Starting phenix.real_space_refine on Sun Jul 5 02:43:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsk_61775/07_2026/9jsk_61775.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsk_61775/07_2026/9jsk_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_61775/07_2026/9jsk_61775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsk_61775/07_2026/9jsk_61775.map" model { file = "/net/cci-nas-00/data/ceres_data/9jsk_61775/07_2026/9jsk_61775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsk_61775/07_2026/9jsk_61775.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Time building chain proxies: 6.12, per 1000 atoms: 0.24 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: 2.23 Conformation dependent library (CDL) restraints added in 1.1 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: 0.88 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: 4.55 Time building geometry restraints manager: 2.94 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 903)) selection = (chain 'C' and (resid 216 through 306 or resid 308 through 386 or resid 389 thro \ ugh 449 or resid 461 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 23.470 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 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 : 7.37 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (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 ARG 0.000 0.000 ARG G 324 TYR 0.013 0.001 TYR G 260 PHE 0.011 0.001 PHE G 565 TRP 0.005 0.001 TRP B 502 HIS 0.002 0.001 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (26217) covalent geometry : angle 0.50102 / 0.28 (35401) hydrogen bonds : bond 0.25860 / 16.81 ( 702) hydrogen bonds : angle 9.75013 / 6.73 ( 1821) *********************** 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 : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 711 GLU cc_start: 0.7571 (mp0) cc_final: 0.6845 (tp30) REVERT: G 334 ASN cc_start: 0.6737 (m-40) cc_final: 0.6459 (m-40) outliers start: 4 outliers final: 3 residues processed: 339 average time/residue: 0.1450 time to fit residues: 80.5511 Evaluate side-chains 193 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 197 optimal weight: 40.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 10.0000 overall best weight: 10.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 647 ASN D 251 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 566 ASN ** 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 = 0.3546 r_free = 0.3546 target = 0.079545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.058348 restraints weight = 97713.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.060058 restraints weight = 50139.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.061168 restraints weight = 33383.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.061852 restraints weight = 25931.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.062226 restraints weight = 22265.933| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 26217 Z= 0.281 Angle : 0.682 10.596 35401 Z= 0.373 Chirality : 0.047 0.189 4096 Planarity : 0.004 0.049 4613 Dihedral : 4.821 52.877 3326 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.15 % Allowed : 8.92 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3293 helix: -0.41 (0.25), residues: 433 sheet: 0.63 (0.20), residues: 730 loop : -0.99 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 527 TYR 0.014 0.002 TYR D 260 PHE 0.012 0.002 PHE G 565 TRP 0.007 0.001 TRP F 244 HIS 0.003 0.002 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.28 (26217) covalent geometry : angle 0.68166 / 0.37 (35401) hydrogen bonds : bond 0.04559 / 2.97 ( 702) hydrogen bonds : angle 6.68294 / 4.58 ( 1821) *********************** 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 210 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.7567 (tpp) cc_final: 0.7250 (mpp) REVERT: A 695 ASP cc_start: 0.7550 (m-30) cc_final: 0.7247 (m-30) REVERT: A 732 LEU cc_start: 0.8414 (mt) cc_final: 0.8213 (pp) REVERT: C 451 MET cc_start: 0.7093 (ttt) cc_final: 0.6817 (ttm) REVERT: E 287 GLU cc_start: 0.8623 (pm20) cc_final: 0.8371 (pm20) REVERT: E 561 GLU cc_start: 0.7968 (pm20) cc_final: 0.7669 (pp20) REVERT: E 688 LYS cc_start: 0.8500 (mttp) cc_final: 0.8277 (tptp) REVERT: G 519 ASP cc_start: 0.8752 (t0) cc_final: 0.8399 (t0) outliers start: 34 outliers final: 26 residues processed: 198 average time/residue: 0.1325 time to fit residues: 44.3276 Evaluate side-chains 177 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 650 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 463 TYR Chi-restraints excluded: chain D residue 506 ILE 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 564 TYR 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 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 650 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 206 optimal weight: 8.9990 chunk 132 optimal weight: 0.0270 chunk 39 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 127 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 overall best weight: 5.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 692 GLN ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.079937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.058718 restraints weight = 97841.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.060480 restraints weight = 49938.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.061602 restraints weight = 32971.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.062292 restraints weight = 25570.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.062715 restraints weight = 21920.580| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26217 Z= 0.175 Angle : 0.576 10.641 35401 Z= 0.319 Chirality : 0.045 0.169 4096 Planarity : 0.004 0.046 4613 Dihedral : 4.550 55.628 3322 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.52 % Allowed : 10.78 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3293 helix: -0.20 (0.25), residues: 444 sheet: 0.54 (0.19), residues: 772 loop : -0.95 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 667 TYR 0.013 0.001 TYR D 260 PHE 0.016 0.001 PHE E 731 TRP 0.007 0.001 TRP F 244 HIS 0.002 0.001 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (26217) covalent geometry : angle 0.57584 / 0.32 (35401) hydrogen bonds : bond 0.03631 / 2.36 ( 702) hydrogen bonds : angle 6.09269 / 4.18 ( 1821) *********************** 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 217 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8627 (tp) REVERT: A 695 ASP cc_start: 0.7511 (m-30) cc_final: 0.7244 (m-30) REVERT: A 732 LEU cc_start: 0.8386 (mt) cc_final: 0.8145 (pp) REVERT: C 659 MET cc_start: 0.7274 (tpp) cc_final: 0.6479 (mmm) REVERT: E 287 GLU cc_start: 0.8534 (pm20) cc_final: 0.8304 (pm20) REVERT: E 688 LYS cc_start: 0.8468 (mttp) cc_final: 0.8246 (tptp) REVERT: G 519 ASP cc_start: 0.8725 (t0) cc_final: 0.8351 (t0) outliers start: 45 outliers final: 28 residues processed: 199 average time/residue: 0.1264 time to fit residues: 42.6444 Evaluate side-chains 188 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 388 ILE 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 458 LEU 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 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 392 VAL 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 268 optimal weight: 10.0000 chunk 300 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 chunk 313 optimal weight: 9.9990 chunk 273 optimal weight: 6.9990 chunk 280 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 GLN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN D 431 ASN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 638 ASN ** 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 = 0.3560 r_free = 0.3560 target = 0.079917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.058721 restraints weight = 96905.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.060453 restraints weight = 49381.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.061584 restraints weight = 32791.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.062284 restraints weight = 25379.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.062710 restraints weight = 21745.957| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26217 Z= 0.152 Angle : 0.553 11.584 35401 Z= 0.306 Chirality : 0.044 0.162 4096 Planarity : 0.003 0.044 4613 Dihedral : 4.300 57.342 3320 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.62 % Allowed : 11.93 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.14), residues: 3293 helix: 0.07 (0.26), residues: 443 sheet: 0.49 (0.19), residues: 793 loop : -0.90 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 667 TYR 0.012 0.001 TYR D 260 PHE 0.011 0.001 PHE G 565 TRP 0.007 0.001 TRP E 631 HIS 0.002 0.001 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (26217) covalent geometry : angle 0.55303 / 0.31 (35401) hydrogen bonds : bond 0.03199 / 2.08 ( 702) hydrogen bonds : angle 5.73504 / 3.95 ( 1821) *********************** 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 220 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 172 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8632 (tp) REVERT: A 695 ASP cc_start: 0.7505 (m-30) cc_final: 0.7277 (m-30) REVERT: A 732 LEU cc_start: 0.8332 (mt) cc_final: 0.8099 (pp) REVERT: B 608 MET cc_start: 0.8720 (mtt) cc_final: 0.8471 (mtm) REVERT: C 476 LYS cc_start: 0.9056 (tppt) cc_final: 0.8821 (tppt) REVERT: D 659 MET cc_start: 0.7425 (tmm) cc_final: 0.6928 (tmm) REVERT: E 287 GLU cc_start: 0.8501 (pm20) cc_final: 0.8234 (pm20) REVERT: E 332 ASP cc_start: 0.7146 (m-30) cc_final: 0.6944 (m-30) REVERT: E 688 LYS cc_start: 0.8444 (mttp) cc_final: 0.8184 (tptp) REVERT: G 519 ASP cc_start: 0.8662 (t0) cc_final: 0.8295 (t0) outliers start: 48 outliers final: 31 residues processed: 207 average time/residue: 0.1283 time to fit residues: 45.4485 Evaluate side-chains 187 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU 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 488 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 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 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 479 THR Chi-restraints excluded: chain E residue 564 TYR 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 124 optimal weight: 40.0000 chunk 249 optimal weight: 0.8980 chunk 272 optimal weight: 10.0000 chunk 310 optimal weight: 8.9990 chunk 260 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 ASN A 494 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN C 474 GLN D 410 ASN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 ASN ** 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 328 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 = 0.3542 r_free = 0.3542 target = 0.079038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.057938 restraints weight = 97242.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.059665 restraints weight = 49901.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.060791 restraints weight = 33136.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.061476 restraints weight = 25677.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.061895 restraints weight = 22004.612| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2616 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= 0.176 Angle : 0.558 11.702 35401 Z= 0.309 Chirality : 0.044 0.158 4096 Planarity : 0.004 0.043 4613 Dihedral : 4.331 59.128 3320 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.66 % Allowed : 13.12 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.14), residues: 3293 helix: 0.15 (0.26), residues: 438 sheet: 0.56 (0.19), residues: 766 loop : -0.91 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 324 TYR 0.012 0.001 TYR D 260 PHE 0.010 0.001 PHE D 554 TRP 0.006 0.001 TRP E 631 HIS 0.002 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (26217) covalent geometry : angle 0.55799 / 0.31 (35401) hydrogen bonds : bond 0.03125 / 2.03 ( 702) hydrogen bonds : angle 5.52472 / 3.80 ( 1821) *********************** 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 205 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7683 (mp0) cc_final: 0.7442 (mp0) REVERT: A 286 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8610 (tp) REVERT: A 690 LYS cc_start: 0.4952 (OUTLIER) cc_final: 0.4294 (mmtm) REVERT: A 695 ASP cc_start: 0.7532 (m-30) cc_final: 0.7208 (m-30) REVERT: D 587 ILE cc_start: 0.9492 (mm) cc_final: 0.9255 (tp) REVERT: E 287 GLU cc_start: 0.8516 (pm20) cc_final: 0.8236 (pm20) REVERT: E 688 LYS cc_start: 0.8492 (mttp) cc_final: 0.8168 (tptp) REVERT: G 519 ASP cc_start: 0.8684 (t0) cc_final: 0.8360 (t0) outliers start: 49 outliers final: 33 residues processed: 194 average time/residue: 0.1347 time to fit residues: 44.7525 Evaluate side-chains 183 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU 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 690 LYS Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 724 LEU 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 477 LEU 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 376 THR Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 443 LEU 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 411 LEU Chi-restraints excluded: chain F residue 536 ASN 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 684 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 83 optimal weight: 40.0000 chunk 2 optimal weight: 20.0000 chunk 318 optimal weight: 9.9990 chunk 243 optimal weight: 20.0000 chunk 281 optimal weight: 20.0000 chunk 220 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 320 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 159 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 ASN ** 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 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 = 0.3524 r_free = 0.3524 target = 0.078116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.057105 restraints weight = 97307.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.058820 restraints weight = 50063.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.059919 restraints weight = 33271.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.060602 restraints weight = 25839.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.060975 restraints weight = 22186.735| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2863 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= 0.200 Angle : 0.581 12.396 35401 Z= 0.319 Chirality : 0.045 0.157 4096 Planarity : 0.004 0.044 4613 Dihedral : 4.463 59.639 3320 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.83 % Allowed : 13.69 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.14), residues: 3293 helix: 0.08 (0.25), residues: 450 sheet: 0.54 (0.19), residues: 768 loop : -0.96 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 667 TYR 0.012 0.001 TYR D 260 PHE 0.010 0.001 PHE F 710 TRP 0.006 0.001 TRP E 631 HIS 0.003 0.001 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (26217) covalent geometry : angle 0.58085 / 0.32 (35401) hydrogen bonds : bond 0.03131 / 2.06 ( 702) hydrogen bonds : angle 5.48721 / 3.78 ( 1821) *********************** 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 211 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 157 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7649 (mp0) cc_final: 0.7393 (mp0) REVERT: A 286 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8600 (tp) REVERT: A 695 ASP cc_start: 0.7607 (m-30) cc_final: 0.7219 (m-30) REVERT: A 732 LEU cc_start: 0.8371 (mt) cc_final: 0.8145 (pp) REVERT: B 643 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7108 (pm20) REVERT: D 587 ILE cc_start: 0.9469 (mm) cc_final: 0.9248 (tp) REVERT: E 287 GLU cc_start: 0.8445 (pm20) cc_final: 0.8197 (pm20) REVERT: E 688 LYS cc_start: 0.8453 (mttp) cc_final: 0.8195 (tptp) REVERT: G 519 ASP cc_start: 0.8659 (t0) cc_final: 0.8353 (t0) outliers start: 54 outliers final: 41 residues processed: 198 average time/residue: 0.1532 time to fit residues: 51.5507 Evaluate side-chains 189 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU 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 A residue 724 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 643 GLN 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 308 ILE Chi-restraints excluded: chain D residue 463 TYR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 570 ILE 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 392 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 443 LEU 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 411 LEU Chi-restraints excluded: chain F residue 536 ASN Chi-restraints excluded: chain F residue 636 THR 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 606 ARG Chi-restraints excluded: chain G residue 684 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 210 optimal weight: 6.9990 chunk 111 optimal weight: 0.3980 chunk 149 optimal weight: 20.0000 chunk 230 optimal weight: 20.0000 chunk 214 optimal weight: 8.9990 chunk 284 optimal weight: 7.9990 chunk 163 optimal weight: 0.2980 chunk 270 optimal weight: 7.9990 chunk 182 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.079182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.058325 restraints weight = 96340.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.060044 restraints weight = 49221.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.061159 restraints weight = 32603.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.061857 restraints weight = 25205.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.062236 restraints weight = 21561.529| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26217 Z= 0.137 Angle : 0.556 12.748 35401 Z= 0.305 Chirality : 0.044 0.171 4096 Planarity : 0.003 0.042 4613 Dihedral : 4.257 58.794 3320 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.66 % Allowed : 14.13 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 3293 helix: 0.26 (0.26), residues: 450 sheet: 0.63 (0.19), residues: 774 loop : -0.87 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 527 TYR 0.011 0.001 TYR D 260 PHE 0.009 0.001 PHE A 710 TRP 0.008 0.001 TRP E 631 HIS 0.002 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (26217) covalent geometry : angle 0.55632 / 0.30 (35401) hydrogen bonds : bond 0.02810 / 1.83 ( 702) hydrogen bonds : angle 5.29263 / 3.64 ( 1821) *********************** 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 213 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7561 (mp0) cc_final: 0.7299 (mp0) REVERT: A 286 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8601 (tp) REVERT: A 695 ASP cc_start: 0.7618 (m-30) cc_final: 0.7244 (m-30) REVERT: B 643 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7102 (pm20) REVERT: C 303 MET cc_start: 0.8426 (tpp) cc_final: 0.8206 (tpp) REVERT: C 692 GLN cc_start: 0.7596 (tp-100) cc_final: 0.7087 (tp-100) REVERT: D 587 ILE cc_start: 0.9485 (mm) cc_final: 0.9242 (tp) REVERT: D 659 MET cc_start: 0.7399 (tmm) cc_final: 0.7059 (tmm) REVERT: E 287 GLU cc_start: 0.8406 (pm20) cc_final: 0.8191 (pt0) REVERT: E 688 LYS cc_start: 0.8425 (mttp) cc_final: 0.8161 (tptp) REVERT: G 336 VAL cc_start: 0.9140 (OUTLIER) cc_final: 0.8865 (p) REVERT: G 519 ASP cc_start: 0.8598 (t0) cc_final: 0.8274 (t0) outliers start: 49 outliers final: 36 residues processed: 200 average time/residue: 0.1539 time to fit residues: 53.0934 Evaluate side-chains 186 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 307 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 A residue 724 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 643 GLN Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 707 SER 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 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 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 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 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 336 VAL Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 606 ARG Chi-restraints excluded: chain G residue 684 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 231 optimal weight: 30.0000 chunk 171 optimal weight: 10.0000 chunk 270 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 169 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 259 optimal weight: 9.9990 chunk 206 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.077596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.056757 restraints weight = 98402.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.058451 restraints weight = 50543.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.059548 restraints weight = 33619.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.060169 restraints weight = 26102.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.060620 restraints weight = 22531.094| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 26217 Z= 0.217 Angle : 0.599 12.659 35401 Z= 0.328 Chirality : 0.045 0.174 4096 Planarity : 0.004 0.043 4613 Dihedral : 4.516 58.091 3320 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.99 % Allowed : 14.33 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3293 helix: 0.13 (0.25), residues: 450 sheet: 0.50 (0.19), residues: 774 loop : -0.94 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 324 TYR 0.011 0.001 TYR D 260 PHE 0.010 0.001 PHE A 710 TRP 0.006 0.001 TRP E 502 HIS 0.003 0.002 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 (26217) covalent geometry : angle 0.59909 / 0.33 (35401) hydrogen bonds : bond 0.03093 / 2.04 ( 702) hydrogen bonds : angle 5.40635 / 3.71 ( 1821) *********************** 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 206 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 147 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7674 (mp0) cc_final: 0.7413 (mp0) REVERT: A 286 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8609 (tp) REVERT: A 303 MET cc_start: 0.7324 (mpp) cc_final: 0.6865 (mpp) REVERT: A 451 MET cc_start: 0.7102 (pmm) cc_final: 0.6639 (pmm) REVERT: A 695 ASP cc_start: 0.7648 (m-30) cc_final: 0.7301 (m-30) REVERT: A 732 LEU cc_start: 0.8426 (mt) cc_final: 0.8141 (pp) REVERT: B 643 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7152 (pm20) REVERT: C 303 MET cc_start: 0.8406 (tpp) cc_final: 0.8200 (tpp) REVERT: C 692 GLN cc_start: 0.7651 (tp-100) cc_final: 0.7317 (mm110) REVERT: F 258 SER cc_start: 0.9429 (OUTLIER) cc_final: 0.9211 (p) REVERT: F 303 MET cc_start: 0.8217 (tpt) cc_final: 0.7991 (tpt) REVERT: F 461 ILE cc_start: 0.3708 (OUTLIER) cc_final: 0.3427 (mt) REVERT: G 336 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8868 (p) REVERT: G 519 ASP cc_start: 0.8657 (t0) cc_final: 0.8393 (t0) outliers start: 59 outliers final: 42 residues processed: 197 average time/residue: 0.1523 time to fit residues: 51.2862 Evaluate side-chains 190 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 634 ILE 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 488 THR Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 643 GLN Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 707 SER 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 308 ILE Chi-restraints excluded: chain D residue 411 LEU 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 286 LEU 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 479 THR Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 461 ILE 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 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 606 ARG Chi-restraints excluded: chain G residue 684 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 99 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 170 optimal weight: 7.9990 chunk 325 optimal weight: 9.9990 chunk 289 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 239 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.078470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.057787 restraints weight = 98058.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.059525 restraints weight = 49652.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.060648 restraints weight = 32748.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.061335 restraints weight = 25354.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.061750 restraints weight = 21764.557| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26217 Z= 0.168 Angle : 0.578 14.231 35401 Z= 0.316 Chirality : 0.045 0.166 4096 Planarity : 0.003 0.042 4613 Dihedral : 4.414 57.427 3320 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.83 % Allowed : 14.74 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 3293 helix: 0.24 (0.26), residues: 444 sheet: 0.48 (0.19), residues: 778 loop : -0.90 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 289 TYR 0.012 0.001 TYR D 260 PHE 0.009 0.001 PHE A 710 TRP 0.008 0.001 TRP E 631 HIS 0.003 0.001 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (26217) covalent geometry : angle 0.57792 / 0.32 (35401) hydrogen bonds : bond 0.02874 / 1.87 ( 702) hydrogen bonds : angle 5.29416 / 3.64 ( 1821) *********************** 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 206 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 152 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7574 (mp0) cc_final: 0.7327 (mp0) REVERT: A 286 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8555 (tp) REVERT: A 303 MET cc_start: 0.7284 (mpp) cc_final: 0.6787 (mpp) REVERT: A 695 ASP cc_start: 0.7609 (m-30) cc_final: 0.7303 (m-30) REVERT: A 711 GLU cc_start: 0.7715 (mp0) cc_final: 0.6568 (tm-30) REVERT: A 732 LEU cc_start: 0.8361 (mt) cc_final: 0.8110 (pp) REVERT: B 526 GLU cc_start: 0.7210 (tp30) cc_final: 0.7001 (tp30) REVERT: C 692 GLN cc_start: 0.7609 (tp-100) cc_final: 0.7284 (mm110) REVERT: D 587 ILE cc_start: 0.9454 (mm) cc_final: 0.9232 (tp) REVERT: F 303 MET cc_start: 0.8116 (tpt) cc_final: 0.7880 (tpt) REVERT: F 461 ILE cc_start: 0.3780 (OUTLIER) cc_final: 0.3489 (mt) REVERT: G 336 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8833 (p) REVERT: G 519 ASP cc_start: 0.8586 (t0) cc_final: 0.8304 (t0) outliers start: 54 outliers final: 44 residues processed: 197 average time/residue: 0.1512 time to fit residues: 51.1382 Evaluate side-chains 194 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 634 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 544 ILE Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 707 SER 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 308 ILE Chi-restraints excluded: chain D residue 411 LEU 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 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 479 THR Chi-restraints excluded: chain E residue 564 TYR 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 411 LEU Chi-restraints excluded: chain F residue 461 ILE 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 F residue 737 ILE 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 606 ARG Chi-restraints excluded: chain G residue 684 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 224 optimal weight: 30.0000 chunk 263 optimal weight: 3.9990 chunk 85 optimal weight: 0.0980 chunk 321 optimal weight: 0.9980 chunk 153 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 272 optimal weight: 40.0000 chunk 59 optimal weight: 0.9990 chunk 2 optimal weight: 20.0000 chunk 88 optimal weight: 8.9990 chunk 135 optimal weight: 20.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.079624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058872 restraints weight = 97638.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.060685 restraints weight = 49567.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061818 restraints weight = 32556.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.062525 restraints weight = 25198.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.062973 restraints weight = 21557.457| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26217 Z= 0.132 Angle : 0.570 14.627 35401 Z= 0.310 Chirality : 0.044 0.167 4096 Planarity : 0.003 0.042 4613 Dihedral : 4.214 56.423 3320 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.49 % Allowed : 15.28 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.15), residues: 3293 helix: 0.30 (0.26), residues: 449 sheet: 0.57 (0.19), residues: 798 loop : -0.84 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 324 TYR 0.011 0.001 TYR A 708 PHE 0.008 0.001 PHE A 710 TRP 0.008 0.001 TRP E 631 HIS 0.002 0.001 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (26217) covalent geometry : angle 0.56975 / 0.31 (35401) hydrogen bonds : bond 0.02672 / 1.72 ( 702) hydrogen bonds : angle 5.12595 / 3.53 ( 1821) ********************** 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 200 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7522 (mp0) cc_final: 0.7246 (mp0) REVERT: A 303 MET cc_start: 0.7222 (mpp) cc_final: 0.6783 (mpp) REVERT: A 695 ASP cc_start: 0.7655 (m-30) cc_final: 0.7334 (m-30) REVERT: B 526 GLU cc_start: 0.7208 (tp30) cc_final: 0.6980 (tp30) REVERT: C 692 GLN cc_start: 0.7614 (tp-100) cc_final: 0.7146 (tp-100) REVERT: C 724 LEU cc_start: 0.9127 (tt) cc_final: 0.8742 (pp) REVERT: D 587 ILE cc_start: 0.9474 (mm) cc_final: 0.9241 (tp) REVERT: F 303 MET cc_start: 0.8137 (tpt) cc_final: 0.7856 (tpt) REVERT: F 461 ILE cc_start: 0.3715 (OUTLIER) cc_final: 0.3425 (mt) REVERT: G 336 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8847 (p) REVERT: G 519 ASP cc_start: 0.8573 (t0) cc_final: 0.8246 (t0) outliers start: 44 outliers final: 39 residues processed: 190 average time/residue: 0.1472 time to fit residues: 48.0419 Evaluate side-chains 193 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 406 THR 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 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 653 THR Chi-restraints excluded: chain B residue 707 SER 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 308 ILE 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 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 479 THR Chi-restraints excluded: chain E residue 564 TYR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 332 ASP 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 461 ILE 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 F residue 737 ILE Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 606 ARG Chi-restraints excluded: chain G residue 684 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 130 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 21 optimal weight: 0.0870 chunk 67 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 overall best weight: 5.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.3554 r_free = 0.3554 target = 0.079023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.058284 restraints weight = 97291.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.060051 restraints weight = 49781.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.061180 restraints weight = 32948.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.061808 restraints weight = 25538.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.062281 restraints weight = 22082.214| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26217 Z= 0.159 Angle : 0.579 14.498 35401 Z= 0.314 Chirality : 0.044 0.164 4096 Planarity : 0.003 0.042 4613 Dihedral : 4.237 55.842 3320 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.49 % Allowed : 15.45 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 3293 helix: 0.24 (0.26), residues: 448 sheet: 0.55 (0.19), residues: 779 loop : -0.82 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 457 TYR 0.011 0.001 TYR D 260 PHE 0.009 0.001 PHE A 710 TRP 0.006 0.001 TRP E 631 HIS 0.002 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (26217) covalent geometry : angle 0.57872 / 0.31 (35401) hydrogen bonds : bond 0.02740 / 1.77 ( 702) hydrogen bonds : angle 5.10853 / 3.51 ( 1821) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3646.41 seconds wall clock time: 64 minutes 25.92 seconds (3865.92 seconds total)