE cc_start: 0.8279 (t80) cc_final: 0.7133 (t80) REVERT: C 420 MET cc_start: 0.7974 (tmm) cc_final: 0.7632 (tmm) REVERT: C 425 GLU cc_start: 0.9254 (tt0) cc_final: 0.8854 (tm-30) REVERT: C 426 VAL cc_start: 0.9048 (t) cc_final: 0.8772 (t) REVERT: C 441 LEU cc_start: 0.8306 (mp) cc_final: 0.7868 (mp) REVERT: C 541 LEU cc_start: 0.9115 (tp) cc_final: 0.8704 (tp) REVERT: D 369 GLU cc_start: 0.7253 (mt-10) cc_final: 0.7037 (tt0) REVERT: D 406 LYS cc_start: 0.8980 (mttt) cc_final: 0.8681 (mtpt) REVERT: D 425 GLU cc_start: 0.8268 (tt0) cc_final: 0.7475 (tp30) REVERT: D 447 ILE cc_start: 0.9569 (pt) cc_final: 0.9101 (mp) REVERT: D 496 MET cc_start: 0.8253 (mtp) cc_final: 0.7731 (ttt) REVERT: D 521 MET cc_start: 0.8549 (mpp) cc_final: 0.8283 (mpp) REVERT: D 602 MET cc_start: 0.8317 (tmm) cc_final: 0.7789 (tmm) REVERT: D 632 ARG cc_start: 0.8351 (ptt180) cc_final: 0.7722 (tpm170) REVERT: E 432 TYR cc_start: 0.8820 (t80) cc_final: 0.8526 (t80) REVERT: E 459 MET cc_start: 0.9128 (mtp) cc_final: 0.8421 (mtp) REVERT: E 540 ARG cc_start: 0.8358 (mtt180) cc_final: 0.7866 (mtm-85) REVERT: E 675 HIS cc_start: 0.7785 (m-70) cc_final: 0.7491 (m90) REVERT: F 371 GLN cc_start: 0.8655 (tt0) cc_final: 0.8339 (tm-30) REVERT: F 378 VAL cc_start: 0.9046 (t) cc_final: 0.8763 (p) REVERT: F 418 ARG cc_start: 0.8354 (ttp-170) cc_final: 0.7309 (ttp-170) REVERT: F 441 LEU cc_start: 0.8976 (mt) cc_final: 0.8740 (mt) REVERT: F 479 MET cc_start: 0.9114 (mtm) cc_final: 0.8737 (mtm) REVERT: F 641 LEU cc_start: 0.8974 (mp) cc_final: 0.7907 (mp) REVERT: F 659 ASP cc_start: 0.7412 (m-30) cc_final: 0.7154 (m-30) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.1332 time to fit residues: 83.5129 Evaluate side-chains 325 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [32, 54, 220, 223, 160, 210, 196, 50, 228, 214, 163] chunk 32 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 223 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 210 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 228 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 692 HIS ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS F 617 GLN F 666 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.089247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.072374 restraints weight = 56113.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.074087 restraints weight = 36327.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.075299 restraints weight = 26406.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.076145 restraints weight = 20832.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.076731 restraints weight = 17532.258| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19276 Z= 0.180 Angle : 0.792 13.145 26313 Z= 0.381 Chirality : 0.049 0.370 3140 Planarity : 0.005 0.067 3226 Dihedral : 14.574 159.503 2973 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -1.90 (0.17), residues: 2343 helix: -0.18 (0.17), residues: 911 sheet: -1.06 (0.26), residues: 379 loop : -2.32 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 529 TYR 0.030 0.002 TYR C 507 PHE 0.013 0.002 PHE A 553 TRP 0.015 0.002 TRP B 530 HIS 0.005 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (19276) covalent geometry : angle 0.79215 / 0.38 (26313) hydrogen bonds : bond 0.04166 / 2.80 ( 729) hydrogen bonds : angle 5.39348 / 3.73 ( 2068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 HIS cc_start: 0.8997 (t-90) cc_final: 0.8778 (t-90) REVERT: A 500 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8288 (ttpt) REVERT: A 542 MET cc_start: 0.8057 (mmt) cc_final: 0.7790 (mmt) REVERT: A 626 LEU cc_start: 0.9655 (tp) cc_final: 0.9452 (tp) REVERT: A 632 ARG cc_start: 0.8512 (ptp-110) cc_final: 0.8276 (ptp-170) REVERT: A 699 ASP cc_start: 0.8662 (t0) cc_final: 0.8422 (t70) REVERT: B 419 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 445 HIS cc_start: 0.8359 (m-70) cc_final: 0.7728 (m-70) REVERT: B 447 ILE cc_start: 0.8380 (mm) cc_final: 0.8146 (mp) REVERT: B 542 MET cc_start: 0.9193 (ttp) cc_final: 0.8542 (ttp) REVERT: B 545 MET cc_start: 0.7885 (mpp) cc_final: 0.7427 (mpp) REVERT: B 556 LYS cc_start: 0.9265 (mmpt) cc_final: 0.8925 (pttp) REVERT: C 420 MET cc_start: 0.7996 (tmm) cc_final: 0.7624 (tmm) REVERT: C 425 GLU cc_start: 0.9231 (tt0) cc_final: 0.8845 (tm-30) REVERT: C 426 VAL cc_start: 0.9034 (t) cc_final: 0.8769 (t) REVERT: C 522 LYS cc_start: 0.8486 (mmpt) cc_final: 0.7546 (mtmt) REVERT: C 535 MET cc_start: 0.9111 (tmm) cc_final: 0.8872 (tmm) REVERT: C 539 TYR cc_start: 0.7181 (m-80) cc_final: 0.6961 (m-10) REVERT: C 541 LEU cc_start: 0.9091 (tp) cc_final: 0.8605 (tp) REVERT: D 369 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6962 (tt0) REVERT: D 406 LYS cc_start: 0.8995 (mttt) cc_final: 0.8673 (mtpt) REVERT: D 425 GLU cc_start: 0.8258 (tt0) cc_final: 0.7431 (tp30) REVERT: D 447 ILE cc_start: 0.9560 (pt) cc_final: 0.9104 (mp) REVERT: D 496 MET cc_start: 0.8273 (mtp) cc_final: 0.7650 (ttt) REVERT: D 603 ILE cc_start: 0.6950 (tt) cc_final: 0.6541 (tt) REVERT: D 632 ARG cc_start: 0.8316 (ptt180) cc_final: 0.7668 (tpm170) REVERT: D 678 MET cc_start: 0.8182 (mtm) cc_final: 0.7742 (mtm) REVERT: E 432 TYR cc_start: 0.8766 (t80) cc_final: 0.8447 (t80) REVERT: E 459 MET cc_start: 0.9121 (mtp) cc_final: 0.8573 (mtp) REVERT: E 461 HIS cc_start: 0.8543 (m-70) cc_final: 0.8187 (m-70) REVERT: E 540 ARG cc_start: 0.8479 (mtt180) cc_final: 0.7850 (mtm-85) REVERT: E 670 GLU cc_start: 0.8693 (pm20) cc_final: 0.8462 (pm20) REVERT: E 675 HIS cc_start: 0.7704 (m-70) cc_final: 0.7463 (m90) REVERT: F 371 GLN cc_start: 0.8632 (tt0) cc_final: 0.8316 (tm-30) REVERT: F 601 MET cc_start: 0.7791 (tmm) cc_final: 0.7447 (tmm) REVERT: F 641 LEU cc_start: 0.8938 (mp) cc_final: 0.7973 (mp) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.1341 time to fit residues: 86.0610 Evaluate side-chains 324 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [223, 173, 94, 40, 196, 218, 5, 225, 4, 117, 192] chunk 223 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 225 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 117 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 477 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 ASN F 435 HIS F 617 GLN F 666 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.088984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.071974 restraints weight = 56552.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.073705 restraints weight = 36154.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.074932 restraints weight = 26132.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.075804 restraints weight = 20537.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.076357 restraints weight = 17206.161| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19276 Z= 0.196 Angle : 0.795 11.616 26313 Z= 0.384 Chirality : 0.049 0.225 3140 Planarity : 0.005 0.054 3226 Dihedral : 14.453 160.510 2973 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -1.77 (0.17), residues: 2343 helix: -0.08 (0.18), residues: 914 sheet: -1.03 (0.27), residues: 369 loop : -2.21 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 529 TYR 0.031 0.002 TYR C 507 PHE 0.019 0.002 PHE A 695 TRP 0.015 0.002 TRP B 530 HIS 0.010 0.001 HIS E 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (19276) covalent geometry : angle 0.79488 / 0.38 (26313) hydrogen bonds : bond 0.04077 / 2.77 ( 729) hydrogen bonds : angle 5.42239 / 3.78 ( 2068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 MET cc_start: 0.8033 (mmt) cc_final: 0.7828 (mmt) REVERT: A 618 LYS cc_start: 0.7922 (ptpt) cc_final: 0.7595 (ptpt) REVERT: A 626 LEU cc_start: 0.9692 (tp) cc_final: 0.9477 (tp) REVERT: A 632 ARG cc_start: 0.8449 (ptp-110) cc_final: 0.8132 (ptp-170) REVERT: A 695 PHE cc_start: 0.8477 (t80) cc_final: 0.8187 (t80) REVERT: A 699 ASP cc_start: 0.8596 (t0) cc_final: 0.8316 (t70) REVERT: B 419 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7474 (tm-30) REVERT: B 445 HIS cc_start: 0.8297 (m-70) cc_final: 0.7760 (m-70) REVERT: B 447 ILE cc_start: 0.8371 (mm) cc_final: 0.8132 (mp) REVERT: B 535 MET cc_start: 0.9325 (tmm) cc_final: 0.9039 (tmm) REVERT: B 542 MET cc_start: 0.9107 (ttp) cc_final: 0.8402 (ttp) REVERT: B 545 MET cc_start: 0.7852 (mpp) cc_final: 0.7305 (mpp) REVERT: B 556 LYS cc_start: 0.9246 (mmpt) cc_final: 0.8912 (pttp) REVERT: C 420 MET cc_start: 0.8045 (tmm) cc_final: 0.7662 (tmm) REVERT: C 425 GLU cc_start: 0.9216 (tt0) cc_final: 0.8841 (tm-30) REVERT: C 426 VAL cc_start: 0.9066 (t) cc_final: 0.8808 (t) REVERT: C 441 LEU cc_start: 0.8493 (mp) cc_final: 0.7975 (mp) REVERT: C 522 LYS cc_start: 0.8496 (mmpt) cc_final: 0.7537 (mtmt) REVERT: C 541 LEU cc_start: 0.9099 (tp) cc_final: 0.8429 (tp) REVERT: D 369 GLU cc_start: 0.7254 (mt-10) cc_final: 0.7002 (tt0) REVERT: D 406 LYS cc_start: 0.8991 (mttt) cc_final: 0.8664 (mtpt) REVERT: D 425 GLU cc_start: 0.8163 (tt0) cc_final: 0.7407 (tp30) REVERT: D 447 ILE cc_start: 0.9560 (pt) cc_final: 0.9101 (mp) REVERT: D 601 MET cc_start: 0.8398 (tmm) cc_final: 0.8155 (tmm) REVERT: D 632 ARG cc_start: 0.8376 (ptt180) cc_final: 0.7706 (tpm170) REVERT: E 459 MET cc_start: 0.9094 (mtp) cc_final: 0.8528 (mtp) REVERT: E 461 HIS cc_start: 0.8621 (m-70) cc_final: 0.8099 (m-70) REVERT: E 521 MET cc_start: 0.7513 (tmm) cc_final: 0.6578 (tmm) REVERT: E 540 ARG cc_start: 0.8434 (mtt180) cc_final: 0.7927 (mtm-85) REVERT: E 670 GLU cc_start: 0.8697 (pm20) cc_final: 0.8473 (pm20) REVERT: E 675 HIS cc_start: 0.7728 (m-70) cc_final: 0.7455 (m90) REVERT: E 678 MET cc_start: 0.7922 (mtp) cc_final: 0.7571 (mtp) REVERT: F 371 GLN cc_start: 0.8564 (tt0) cc_final: 0.8251 (tm-30) REVERT: F 441 LEU cc_start: 0.9026 (mp) cc_final: 0.8542 (mt) REVERT: F 479 MET cc_start: 0.9016 (mtm) cc_final: 0.8794 (mtm) REVERT: F 601 MET cc_start: 0.7713 (tmm) cc_final: 0.7370 (tmm) REVERT: F 641 LEU cc_start: 0.8908 (mp) cc_final: 0.8111 (mp) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.1351 time to fit residues: 87.5795 Evaluate side-chains 323 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [97, 1, 181, 185, 135, 139, 55, 216, 208, 232, 142] chunk 97 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 181 optimal weight: 0.0870 chunk 185 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 216 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 142 optimal weight: 0.5980 overall best weight: 2.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN F 435 HIS F 617 GLN F 666 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.088180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.071123 restraints weight = 56757.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.072897 restraints weight = 36480.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.074123 restraints weight = 26290.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.074974 restraints weight = 20717.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.075589 restraints weight = 17430.283| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19276 Z= 0.210 Angle : 0.801 12.031 26313 Z= 0.384 Chirality : 0.050 0.344 3140 Planarity : 0.005 0.055 3226 Dihedral : 14.354 157.438 2973 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -1.64 (0.18), residues: 2343 helix: -0.01 (0.17), residues: 921 sheet: -0.95 (0.27), residues: 390 loop : -2.14 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 529 TYR 0.030 0.002 TYR C 507 PHE 0.019 0.002 PHE A 553 TRP 0.016 0.002 TRP B 530 HIS 0.004 0.001 HIS F 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (19276) covalent geometry : angle 0.80110 / 0.38 (26313) hydrogen bonds : bond 0.04048 / 2.74 ( 729) hydrogen bonds : angle 5.36695 / 3.72 ( 2068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 VAL cc_start: 0.9305 (t) cc_final: 0.9019 (p) REVERT: A 542 MET cc_start: 0.8066 (mmt) cc_final: 0.7768 (mmt) REVERT: A 626 LEU cc_start: 0.9682 (tp) cc_final: 0.9458 (tp) REVERT: A 695 PHE cc_start: 0.8483 (t80) cc_final: 0.8206 (t80) REVERT: A 699 ASP cc_start: 0.8606 (t0) cc_final: 0.8349 (t70) REVERT: B 419 GLN cc_start: 0.8303 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 445 HIS cc_start: 0.8369 (m-70) cc_final: 0.7843 (m-70) REVERT: B 447 ILE cc_start: 0.8433 (mm) cc_final: 0.8192 (mp) REVERT: B 535 MET cc_start: 0.9364 (tmm) cc_final: 0.9080 (tmm) REVERT: B 542 MET cc_start: 0.9077 (ttp) cc_final: 0.8366 (ttp) REVERT: C 420 MET cc_start: 0.8093 (tmm) cc_final: 0.7708 (tmm) REVERT: C 425 GLU cc_start: 0.9227 (tt0) cc_final: 0.8844 (tm-30) REVERT: C 426 VAL cc_start: 0.9075 (t) cc_final: 0.8853 (t) REVERT: C 479 MET cc_start: 0.8985 (mtp) cc_final: 0.8604 (mtm) REVERT: C 522 LYS cc_start: 0.8466 (mmpt) cc_final: 0.7490 (mtmt) REVERT: C 541 LEU cc_start: 0.9163 (tp) cc_final: 0.8730 (tp) REVERT: D 318 LEU cc_start: 0.8668 (mp) cc_final: 0.8331 (tp) REVERT: D 369 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7105 (mt-10) REVERT: D 425 GLU cc_start: 0.8199 (tt0) cc_final: 0.7444 (tp30) REVERT: D 447 ILE cc_start: 0.9571 (pt) cc_final: 0.9073 (mp) REVERT: D 521 MET cc_start: 0.8504 (mpp) cc_final: 0.8065 (mtt) REVERT: D 603 ILE cc_start: 0.6941 (tt) cc_final: 0.6618 (tt) REVERT: D 631 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8208 (mm-40) REVERT: D 632 ARG cc_start: 0.8410 (ptt180) cc_final: 0.7725 (tpm170) REVERT: E 432 TYR cc_start: 0.8778 (t80) cc_final: 0.8498 (t80) REVERT: E 459 MET cc_start: 0.9094 (mtp) cc_final: 0.8465 (mtp) REVERT: E 461 HIS cc_start: 0.8729 (m-70) cc_final: 0.8256 (m-70) REVERT: E 540 ARG cc_start: 0.8416 (mtt180) cc_final: 0.7923 (mtm-85) REVERT: E 675 HIS cc_start: 0.7687 (m-70) cc_final: 0.7446 (m90) REVERT: E 678 MET cc_start: 0.8010 (mtp) cc_final: 0.7659 (mtp) REVERT: F 371 GLN cc_start: 0.8577 (tt0) cc_final: 0.8262 (tm-30) REVERT: F 441 LEU cc_start: 0.8981 (mp) cc_final: 0.8595 (mt) REVERT: F 479 MET cc_start: 0.9069 (mtm) cc_final: 0.8809 (mtm) REVERT: F 601 MET cc_start: 0.7716 (tmm) cc_final: 0.7234 (tmm) REVERT: F 641 LEU cc_start: 0.8904 (mp) cc_final: 0.8234 (mp) REVERT: F 680 TYR cc_start: 0.8943 (t80) cc_final: 0.8665 (t80) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.1243 time to fit residues: 78.9323 Evaluate side-chains 315 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [168, 5, 188, 226, 85, 20, 157, 169, 1, 125, 26] chunk 168 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 617 GLN A 631 GLN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN F 435 HIS F 617 GLN F 666 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.090808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.073869 restraints weight = 55274.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.075715 restraints weight = 34956.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.076992 restraints weight = 24906.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.077894 restraints weight = 19346.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.078516 restraints weight = 16080.937| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19276 Z= 0.140 Angle : 0.789 12.058 26313 Z= 0.374 Chirality : 0.049 0.270 3140 Planarity : 0.005 0.065 3226 Dihedral : 14.148 142.667 2973 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.05 % Allowed : 0.85 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -1.46 (0.18), residues: 2343 helix: 0.14 (0.18), residues: 925 sheet: -0.71 (0.28), residues: 370 loop : -2.08 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 529 TYR 0.030 0.002 TYR C 507 PHE 0.024 0.002 PHE D 553 TRP 0.019 0.002 TRP B 530 HIS 0.011 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (19276) covalent geometry : angle 0.78908 / 0.37 (26313) hydrogen bonds : bond 0.03779 / 2.57 ( 729) hydrogen bonds : angle 5.18683 / 3.60 ( 2068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 424 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 VAL cc_start: 0.9250 (t) cc_final: 0.8959 (p) REVERT: A 609 GLU cc_start: 0.8126 (tp30) cc_final: 0.7903 (tp30) REVERT: A 626 LEU cc_start: 0.9701 (tp) cc_final: 0.9494 (tp) REVERT: A 695 PHE cc_start: 0.8525 (t80) cc_final: 0.8249 (t80) REVERT: B 419 GLN cc_start: 0.8344 (tm-30) cc_final: 0.8031 (tm-30) REVERT: B 445 HIS cc_start: 0.8288 (m-70) cc_final: 0.7719 (m-70) REVERT: B 446 ASP cc_start: 0.8018 (m-30) cc_final: 0.7757 (m-30) REVERT: B 447 ILE cc_start: 0.8376 (mm) cc_final: 0.8167 (mp) REVERT: B 535 MET cc_start: 0.9330 (tmm) cc_final: 0.9062 (tmm) REVERT: B 542 MET cc_start: 0.9070 (ttp) cc_final: 0.8545 (ttp) REVERT: B 556 LYS cc_start: 0.9228 (mmpt) cc_final: 0.8909 (pttp) REVERT: C 420 MET cc_start: 0.8145 (tmm) cc_final: 0.7646 (tmm) REVERT: C 425 GLU cc_start: 0.9214 (tt0) cc_final: 0.8834 (tm-30) REVERT: C 522 LYS cc_start: 0.8417 (mmpt) cc_final: 0.7475 (mtmt) REVERT: C 661 ARG cc_start: 0.8627 (ptp-110) cc_final: 0.8424 (ttm110) REVERT: D 318 LEU cc_start: 0.8608 (mp) cc_final: 0.8268 (tp) REVERT: D 425 GLU cc_start: 0.8080 (tt0) cc_final: 0.7284 (tp30) REVERT: D 426 VAL cc_start: 0.9058 (t) cc_final: 0.8788 (t) REVERT: D 447 ILE cc_start: 0.9559 (pt) cc_final: 0.9163 (mp) REVERT: D 521 MET cc_start: 0.8499 (mpp) cc_final: 0.8071 (mtt) REVERT: D 603 ILE cc_start: 0.6734 (tt) cc_final: 0.6000 (tt) REVERT: D 631 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8214 (mm-40) REVERT: D 632 ARG cc_start: 0.8204 (ptt180) cc_final: 0.7554 (tpm170) REVERT: E 369 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7288 (mt-10) REVERT: E 456 LEU cc_start: 0.9231 (tp) cc_final: 0.8988 (tp) REVERT: E 459 MET cc_start: 0.8967 (mtp) cc_final: 0.8350 (mtp) REVERT: E 461 HIS cc_start: 0.8609 (m-70) cc_final: 0.8043 (m-70) REVERT: E 521 MET cc_start: 0.7521 (tmm) cc_final: 0.6891 (tmm) REVERT: E 540 ARG cc_start: 0.8409 (mtt180) cc_final: 0.7948 (mtm-85) REVERT: E 617 GLN cc_start: 0.8427 (mm110) cc_final: 0.8121 (tp40) REVERT: E 650 ILE cc_start: 0.9011 (tp) cc_final: 0.8379 (tp) REVERT: E 675 HIS cc_start: 0.7607 (m-70) cc_final: 0.7362 (m90) REVERT: F 371 GLN cc_start: 0.8573 (tt0) cc_final: 0.8224 (tm-30) REVERT: F 419 GLN cc_start: 0.8973 (tt0) cc_final: 0.8430 (tm-30) REVERT: F 480 LEU cc_start: 0.9639 (mm) cc_final: 0.9405 (mt) REVERT: F 500 LYS cc_start: 0.8032 (pttt) cc_final: 0.7797 (pttt) REVERT: F 601 MET cc_start: 0.7802 (tmm) cc_final: 0.7373 (tmm) REVERT: F 641 LEU cc_start: 0.8913 (mp) cc_final: 0.8076 (mp) outliers start: 1 outliers final: 0 residues processed: 425 average time/residue: 0.1290 time to fit residues: 85.2581 Evaluate side-chains 322 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [33, 142, 182, 188, 136, 99, 224, 2, 221, 144, 129] chunk 33 optimal weight: 0.8980 chunk 142 optimal weight: 0.4980 chunk 182 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 224 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 129 optimal weight: 0.1980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 ASN A 617 GLN ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 666 GLN F 435 HIS ** F 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 666 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.091260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.074489 restraints weight = 55810.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.076244 restraints weight = 36215.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.077445 restraints weight = 26269.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.078317 restraints weight = 20765.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.078867 restraints weight = 17463.807| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19276 Z= 0.138 Angle : 0.773 11.995 26313 Z= 0.368 Chirality : 0.049 0.254 3140 Planarity : 0.005 0.071 3226 Dihedral : 14.006 143.306 2973 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -1.32 (0.18), residues: 2343 helix: 0.22 (0.18), residues: 932 sheet: -0.78 (0.27), residues: 391 loop : -1.94 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 529 TYR 0.031 0.002 TYR C 507 PHE 0.023 0.002 PHE A 485 TRP 0.020 0.002 TRP B 530 HIS 0.010 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (19276) covalent geometry : angle 0.77260 / 0.37 (26313) hydrogen bonds : bond 0.03720 / 2.53 ( 729) hydrogen bonds : angle 5.11157 / 3.54 ( 2068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.871 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: A 349 GLU cc_start: 0.8450 (pm20) cc_final: 0.8229 (mp0) REVERT: A 474 VAL cc_start: 0.9280 (t) cc_final: 0.8965 (p) REVERT: A 609 GLU cc_start: 0.8127 (tp30) cc_final: 0.7914 (tp30) REVERT: A 626 LEU cc_start: 0.9690 (tp) cc_final: 0.9486 (tp) REVERT: A 628 LEU cc_start: 0.9656 (mt) cc_final: 0.9399 (mt) REVERT: A 695 PHE cc_start: 0.8468 (t80) cc_final: 0.8258 (t80) REVERT: B 419 GLN cc_start: 0.8336 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 445 HIS cc_start: 0.8298 (m-70) cc_final: 0.7722 (m-70) REVERT: B 535 MET cc_start: 0.9304 (tmm) cc_final: 0.8951 (tmm) REVERT: B 542 MET cc_start: 0.9067 (ttp) cc_final: 0.8535 (ttp) REVERT: B 556 LYS cc_start: 0.9248 (mmpt) cc_final: 0.8926 (pttp) REVERT: B 611 LEU cc_start: 0.7627 (tt) cc_final: 0.7343 (tt) REVERT: C 420 MET cc_start: 0.8041 (tmm) cc_final: 0.7646 (tmm) REVERT: C 425 GLU cc_start: 0.9263 (tt0) cc_final: 0.8828 (tm-30) REVERT: C 496 MET cc_start: 0.7961 (ppp) cc_final: 0.7542 (ppp) REVERT: C 522 LYS cc_start: 0.8389 (mmpt) cc_final: 0.7465 (mtmt) REVERT: C 541 LEU cc_start: 0.9192 (tp) cc_final: 0.8967 (tp) REVERT: C 545 MET cc_start: 0.8383 (mmp) cc_final: 0.8174 (mmp) REVERT: C 617 GLN cc_start: 0.8357 (tp40) cc_final: 0.8049 (tp40) REVERT: C 661 ARG cc_start: 0.8681 (ptp-110) cc_final: 0.8460 (ttm110) REVERT: D 318 LEU cc_start: 0.8635 (mp) cc_final: 0.8282 (tp) REVERT: D 425 GLU cc_start: 0.8103 (tt0) cc_final: 0.7274 (tp30) REVERT: D 426 VAL cc_start: 0.8989 (t) cc_final: 0.8748 (t) REVERT: D 447 ILE cc_start: 0.9558 (pt) cc_final: 0.9155 (mp) REVERT: D 632 ARG cc_start: 0.8108 (ptt180) cc_final: 0.7565 (tpm170) REVERT: E 369 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7161 (mt-10) REVERT: E 400 VAL cc_start: 0.9611 (t) cc_final: 0.9238 (p) REVERT: E 456 LEU cc_start: 0.9233 (tp) cc_final: 0.9016 (tp) REVERT: E 459 MET cc_start: 0.8985 (mtp) cc_final: 0.8386 (mtp) REVERT: E 461 HIS cc_start: 0.8594 (m-70) cc_final: 0.8048 (m-70) REVERT: E 521 MET cc_start: 0.7340 (tmm) cc_final: 0.6936 (tmm) REVERT: E 540 ARG cc_start: 0.8423 (mtt180) cc_final: 0.7953 (mtm-85) REVERT: E 675 HIS cc_start: 0.7662 (m-70) cc_final: 0.7431 (m90) REVERT: F 371 GLN cc_start: 0.8575 (tt0) cc_final: 0.8216 (tm-30) REVERT: F 419 GLN cc_start: 0.8968 (tt0) cc_final: 0.8502 (tm-30) REVERT: F 480 LEU cc_start: 0.9641 (mm) cc_final: 0.9389 (mt) REVERT: F 510 ILE cc_start: 0.9235 (pt) cc_final: 0.8854 (mt) REVERT: F 641 LEU cc_start: 0.8952 (mp) cc_final: 0.8112 (mp) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.1319 time to fit residues: 85.1204 Evaluate side-chains 330 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [212, 203, 105, 89, 102, 113, 116, 52, 148, 99, 145] chunk 212 optimal weight: 4.9990 chunk 203 optimal weight: 0.3980 chunk 105 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 631 GLN ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN F 435 HIS ** F 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 666 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.090928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.074003 restraints weight = 56043.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.075810 restraints weight = 35693.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.077049 restraints weight = 25559.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.077854 restraints weight = 20050.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.078494 restraints weight = 16912.326| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19276 Z= 0.155 Angle : 0.773 12.941 26313 Z= 0.368 Chirality : 0.048 0.264 3140 Planarity : 0.005 0.076 3226 Dihedral : 13.874 144.685 2973 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -1.21 (0.18), residues: 2343 helix: 0.31 (0.18), residues: 927 sheet: -0.70 (0.27), residues: 390 loop : -1.88 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 529 TYR 0.027 0.002 TYR C 539 PHE 0.033 0.002 PHE E 652 TRP 0.023 0.002 TRP B 530 HIS 0.010 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (19276) covalent geometry : angle 0.77289 / 0.37 (26313) hydrogen bonds : bond 0.03753 / 2.55 ( 729) hydrogen bonds : angle 5.09203 / 3.54 ( 2068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2941.33 seconds wall clock time: 51 minutes 40.76 seconds (3100.76 seconds total)