Starting phenix.real_space_refine on Sat Jun 21 17:32:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsk_61775/06_2025/9jsk_61775.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsk_61775/06_2025/9jsk_61775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jsk_61775/06_2025/9jsk_61775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsk_61775/06_2025/9jsk_61775.map" model { file = "/net/cci-nas-00/data/ceres_data/9jsk_61775/06_2025/9jsk_61775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsk_61775/06_2025/9jsk_61775.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.087 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 Ca 21 9.91 5 S 38 5.16 5 C 16372 2.51 5 N 4118 2.21 5 O 5264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25813 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3494 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 431} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3488 Classifications: {'peptide': 450} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 430} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3475 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3830 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 478} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3845 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 479} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 3806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3806 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 474} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "G" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3854 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 480} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 15.24, per 1000 atoms: 0.59 Number of scatterers: 25813 At special positions: 0 Unit cell: (176.88, 176, 96.8, 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) Ca 21 19.99 S 38 16.00 O 5264 8.00 N 4118 7.00 C 16372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.31 Conformation dependent library (CDL) restraints added in 3.4 seconds 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6274 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 68 sheets defined 16.7% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 424 through 428 removed outlier: 4.194A pdb=" N ILE A 428 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.741A pdb=" N LEU A 466 " --> pdb=" O ASN A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 Processing helix chain 'A' and resid 580 through 592 removed outlier: 4.155A pdb=" N LYS A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 662 removed outlier: 3.778A pdb=" N LYS A 661 " --> pdb=" O PRO A 658 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 662 " --> pdb=" O MET A 659 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 658 through 662' Processing helix chain 'B' and resid 226 through 232 removed outlier: 3.570A pdb=" N ASN B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.592A pdb=" N ALA B 249 " --> pdb=" O ASP B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 285 through 289 Processing helix chain 'B' and resid 463 through 471 Processing helix chain 'B' and resid 503 through 508 removed outlier: 4.584A pdb=" N SER B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 503 through 508' Processing helix chain 'B' and resid 545 through 555 Processing helix chain 'B' and resid 571 through 575 removed outlier: 3.768A pdb=" N VAL B 575 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 592 removed outlier: 3.862A pdb=" N LYS B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 602 Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 285 through 290 removed outlier: 3.652A pdb=" N ASP C 290 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 472 removed outlier: 3.813A pdb=" N SER C 471 " --> pdb=" O LYS C 467 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 510 removed outlier: 4.509A pdb=" N SER C 507 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN C 508 " --> pdb=" O ASN C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 555 Processing helix chain 'C' and resid 571 through 575 removed outlier: 3.843A pdb=" N VAL C 575 " --> pdb=" O GLU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 593 removed outlier: 4.096A pdb=" N LYS C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR C 593 " --> pdb=" O GLU C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 602 removed outlier: 3.541A pdb=" N ASN C 601 " --> pdb=" O LYS C 598 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 602 " --> pdb=" O ILE C 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 598 through 602' Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 245 through 252 removed outlier: 3.845A pdb=" N ALA D 249 " --> pdb=" O ASP D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 278 Processing helix chain 'D' and resid 285 through 290 removed outlier: 3.766A pdb=" N ASP D 290 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 337 removed outlier: 4.437A pdb=" N GLY D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 471 Processing helix chain 'D' and resid 502 through 510 removed outlier: 4.821A pdb=" N SER D 507 " --> pdb=" O SER D 503 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLN D 508 " --> pdb=" O ASN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 555 Processing helix chain 'D' and resid 580 through 592 removed outlier: 4.220A pdb=" N LYS D 592 " --> pdb=" O LYS D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 602 Processing helix chain 'D' and resid 658 through 662 Processing helix chain 'E' and resid 226 through 232 Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 271 through 278 Processing helix chain 'E' and resid 331 through 337 removed outlier: 3.527A pdb=" N THR E 335 " --> pdb=" O THR E 331 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 416 removed outlier: 3.948A pdb=" N GLU E 416 " --> pdb=" O LEU E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 470 Processing helix chain 'E' and resid 505 through 510 Processing helix chain 'E' and resid 545 through 555 Processing helix chain 'E' and resid 580 through 592 removed outlier: 3.798A pdb=" N LYS E 592 " --> pdb=" O LYS E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 602 Processing helix chain 'E' and resid 658 through 662 Processing helix chain 'F' and resid 226 through 233 Processing helix chain 'F' and resid 247 through 252 removed outlier: 4.408A pdb=" N GLN F 251 " --> pdb=" O SER F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 278 Processing helix chain 'F' and resid 332 through 337 removed outlier: 4.536A pdb=" N GLY F 337 " --> pdb=" O ALA F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 472 removed outlier: 3.600A pdb=" N LEU F 466 " --> pdb=" O ASN F 462 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER F 471 " --> pdb=" O LYS F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 507 removed outlier: 4.364A pdb=" N SER F 507 " --> pdb=" O SER F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 555 Processing helix chain 'F' and resid 581 through 592 removed outlier: 3.781A pdb=" N LYS F 592 " --> pdb=" O LYS F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 602 Processing helix chain 'F' and resid 658 through 662 Processing helix chain 'G' and resid 226 through 233 Processing helix chain 'G' and resid 247 through 252 removed outlier: 4.207A pdb=" N GLN G 251 " --> pdb=" O SER G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 278 Processing helix chain 'G' and resid 285 through 290 removed outlier: 3.962A pdb=" N ASP G 290 " --> pdb=" O GLU G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 337 removed outlier: 3.860A pdb=" N GLY G 337 " --> pdb=" O ALA G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 470 removed outlier: 3.974A pdb=" N LEU G 466 " --> pdb=" O ASN G 462 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP G 470 " --> pdb=" O LEU G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 510 removed outlier: 4.711A pdb=" N SER G 507 " --> pdb=" O SER G 503 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN G 508 " --> pdb=" O ASN G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 555 Processing helix chain 'G' and resid 571 through 575 removed outlier: 3.704A pdb=" N VAL G 575 " --> pdb=" O GLU G 572 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 592 removed outlier: 3.862A pdb=" N LYS G 592 " --> pdb=" O LYS G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 602 Processing helix chain 'G' and resid 658 through 662 Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 237 Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 308 removed outlier: 5.358A pdb=" N VAL A 301 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR A 395 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N MET A 303 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG A 393 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 305 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 390 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 405 removed outlier: 6.883A pdb=" N TYR A 403 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN A 431 " --> pdb=" O TYR A 403 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 429 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 417 through 422 removed outlier: 3.948A pdb=" N ALA A 419 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR A 408 " --> pdb=" O THR A 480 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 528 removed outlier: 3.748A pdb=" N LYS A 613 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU A 576 " --> pdb=" O LYS A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 558 Processing sheet with id=AA8, first strand: chain 'A' and resid 617 through 619 removed outlier: 3.564A pdb=" N THR A 619 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 735 " --> pdb=" O THR A 619 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 684 " --> pdb=" O THR A 725 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 647 through 656 removed outlier: 5.887A pdb=" N ASN A 647 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE A 730 " --> pdb=" O ASN A 647 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 649 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY A 728 " --> pdb=" O LEU A 649 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY A 651 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU A 732 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS A 675 " --> pdb=" O LEU A 732 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASN A 734 " --> pdb=" O TYR A 673 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR A 673 " --> pdb=" O ASN A 734 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ARG A 667 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB2, first strand: chain 'B' and resid 299 through 309 removed outlier: 5.235A pdb=" N VAL B 301 " --> pdb=" O TYR B 395 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR B 395 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N MET B 303 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ARG B 393 " --> pdb=" O MET B 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 299 through 309 removed outlier: 5.235A pdb=" N VAL B 301 " --> pdb=" O TYR B 395 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR B 395 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N MET B 303 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ARG B 393 " --> pdb=" O MET B 303 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 417 through 422 removed outlier: 3.500A pdb=" N ALA B 419 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS B 404 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY B 484 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR B 406 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL B 482 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR B 408 " --> pdb=" O THR B 480 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 488 through 489 removed outlier: 3.694A pdb=" N ILE B 496 " --> pdb=" O THR B 488 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 524 through 530 removed outlier: 3.652A pdb=" N GLU B 576 " --> pdb=" O LYS B 613 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 557 through 559 removed outlier: 4.086A pdb=" N LEU B 562 " --> pdb=" O ASN B 559 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 617 through 619 removed outlier: 3.701A pdb=" N GLU B 721 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP B 695 " --> pdb=" O VAL B 685 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 693 " --> pdb=" O ILE B 687 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 647 through 656 removed outlier: 3.815A pdb=" N GLY B 651 " --> pdb=" O GLY B 728 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLY B 728 " --> pdb=" O GLY B 651 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR B 653 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N SER B 726 " --> pdb=" O THR B 653 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE B 655 " --> pdb=" O LEU B 724 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU B 724 " --> pdb=" O ILE B 655 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU B 735 " --> pdb=" O SER B 671 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER B 671 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE B 737 " --> pdb=" O VAL B 669 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 669 " --> pdb=" O ILE B 737 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU B 739 " --> pdb=" O ARG B 667 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG B 667 " --> pdb=" O GLU B 739 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 672 " --> pdb=" O PHE B 706 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 234 through 237 Processing sheet with id=AC2, first strand: chain 'C' and resid 299 through 307 removed outlier: 5.663A pdb=" N VAL C 301 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR C 395 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N MET C 303 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG C 393 " --> pdb=" O MET C 303 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 299 through 307 removed outlier: 5.663A pdb=" N VAL C 301 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR C 395 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N MET C 303 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG C 393 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 390 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 446 " --> pdb=" O VAL C 392 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 417 through 422 removed outlier: 6.808A pdb=" N LEU C 411 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR C 420 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR C 409 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS C 422 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL C 405 " --> pdb=" O SER C 483 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER C 483 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN C 481 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C 409 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR C 479 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU C 411 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU C 477 " --> pdb=" O LEU C 411 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC6, first strand: chain 'C' and resid 524 through 530 removed outlier: 9.248A pdb=" N ILE C 610 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER C 515 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE C 612 " --> pdb=" O SER C 515 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 517 " --> pdb=" O ILE C 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 557 through 559 removed outlier: 3.500A pdb=" N TYR C 564 " --> pdb=" O THR C 557 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 562 " --> pdb=" O ASN C 559 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 617 through 619 removed outlier: 3.565A pdb=" N THR C 684 " --> pdb=" O THR C 725 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 647 through 656 removed outlier: 5.606A pdb=" N ASN C 647 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE C 730 " --> pdb=" O ASN C 647 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU C 649 " --> pdb=" O GLY C 728 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLY C 728 " --> pdb=" O LEU C 649 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY C 651 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 722 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU C 732 " --> pdb=" O LYS C 675 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LYS C 675 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASN C 734 " --> pdb=" O TYR C 673 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR C 673 " --> pdb=" O ASN C 734 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG C 667 " --> pdb=" O LEU C 740 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 672 " --> pdb=" O PHE C 706 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 234 through 237 Processing sheet with id=AD2, first strand: chain 'D' and resid 299 through 303 removed outlier: 3.513A pdb=" N GLY D 302 " --> pdb=" O ARG D 393 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 326 through 329 removed outlier: 3.803A pdb=" N THR D 327 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA D 365 " --> pdb=" O THR D 327 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 351 through 352 removed outlier: 6.609A pdb=" N ASN D 351 " --> pdb=" O PHE D 579 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 613 " --> pdb=" O GLU D 576 " (cutoff:3.500A) removed outlier: 9.349A pdb=" N ILE D 610 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER D 515 " --> pdb=" O ILE D 610 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ILE D 612 " --> pdb=" O SER D 515 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE D 517 " --> pdb=" O ILE D 612 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 403 through 410 removed outlier: 5.847A pdb=" N LYS D 404 " --> pdb=" O ASN D 485 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN D 485 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN D 481 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASN D 410 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR D 479 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 564 through 565 Processing sheet with id=AD7, first strand: chain 'D' and resid 617 through 619 Processing sheet with id=AD8, first strand: chain 'D' and resid 617 through 619 removed outlier: 5.363A pdb=" N LEU D 732 " --> pdb=" O LYS D 675 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS D 675 " --> pdb=" O LEU D 732 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASN D 734 " --> pdb=" O TYR D 673 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR D 673 " --> pdb=" O ASN D 734 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 652 through 657 removed outlier: 3.968A pdb=" N ILE D 655 " --> pdb=" O ILE D 722 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE D 722 " --> pdb=" O ILE D 655 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D 657 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU D 721 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS D 688 " --> pdb=" O GLU D 721 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN D 686 " --> pdb=" O THR D 723 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 684 " --> pdb=" O THR D 725 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS D 693 " --> pdb=" O ILE D 687 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 234 through 237 Processing sheet with id=AE2, first strand: chain 'E' and resid 299 through 305 removed outlier: 7.047A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 299 through 305 removed outlier: 7.047A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA E 390 " --> pdb=" O LEU E 448 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 327 through 329 removed outlier: 3.770A pdb=" N SER E 363 " --> pdb=" O SER E 329 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN E 362 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU E 477 " --> pdb=" O ASN E 362 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU E 478 " --> pdb=" O ASN E 410 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 351 through 352 removed outlier: 3.563A pdb=" N LYS E 613 " --> pdb=" O GLU E 576 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N ILE E 610 " --> pdb=" O SER E 513 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N SER E 515 " --> pdb=" O ILE E 610 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE E 612 " --> pdb=" O SER E 515 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE E 517 " --> pdb=" O ILE E 612 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU E 518 " --> pdb=" O PHE E 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 488 through 489 Processing sheet with id=AE7, first strand: chain 'E' and resid 564 through 565 Processing sheet with id=AE8, first strand: chain 'E' and resid 617 through 619 removed outlier: 3.798A pdb=" N TYR E 617 " --> pdb=" O ILE E 737 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 617 through 619 removed outlier: 3.798A pdb=" N TYR E 617 " --> pdb=" O ILE E 737 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ASP E 733 " --> pdb=" O LYS E 675 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LYS E 675 " --> pdb=" O ASP E 733 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU E 735 " --> pdb=" O TYR E 673 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N TYR E 673 " --> pdb=" O LEU E 735 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE E 737 " --> pdb=" O SER E 671 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER E 671 " --> pdb=" O ILE E 737 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLU E 739 " --> pdb=" O VAL E 669 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL E 669 " --> pdb=" O GLU E 739 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN E 741 " --> pdb=" O ARG E 667 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE E 710 " --> pdb=" O TYR E 668 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY E 672 " --> pdb=" O PHE E 706 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 652 through 657 removed outlier: 3.697A pdb=" N ILE E 655 " --> pdb=" O ILE E 722 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE E 722 " --> pdb=" O ILE E 655 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN E 686 " --> pdb=" O THR E 723 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS E 693 " --> pdb=" O ILE E 687 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 234 through 237 Processing sheet with id=AF3, first strand: chain 'F' and resid 324 through 325 removed outlier: 3.934A pdb=" N ARG F 324 " --> pdb=" O LEU F 306 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU F 306 " --> pdb=" O ARG F 324 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN F 391 " --> pdb=" O GLU F 304 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 324 through 325 removed outlier: 3.934A pdb=" N ARG F 324 " --> pdb=" O LEU F 306 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU F 306 " --> pdb=" O ARG F 324 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN F 391 " --> pdb=" O GLU F 304 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 327 through 329 Processing sheet with id=AF6, first strand: chain 'F' and resid 350 through 353 removed outlier: 3.943A pdb=" N GLU F 576 " --> pdb=" O LYS F 613 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS F 613 " --> pdb=" O GLU F 576 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASP F 580 " --> pdb=" O ASN F 609 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASN F 609 " --> pdb=" O ASP F 580 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 420 through 422 removed outlier: 3.902A pdb=" N GLN F 481 " --> pdb=" O THR F 408 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASN F 410 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N THR F 479 " --> pdb=" O ASN F 410 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 488 through 489 Processing sheet with id=AF9, first strand: chain 'F' and resid 557 through 559 removed outlier: 3.825A pdb=" N LEU F 562 " --> pdb=" O ASN F 559 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 617 through 619 removed outlier: 3.665A pdb=" N LEU F 732 " --> pdb=" O ASN F 647 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 617 through 619 removed outlier: 4.605A pdb=" N LEU F 735 " --> pdb=" O SER F 671 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N SER F 671 " --> pdb=" O LEU F 735 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE F 737 " --> pdb=" O VAL F 669 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL F 669 " --> pdb=" O ILE F 737 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLU F 739 " --> pdb=" O ARG F 667 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ARG F 667 " --> pdb=" O GLU F 739 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER F 674 " --> pdb=" O THR F 704 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 652 through 657 removed outlier: 3.826A pdb=" N ILE F 722 " --> pdb=" O ILE F 655 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE F 657 " --> pdb=" O ILE F 720 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE F 720 " --> pdb=" O ILE F 657 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU F 721 " --> pdb=" O LYS F 688 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS F 693 " --> pdb=" O ILE F 687 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 234 through 237 Processing sheet with id=AG5, first strand: chain 'G' and resid 299 through 306 removed outlier: 3.599A pdb=" N GLY G 302 " --> pdb=" O ARG G 393 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN G 391 " --> pdb=" O GLU G 304 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 299 through 306 removed outlier: 3.599A pdb=" N GLY G 302 " --> pdb=" O ARG G 393 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN G 391 " --> pdb=" O GLU G 304 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 326 through 328 Processing sheet with id=AG8, first strand: chain 'G' and resid 351 through 352 removed outlier: 3.580A pdb=" N LYS G 613 " --> pdb=" O GLU G 576 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 420 through 422 removed outlier: 3.591A pdb=" N ILE G 421 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR G 403 " --> pdb=" O ASN G 431 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN G 431 " --> pdb=" O TYR G 403 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 420 through 422 removed outlier: 3.591A pdb=" N ILE G 421 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL G 405 " --> pdb=" O SER G 483 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER G 483 " --> pdb=" O VAL G 405 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLN G 481 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR G 409 " --> pdb=" O THR G 479 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR G 479 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU G 411 " --> pdb=" O LEU G 477 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU G 477 " --> pdb=" O LEU G 411 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 488 through 489 Processing sheet with id=AH3, first strand: chain 'G' and resid 557 through 559 Processing sheet with id=AH4, first strand: chain 'G' and resid 617 through 619 removed outlier: 3.682A pdb=" N ILE G 687 " --> pdb=" O LYS G 693 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS G 693 " --> pdb=" O ILE G 687 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 647 through 657 removed outlier: 5.765A pdb=" N ASN G 647 " --> pdb=" O ILE G 730 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE G 730 " --> pdb=" O ASN G 647 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU G 649 " --> pdb=" O GLY G 728 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY G 728 " --> pdb=" O LEU G 649 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY G 651 " --> pdb=" O SER G 726 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 724 " --> pdb=" O THR G 653 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE G 655 " --> pdb=" O ILE G 722 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE G 722 " --> pdb=" O ILE G 655 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LEU G 735 " --> pdb=" O SER G 671 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER G 671 " --> pdb=" O LEU G 735 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ILE G 737 " --> pdb=" O VAL G 669 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL G 669 " --> pdb=" O ILE G 737 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLU G 739 " --> pdb=" O ARG G 667 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ARG G 667 " --> pdb=" O GLU G 739 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS G 666 " --> pdb=" O THR G 712 " (cutoff:3.500A) 738 hydrogen bonds defined for protein. 1821 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.02 Time building geometry restraints manager: 7.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8414 1.34 - 1.46: 4585 1.46 - 1.57: 13149 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 26217 Sorted by residual: bond pdb=" CD2 TRP F 374 " pdb=" CE2 TRP F 374 " ideal model delta sigma weight residual 1.409 1.447 -0.038 1.70e-02 3.46e+03 4.88e+00 bond pdb=" CD2 TRP G 374 " pdb=" CE2 TRP G 374 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.84e+00 bond pdb=" CD2 TRP F 631 " pdb=" CE2 TRP F 631 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.83e+00 bond pdb=" CD2 TRP E 374 " pdb=" CE2 TRP E 374 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.80e+00 bond pdb=" CD2 TRP A 631 " pdb=" CE2 TRP A 631 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.79e+00 ... (remaining 26212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 35002 1.95 - 3.90: 345 3.90 - 5.85: 47 5.85 - 7.80: 5 7.80 - 9.75: 2 Bond angle restraints: 35401 Sorted by residual: angle pdb=" CD2 TRP A 631 " pdb=" CE3 TRP A 631 " pdb=" CZ3 TRP A 631 " ideal model delta sigma weight residual 118.60 124.05 -5.45 1.30e+00 5.92e-01 1.76e+01 angle pdb=" CD2 TRP E 631 " pdb=" CE3 TRP E 631 " pdb=" CZ3 TRP E 631 " ideal model delta sigma weight residual 118.60 124.01 -5.41 1.30e+00 5.92e-01 1.73e+01 angle pdb=" CD2 TRP G 374 " pdb=" CE3 TRP G 374 " pdb=" CZ3 TRP G 374 " ideal model delta sigma weight residual 118.60 124.01 -5.41 1.30e+00 5.92e-01 1.73e+01 angle pdb=" CD2 TRP D 374 " pdb=" CE3 TRP D 374 " pdb=" CZ3 TRP D 374 " ideal model delta sigma weight residual 118.60 124.00 -5.40 1.30e+00 5.92e-01 1.73e+01 angle pdb=" CD2 TRP F 374 " pdb=" CE3 TRP F 374 " pdb=" CZ3 TRP F 374 " ideal model delta sigma weight residual 118.60 124.00 -5.40 1.30e+00 5.92e-01 1.72e+01 ... (remaining 35396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 14268 17.97 - 35.93: 1361 35.93 - 53.90: 200 53.90 - 71.86: 48 71.86 - 89.83: 27 Dihedral angle restraints: 15904 sinusoidal: 6312 harmonic: 9592 Sorted by residual: dihedral pdb=" CA PRO A 460 " pdb=" C PRO A 460 " pdb=" N ILE A 461 " pdb=" CA ILE A 461 " ideal model delta harmonic sigma weight residual -180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ILE A 459 " pdb=" C ILE A 459 " pdb=" N PRO A 460 " pdb=" CA PRO A 460 " ideal model delta harmonic sigma weight residual 180.00 163.26 16.74 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA LEU A 458 " pdb=" C LEU A 458 " pdb=" N ILE A 459 " pdb=" CA ILE A 459 " ideal model delta harmonic sigma weight residual -180.00 -163.36 -16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 15901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2614 0.034 - 0.067: 955 0.067 - 0.101: 333 0.101 - 0.134: 190 0.134 - 0.168: 4 Chirality restraints: 4096 Sorted by residual: chirality pdb=" CA ILE F 509 " pdb=" N ILE F 509 " pdb=" C ILE F 509 " pdb=" CB ILE F 509 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CB ILE A 475 " pdb=" CA ILE A 475 " pdb=" CG1 ILE A 475 " pdb=" CG2 ILE A 475 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CB ILE B 657 " pdb=" CA ILE B 657 " pdb=" CG1 ILE B 657 " pdb=" CG2 ILE B 657 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 4093 not shown) Planarity restraints: 4613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 568 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO D 569 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 569 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 569 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 413 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C LEU G 413 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU G 413 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP G 414 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 290 " 0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO B 291 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 291 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 291 " 0.023 5.00e-02 4.00e+02 ... (remaining 4610 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 703 2.69 - 3.24: 24824 3.24 - 3.80: 37190 3.80 - 4.35: 51819 4.35 - 4.90: 87463 Nonbonded interactions: 201999 Sorted by model distance: nonbonded pdb=" OG1 THR F 684 " pdb=" OG1 THR F 725 " model vdw 2.138 3.040 nonbonded pdb=" OD2 ASP D 571 " pdb=" OG SER D 573 " model vdw 2.200 3.040 nonbonded pdb=" O SER F 632 " pdb=" OG1 THR F 653 " model vdw 2.213 3.040 nonbonded pdb=" OD1 ASN A 245 " pdb=" OG SER A 247 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR E 359 " pdb=" OE1 GLU E 526 " model vdw 2.230 3.040 ... (remaining 201994 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 216 through 306 or resid 308 through 309 or resid 386 or r \ esid 389 through 449 or resid 461 through 741 or resid 901 through 903)) selection = (chain 'B' and (resid 216 through 306 or resid 308 through 309 or resid 386 or r \ esid 389 through 449 or resid 461 through 741 or resid 901 through 903)) selection = (chain 'C' and (resid 216 through 306 or resid 308 through 386 or resid 389 thro \ ugh 449 or resid 461 through 741 or resid 901 through 903)) selection = (chain 'D' and (resid 216 through 306 or resid 308 through 309 or resid 365 or r \ esid 389 through 614 or (resid 615 and (name N or name CA or name C or name O or \ name CB or name CG )) or resid 616 through 741 or resid 901 through 903)) selection = (chain 'E' and (resid 216 through 306 or resid 340 through 341 or resid 365 or r \ esid 389 through 449 or resid 461 through 614 or (resid 615 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 616 through 741 or resi \ d 901 through 903)) selection = (chain 'F' and (resid 216 through 306 or resid 308 through 323 or resid 342 or r \ esid 346 or resid 390 through 449 or resid 461 through 614 or (resid 615 and (na \ me N or name CA or name C or name O or name CB or name CG )) or resid 616 throug \ h 741 or resid 901 through 903)) selection = (chain 'G' and (resid 216 through 306 or resid 340 through 341 or resid 365 or r \ esid 389 through 449 or resid 461 through 614 or (resid 615 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 616 through 741 or resi \ d 901 through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.210 Process input model: 59.150 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.110 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 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 : 0.002 0.043 26217 Z= 0.120 Angle : 0.501 9.746 35401 Z= 0.282 Chirality : 0.044 0.168 4096 Planarity : 0.003 0.045 4613 Dihedral : 14.562 89.831 9630 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.14 % Allowed : 0.98 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 3293 helix: -0.78 (0.25), residues: 449 sheet: 0.88 (0.20), residues: 711 loop : -0.92 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 502 HIS 0.002 0.001 HIS G 358 PHE 0.011 0.001 PHE G 565 TYR 0.013 0.001 TYR G 260 ARG 0.000 0.000 ARG G 324 Details of bonding type rmsd hydrogen bonds : bond 0.25860 ( 702) hydrogen bonds : angle 9.75013 ( 1821) covalent geometry : bond 0.00249 (26217) covalent geometry : angle 0.50102 (35401) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 336 time to evaluate : 3.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 334 ASN cc_start: 0.6736 (m-40) cc_final: 0.6447 (m-40) outliers start: 4 outliers final: 3 residues processed: 339 average time/residue: 0.3568 time to fit residues: 196.5419 Evaluate side-chains 191 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 188 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 463 TYR Chi-restraints excluded: chain E residue 564 TYR Chi-restraints excluded: chain G residue 606 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 280 optimal weight: 7.9990 chunk 251 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 260 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 193 optimal weight: 40.0000 chunk 301 optimal weight: 20.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 ASN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 391 ASN G 566 ASN ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.081632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.060423 restraints weight = 97091.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.062223 restraints weight = 49528.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.063376 restraints weight = 32647.281| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26217 Z= 0.182 Angle : 0.607 11.057 35401 Z= 0.335 Chirality : 0.046 0.184 4096 Planarity : 0.004 0.044 4613 Dihedral : 4.417 53.040 3326 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.05 % Allowed : 7.91 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3293 helix: -0.31 (0.25), residues: 447 sheet: 0.82 (0.19), residues: 744 loop : -0.90 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 244 HIS 0.002 0.001 HIS D 358 PHE 0.013 0.001 PHE G 565 TYR 0.015 0.001 TYR C 617 ARG 0.000 0.000 ARG G 667 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 702) hydrogen bonds : angle 6.76332 ( 1821) covalent geometry : bond 0.00394 (26217) covalent geometry : angle 0.60716 (35401) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.7684 (tpp) cc_final: 0.7203 (mpp) REVERT: A 695 ASP cc_start: 0.7494 (m-30) cc_final: 0.7165 (m-30) REVERT: A 732 LEU cc_start: 0.8421 (mt) cc_final: 0.8098 (pp) REVERT: B 303 MET cc_start: 0.9126 (tmm) cc_final: 0.8919 (ttt) REVERT: C 519 ASP cc_start: 0.8654 (t0) cc_final: 0.8422 (t0) REVERT: D 695 ASP cc_start: 0.8173 (p0) cc_final: 0.7328 (m-30) REVERT: D 724 LEU cc_start: 0.9087 (tp) cc_final: 0.8821 (tp) REVERT: E 287 GLU cc_start: 0.8650 (pm20) cc_final: 0.8360 (pm20) REVERT: E 561 GLU cc_start: 0.7779 (pm20) cc_final: 0.7463 (pp20) REVERT: E 688 LYS cc_start: 0.8464 (mttp) cc_final: 0.8240 (tptp) REVERT: F 640 ASP cc_start: 0.8563 (t0) cc_final: 0.8347 (t0) REVERT: G 519 ASP cc_start: 0.8733 (t0) cc_final: 0.8411 (t0) REVERT: G 739 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7582 (mp0) outliers start: 31 outliers final: 23 residues processed: 214 average time/residue: 0.3351 time to fit residues: 119.3794 Evaluate side-chains 191 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 686 ASN Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 463 TYR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 564 TYR Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 536 ASN Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 568 ILE Chi-restraints excluded: chain G residue 739 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 137 optimal weight: 6.9990 chunk 307 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 81 optimal weight: 0.0010 chunk 265 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 278 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 overall best weight: 5.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 GLN ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN D 251 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 ASN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 391 ASN ** F 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.080306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.059194 restraints weight = 97602.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.060955 restraints weight = 49853.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.062087 restraints weight = 32977.511| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26217 Z= 0.178 Angle : 0.573 13.023 35401 Z= 0.316 Chirality : 0.045 0.193 4096 Planarity : 0.003 0.042 4613 Dihedral : 4.381 54.917 3322 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.39 % Allowed : 9.57 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3293 helix: -0.07 (0.25), residues: 439 sheet: 0.67 (0.19), residues: 774 loop : -0.87 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 244 HIS 0.002 0.001 HIS G 358 PHE 0.013 0.001 PHE E 731 TYR 0.012 0.001 TYR D 260 ARG 0.000 0.000 ARG F 667 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 702) hydrogen bonds : angle 6.07784 ( 1821) covalent geometry : bond 0.00386 (26217) covalent geometry : angle 0.57291 (35401) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8032 (mp0) cc_final: 0.7755 (mp0) REVERT: A 303 MET cc_start: 0.7593 (tpp) cc_final: 0.7330 (mpp) REVERT: A 695 ASP cc_start: 0.7534 (m-30) cc_final: 0.7278 (m-30) REVERT: A 732 LEU cc_start: 0.8334 (mt) cc_final: 0.7990 (pp) REVERT: C 659 MET cc_start: 0.7202 (tpp) cc_final: 0.6550 (mmm) REVERT: E 287 GLU cc_start: 0.8587 (pm20) cc_final: 0.8299 (pm20) REVERT: E 332 ASP cc_start: 0.7102 (m-30) cc_final: 0.6874 (m-30) REVERT: E 688 LYS cc_start: 0.8464 (mttp) cc_final: 0.8260 (tptp) REVERT: G 519 ASP cc_start: 0.8739 (t0) cc_final: 0.8351 (t0) outliers start: 41 outliers final: 29 residues processed: 200 average time/residue: 0.3238 time to fit residues: 109.3224 Evaluate side-chains 190 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 463 TYR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 564 TYR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 536 ASN Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain F residue 725 THR Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 568 ILE Chi-restraints excluded: chain G residue 739 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 289 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 89 optimal weight: 40.0000 chunk 322 optimal weight: 0.2980 chunk 22 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 29 optimal weight: 0.0270 chunk 158 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 328 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 overall best weight: 3.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 431 ASN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 638 ASN F 692 GLN ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.080775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.059669 restraints weight = 97606.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.061466 restraints weight = 49041.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.062618 restraints weight = 32155.507| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26217 Z= 0.132 Angle : 0.539 14.198 35401 Z= 0.298 Chirality : 0.044 0.177 4096 Planarity : 0.003 0.042 4613 Dihedral : 4.210 57.062 3322 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.25 % Allowed : 11.02 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3293 helix: 0.12 (0.25), residues: 438 sheet: 0.73 (0.19), residues: 788 loop : -0.80 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 631 HIS 0.002 0.001 HIS G 358 PHE 0.009 0.001 PHE G 565 TYR 0.011 0.001 TYR D 260 ARG 0.000 0.000 ARG G 324 Details of bonding type rmsd hydrogen bonds : bond 0.03071 ( 702) hydrogen bonds : angle 5.62454 ( 1821) covalent geometry : bond 0.00280 (26217) covalent geometry : angle 0.53935 (35401) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7961 (mp0) cc_final: 0.7643 (mp0) REVERT: A 286 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8591 (tp) REVERT: A 695 ASP cc_start: 0.7515 (m-30) cc_final: 0.7283 (m-30) REVERT: A 732 LEU cc_start: 0.8263 (mt) cc_final: 0.7896 (pp) REVERT: C 659 MET cc_start: 0.7229 (tpp) cc_final: 0.6898 (mmm) REVERT: E 287 GLU cc_start: 0.8547 (pm20) cc_final: 0.8262 (pm20) REVERT: E 561 GLU cc_start: 0.7680 (pm20) cc_final: 0.7380 (pp20) REVERT: E 688 LYS cc_start: 0.8478 (mttp) cc_final: 0.8266 (tptp) REVERT: G 519 ASP cc_start: 0.8628 (t0) cc_final: 0.8278 (t0) outliers start: 37 outliers final: 24 residues processed: 206 average time/residue: 0.3265 time to fit residues: 114.6598 Evaluate side-chains 188 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 463 TYR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 536 ASN Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain F residue 725 THR Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 568 ILE Chi-restraints excluded: chain G residue 739 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 205 optimal weight: 6.9990 chunk 270 optimal weight: 5.9990 chunk 304 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 253 optimal weight: 2.9990 chunk 223 optimal weight: 8.9990 chunk 243 optimal weight: 20.0000 chunk 146 optimal weight: 50.0000 chunk 161 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN C 430 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN D 410 ASN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 ASN ** G 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.078929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.057824 restraints weight = 98748.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.059578 restraints weight = 50263.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.060699 restraints weight = 33165.520| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26217 Z= 0.196 Angle : 0.571 14.092 35401 Z= 0.314 Chirality : 0.045 0.173 4096 Planarity : 0.003 0.043 4613 Dihedral : 4.274 58.552 3320 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.52 % Allowed : 12.14 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3293 helix: 0.07 (0.25), residues: 443 sheet: 0.64 (0.19), residues: 781 loop : -0.88 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 244 HIS 0.003 0.001 HIS D 358 PHE 0.020 0.001 PHE A 670 TYR 0.012 0.001 TYR D 260 ARG 0.000 0.000 ARG G 606 Details of bonding type rmsd hydrogen bonds : bond 0.03166 ( 702) hydrogen bonds : angle 5.51064 ( 1821) covalent geometry : bond 0.00425 (26217) covalent geometry : angle 0.57084 (35401) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8618 (tp) REVERT: A 695 ASP cc_start: 0.7567 (m-30) cc_final: 0.7303 (m-30) REVERT: A 732 LEU cc_start: 0.8312 (mt) cc_final: 0.7966 (pp) REVERT: E 287 GLU cc_start: 0.8543 (pm20) cc_final: 0.8253 (pm20) REVERT: E 332 ASP cc_start: 0.7261 (m-30) cc_final: 0.6899 (m-30) REVERT: E 688 LYS cc_start: 0.8475 (mttp) cc_final: 0.8259 (tptp) REVERT: G 519 ASP cc_start: 0.8669 (t0) cc_final: 0.8352 (t0) outliers start: 45 outliers final: 34 residues processed: 186 average time/residue: 0.3200 time to fit residues: 102.9253 Evaluate side-chains 185 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain D residue 463 TYR Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 536 ASN Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 636 THR Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain F residue 725 THR Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 568 ILE Chi-restraints excluded: chain G residue 739 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 154 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 275 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 87 optimal weight: 50.0000 chunk 229 optimal weight: 30.0000 chunk 218 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.078348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.057346 restraints weight = 98336.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.059080 restraints weight = 50232.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.060194 restraints weight = 33180.237| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26217 Z= 0.199 Angle : 0.572 12.628 35401 Z= 0.315 Chirality : 0.045 0.166 4096 Planarity : 0.003 0.043 4613 Dihedral : 4.361 59.608 3320 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.69 % Allowed : 12.64 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3293 helix: 0.13 (0.25), residues: 437 sheet: 0.59 (0.19), residues: 770 loop : -0.92 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 631 HIS 0.003 0.001 HIS D 358 PHE 0.010 0.001 PHE A 710 TYR 0.013 0.001 TYR D 260 ARG 0.000 0.000 ARG F 527 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 702) hydrogen bonds : angle 5.45275 ( 1821) covalent geometry : bond 0.00435 (26217) covalent geometry : angle 0.57232 (35401) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8178 (mp0) cc_final: 0.7909 (mp0) REVERT: A 286 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8607 (tp) REVERT: A 690 LYS cc_start: 0.4992 (OUTLIER) cc_final: 0.4458 (mmtm) REVERT: A 695 ASP cc_start: 0.7609 (m-30) cc_final: 0.7229 (m-30) REVERT: A 732 LEU cc_start: 0.8309 (mt) cc_final: 0.7966 (pp) REVERT: D 741 ASN cc_start: 0.7697 (t0) cc_final: 0.7139 (m-40) REVERT: E 287 GLU cc_start: 0.8497 (pm20) cc_final: 0.8243 (pm20) REVERT: E 332 ASP cc_start: 0.7259 (m-30) cc_final: 0.6861 (m-30) REVERT: E 688 LYS cc_start: 0.8455 (mttp) cc_final: 0.8254 (tptp) REVERT: G 336 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8820 (p) REVERT: G 519 ASP cc_start: 0.8645 (t0) cc_final: 0.8340 (t0) outliers start: 50 outliers final: 39 residues processed: 196 average time/residue: 0.3032 time to fit residues: 102.4163 Evaluate side-chains 192 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 690 LYS Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 463 TYR Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 713 THR Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 536 ASN Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 636 THR Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain F residue 725 THR Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 568 ILE Chi-restraints excluded: chain G residue 684 THR Chi-restraints excluded: chain G residue 739 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 219 optimal weight: 3.9990 chunk 288 optimal weight: 9.9990 chunk 221 optimal weight: 30.0000 chunk 315 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 171 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 299 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 ASN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.078549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.057622 restraints weight = 98100.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.059356 restraints weight = 49834.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.060473 restraints weight = 32871.173| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26217 Z= 0.169 Angle : 0.559 12.656 35401 Z= 0.307 Chirality : 0.044 0.160 4096 Planarity : 0.003 0.042 4613 Dihedral : 4.307 59.106 3320 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.69 % Allowed : 13.69 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3293 helix: 0.16 (0.25), residues: 442 sheet: 0.63 (0.19), residues: 768 loop : -0.91 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 631 HIS 0.003 0.001 HIS D 358 PHE 0.009 0.001 PHE A 710 TYR 0.012 0.001 TYR D 260 ARG 0.000 0.000 ARG C 457 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 702) hydrogen bonds : angle 5.33608 ( 1821) covalent geometry : bond 0.00369 (26217) covalent geometry : angle 0.55923 (35401) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 162 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8237 (mp0) cc_final: 0.7935 (mp0) REVERT: A 286 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8597 (tp) REVERT: A 303 MET cc_start: 0.7304 (mpp) cc_final: 0.7104 (mpp) REVERT: A 695 ASP cc_start: 0.7668 (m-30) cc_final: 0.7326 (m-30) REVERT: A 732 LEU cc_start: 0.8330 (mt) cc_final: 0.7990 (pp) REVERT: D 587 ILE cc_start: 0.9475 (mm) cc_final: 0.9238 (tp) REVERT: D 741 ASN cc_start: 0.7693 (t0) cc_final: 0.7137 (m-40) REVERT: E 287 GLU cc_start: 0.8492 (pm20) cc_final: 0.8231 (pm20) REVERT: E 332 ASP cc_start: 0.7486 (m-30) cc_final: 0.7271 (m-30) REVERT: F 691 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6630 (tm-30) REVERT: G 336 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8819 (p) REVERT: G 519 ASP cc_start: 0.8639 (t0) cc_final: 0.8332 (t0) outliers start: 50 outliers final: 40 residues processed: 197 average time/residue: 0.3170 time to fit residues: 107.1995 Evaluate side-chains 196 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 463 TYR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 713 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 476 LYS Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 536 ASN Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 636 THR Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain F residue 725 THR Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 568 ILE Chi-restraints excluded: chain G residue 684 THR Chi-restraints excluded: chain G residue 739 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 186 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 316 optimal weight: 6.9990 chunk 175 optimal weight: 0.0770 chunk 305 optimal weight: 6.9990 chunk 134 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 overall best weight: 6.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 GLN C 647 ASN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 ASN ** F 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.078060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.057190 restraints weight = 99201.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.058940 restraints weight = 50448.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.060051 restraints weight = 33105.134| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26217 Z= 0.184 Angle : 0.574 12.867 35401 Z= 0.315 Chirality : 0.044 0.187 4096 Planarity : 0.003 0.042 4613 Dihedral : 4.353 58.578 3320 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.59 % Allowed : 14.10 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3293 helix: 0.18 (0.25), residues: 443 sheet: 0.57 (0.19), residues: 773 loop : -0.91 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 631 HIS 0.002 0.001 HIS D 358 PHE 0.010 0.001 PHE A 710 TYR 0.012 0.001 TYR D 260 ARG 0.000 0.000 ARG E 667 Details of bonding type rmsd hydrogen bonds : bond 0.02956 ( 702) hydrogen bonds : angle 5.39180 ( 1821) covalent geometry : bond 0.00404 (26217) covalent geometry : angle 0.57360 (35401) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 3.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8204 (mp0) cc_final: 0.7878 (mp0) REVERT: A 286 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8594 (tp) REVERT: A 303 MET cc_start: 0.7303 (mpp) cc_final: 0.6763 (mpp) REVERT: A 695 ASP cc_start: 0.7617 (m-30) cc_final: 0.7264 (m-30) REVERT: A 732 LEU cc_start: 0.8376 (mt) cc_final: 0.8070 (pp) REVERT: C 303 MET cc_start: 0.8448 (tpp) cc_final: 0.8248 (tpp) REVERT: C 692 GLN cc_start: 0.7700 (tp-100) cc_final: 0.7177 (tp-100) REVERT: D 741 ASN cc_start: 0.7746 (t0) cc_final: 0.7190 (m-40) REVERT: F 702 ASP cc_start: 0.7714 (t0) cc_final: 0.7493 (t0) REVERT: G 336 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8872 (p) REVERT: G 519 ASP cc_start: 0.8635 (t0) cc_final: 0.8336 (t0) outliers start: 47 outliers final: 39 residues processed: 191 average time/residue: 0.3165 time to fit residues: 104.8505 Evaluate side-chains 192 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 463 TYR Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 713 THR Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 476 LYS Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 536 ASN Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 725 THR Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 568 ILE Chi-restraints excluded: chain G residue 684 THR Chi-restraints excluded: chain G residue 739 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 156 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 chunk 301 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 253 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 311 optimal weight: 0.2980 chunk 295 optimal weight: 8.9990 chunk 252 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 259 optimal weight: 9.9990 overall best weight: 5.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.078117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.057363 restraints weight = 99180.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.059096 restraints weight = 50585.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.060203 restraints weight = 33313.396| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26217 Z= 0.173 Angle : 0.572 14.189 35401 Z= 0.314 Chirality : 0.044 0.184 4096 Planarity : 0.003 0.041 4613 Dihedral : 4.340 57.761 3320 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.56 % Allowed : 14.20 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3293 helix: 0.20 (0.25), residues: 443 sheet: 0.55 (0.19), residues: 778 loop : -0.88 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 631 HIS 0.002 0.001 HIS D 358 PHE 0.010 0.001 PHE A 710 TYR 0.012 0.001 TYR D 260 ARG 0.000 0.000 ARG G 667 Details of bonding type rmsd hydrogen bonds : bond 0.02905 ( 702) hydrogen bonds : angle 5.32128 ( 1821) covalent geometry : bond 0.00379 (26217) covalent geometry : angle 0.57216 (35401) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 3.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8244 (mp0) cc_final: 0.7927 (mp0) REVERT: A 286 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8586 (tp) REVERT: A 303 MET cc_start: 0.7369 (mpp) cc_final: 0.6749 (mpp) REVERT: A 695 ASP cc_start: 0.7657 (m-30) cc_final: 0.7160 (m-30) REVERT: A 732 LEU cc_start: 0.8352 (mt) cc_final: 0.8075 (pp) REVERT: C 692 GLN cc_start: 0.7690 (tp-100) cc_final: 0.7177 (tp-100) REVERT: D 587 ILE cc_start: 0.9461 (mm) cc_final: 0.9236 (tp) REVERT: D 741 ASN cc_start: 0.7797 (t0) cc_final: 0.7210 (m-40) REVERT: E 476 LYS cc_start: 0.6206 (OUTLIER) cc_final: 0.5985 (mmmt) REVERT: G 336 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8863 (p) REVERT: G 519 ASP cc_start: 0.8600 (t0) cc_final: 0.8296 (t0) outliers start: 46 outliers final: 37 residues processed: 191 average time/residue: 0.3168 time to fit residues: 105.5793 Evaluate side-chains 194 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 3.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 463 TYR Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 713 THR Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 476 LYS Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 536 ASN Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain F residue 725 THR Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 568 ILE Chi-restraints excluded: chain G residue 684 THR Chi-restraints excluded: chain G residue 739 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 163 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 30.0000 chunk 284 optimal weight: 20.0000 chunk 61 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 270 optimal weight: 10.0000 chunk 319 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.076384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.055649 restraints weight = 99445.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.057328 restraints weight = 51042.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.058414 restraints weight = 33801.176| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 26217 Z= 0.276 Angle : 0.659 13.850 35401 Z= 0.357 Chirality : 0.046 0.192 4096 Planarity : 0.004 0.042 4613 Dihedral : 4.784 57.086 3320 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.49 % Allowed : 14.60 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3293 helix: 0.03 (0.25), residues: 438 sheet: 0.25 (0.19), residues: 767 loop : -0.98 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 502 HIS 0.003 0.002 HIS G 358 PHE 0.012 0.002 PHE A 710 TYR 0.013 0.002 TYR B 505 ARG 0.000 0.000 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 702) hydrogen bonds : angle 5.58663 ( 1821) covalent geometry : bond 0.00609 (26217) covalent geometry : angle 0.65910 (35401) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 4.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8281 (mp0) cc_final: 0.7913 (mp0) REVERT: A 732 LEU cc_start: 0.8401 (mt) cc_final: 0.8127 (pp) REVERT: C 692 GLN cc_start: 0.7765 (tp-100) cc_final: 0.7134 (tp-100) REVERT: G 519 ASP cc_start: 0.8645 (t0) cc_final: 0.8389 (t0) outliers start: 44 outliers final: 39 residues processed: 182 average time/residue: 0.3143 time to fit residues: 99.0903 Evaluate side-chains 179 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 463 TYR Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 713 THR Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 476 LYS Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 536 ASN Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain F residue 725 THR Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 568 ILE Chi-restraints excluded: chain G residue 739 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 234 optimal weight: 10.0000 chunk 317 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 244 optimal weight: 0.0070 chunk 114 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.078705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.057951 restraints weight = 98597.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059720 restraints weight = 49986.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.060806 restraints weight = 32901.913| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26217 Z= 0.138 Angle : 0.577 14.706 35401 Z= 0.314 Chirality : 0.045 0.171 4096 Planarity : 0.003 0.042 4613 Dihedral : 4.374 55.542 3320 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.28 % Allowed : 14.91 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 3293 helix: 0.15 (0.25), residues: 453 sheet: 0.42 (0.19), residues: 786 loop : -0.89 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 631 HIS 0.002 0.001 HIS D 358 PHE 0.009 0.001 PHE G 565 TYR 0.012 0.001 TYR D 260 ARG 0.000 0.000 ARG F 667 Details of bonding type rmsd hydrogen bonds : bond 0.02771 ( 702) hydrogen bonds : angle 5.28530 ( 1821) covalent geometry : bond 0.00297 (26217) covalent geometry : angle 0.57729 (35401) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7056.83 seconds wall clock time: 124 minutes 19.85 seconds (7459.85 seconds total)