Starting phenix.real_space_refine on Sun Jul 5 01:00:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsm_61777/07_2026/9jsm_61777.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsm_61777/07_2026/9jsm_61777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jsm_61777/07_2026/9jsm_61777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsm_61777/07_2026/9jsm_61777.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jsm_61777/07_2026/9jsm_61777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsm_61777/07_2026/9jsm_61777.map" } resolution = 3.73 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= 0.013 sd= 0.084 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 40 5.16 5 C 16020 2.51 5 N 4012 2.21 5 O 5116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s 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: 25209 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3514 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 433} Chain breaks: 1 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: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3514 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 433} Chain breaks: 1 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: 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: "D" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3514 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 433} Chain breaks: 1 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: "E" Number of atoms: 3490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3490 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: "F" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3847 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 479} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 44 Chain: "G" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3821 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 477} 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: 5.89, per 1000 atoms: 0.23 Number of scatterers: 25209 At special positions: 0 Unit cell: (176.88, 176.88, 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 40 16.00 O 5116 8.00 N 4012 7.00 C 16020 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: 2.14 Conformation dependent library (CDL) restraints added in 1.1 seconds 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6124 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 66 sheets defined 17.5% alpha, 33.1% 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 233 removed outlier: 3.698A pdb=" N ASN A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.787A pdb=" N ALA A 249 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.936A pdb=" N ASP A 290 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.952A pdb=" N ILE A 428 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 470 Processing helix chain 'A' and resid 502 through 512 removed outlier: 4.601A pdb=" N SER A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 Processing helix chain 'A' and resid 580 through 592 removed outlier: 3.619A pdb=" N GLU A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.551A pdb=" N ASN B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 252 removed outlier: 3.652A pdb=" N ALA B 249 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU B 250 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 285 through 290 removed outlier: 3.597A pdb=" N ASP B 290 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 470 Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 545 through 555 Processing helix chain 'B' and resid 571 through 575 removed outlier: 3.596A pdb=" N VAL B 575 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 592 removed outlier: 4.007A 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 233 Processing helix chain 'C' and resid 245 through 249 removed outlier: 3.537A pdb=" N ALA C 249 " --> pdb=" O ASP C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 424 through 428 removed outlier: 4.134A pdb=" N ILE C 428 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 471 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 506 through 512 removed outlier: 3.660A pdb=" N VAL C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 555 Processing helix chain 'C' and resid 580 through 593 removed outlier: 3.553A pdb=" N GLU C 589 " --> pdb=" O GLU C 585 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR C 593 " --> pdb=" O GLU C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 602 Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 245 through 249 removed outlier: 3.500A 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 289 removed outlier: 3.658A pdb=" N ARG D 289 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 471 removed outlier: 4.371A pdb=" N LEU D 466 " --> pdb=" O ASN D 462 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 504 No H-bonds generated for 'chain 'D' and resid 502 through 504' Processing helix chain 'D' and resid 505 through 511 removed outlier: 3.792A pdb=" N ILE D 509 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER D 511 " --> pdb=" O SER D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 555 removed outlier: 3.570A pdb=" N LYS D 551 " --> pdb=" O GLY D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 575 removed outlier: 3.871A pdb=" N VAL D 575 " --> pdb=" O GLU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 592 removed outlier: 3.602A pdb=" N GLU D 585 " --> pdb=" O ASP D 581 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 586 " --> pdb=" O ASN D 582 " (cutoff:3.500A) removed outlier: 4.007A 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 'E' and resid 226 through 233 Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 271 through 278 Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 424 through 428 removed outlier: 3.838A pdb=" N ILE E 428 " --> pdb=" O ASP E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 470 removed outlier: 3.829A pdb=" N LYS E 468 " --> pdb=" O ASP E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 512 Processing helix chain 'E' and resid 545 through 554 removed outlier: 3.657A pdb=" N LYS E 551 " --> pdb=" O GLY E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 575 removed outlier: 3.840A pdb=" N VAL E 575 " --> pdb=" O GLU E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 593 removed outlier: 3.523A pdb=" N ILE E 586 " --> pdb=" O ASN E 582 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR E 593 " --> pdb=" O GLU E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 602 Processing helix chain 'F' and resid 226 through 233 removed outlier: 3.524A pdb=" N ASN F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 252 removed outlier: 3.733A pdb=" N ALA F 249 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU F 250 " --> pdb=" O SER F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 278 Processing helix chain 'F' and resid 285 through 289 Processing helix chain 'F' and resid 331 through 336 removed outlier: 3.640A pdb=" N THR F 335 " --> pdb=" O THR F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 502 through 504 No H-bonds generated for 'chain 'F' and resid 502 through 504' Processing helix chain 'F' and resid 505 through 510 Processing helix chain 'F' and resid 545 through 555 Processing helix chain 'F' and resid 571 through 575 removed outlier: 3.810A pdb=" N VAL F 575 " --> pdb=" O GLU F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 592 removed outlier: 3.737A 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 'G' and resid 226 through 233 removed outlier: 3.627A pdb=" N ASN G 232 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 249 removed outlier: 3.701A pdb=" N ALA G 249 " --> pdb=" O ASP G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 278 Processing helix chain 'G' and resid 285 through 290 removed outlier: 3.804A pdb=" N ASP G 290 " --> pdb=" O GLU G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 336 Processing helix chain 'G' and resid 462 through 471 removed outlier: 3.548A pdb=" N LEU G 466 " --> pdb=" O ASN G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 512 removed outlier: 3.762A pdb=" N SER G 511 " --> pdb=" O SER G 507 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL G 512 " --> pdb=" O GLN G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 555 Processing helix chain 'G' and resid 580 through 591 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 309 removed outlier: 5.129A pdb=" N VAL A 301 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR A 395 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N MET A 303 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG A 393 " --> pdb=" O MET A 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 309 removed outlier: 5.129A pdb=" N VAL A 301 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR A 395 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N MET A 303 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG A 393 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 390 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 417 through 422 removed outlier: 3.721A pdb=" N GLN A 481 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN A 410 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR A 479 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL A 412 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU A 477 " --> pdb=" O VAL A 412 " (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 513 through 519 Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 559 removed outlier: 4.151A pdb=" N LEU A 562 " --> pdb=" O ASN A 559 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 576 through 579 removed outlier: 3.624A pdb=" N GLU A 576 " --> pdb=" O LYS A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 617 through 619 removed outlier: 3.536A pdb=" N TYR A 617 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 684 " --> pdb=" O THR A 725 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 647 through 657 removed outlier: 3.865A pdb=" N GLY A 651 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLY A 728 " --> pdb=" O GLY A 651 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR A 653 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N SER A 726 " --> pdb=" O THR A 653 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE A 655 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU A 724 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE A 657 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE A 722 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU A 732 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LYS A 675 " --> pdb=" O LEU A 732 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASN A 734 " --> pdb=" O TYR A 673 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 673 " --> pdb=" O ASN A 734 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG A 667 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 712 " --> pdb=" O LYS A 666 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 672 " --> pdb=" O PHE A 706 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB3, first strand: chain 'B' and resid 299 through 300 Processing sheet with id=AB4, first strand: chain 'B' and resid 303 through 309 removed outlier: 6.710A pdb=" N ASN B 391 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU B 306 " --> pdb=" O ASN B 389 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN B 389 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE B 308 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR B 387 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 417 through 422 removed outlier: 3.930A pdb=" N ALA B 419 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL B 405 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER B 483 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLN B 481 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR B 409 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR B 479 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU B 411 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU B 477 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AB7, first strand: chain 'B' and resid 524 through 530 removed outlier: 3.618A pdb=" N LYS B 613 " --> pdb=" O GLU B 576 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU B 576 " --> pdb=" O LYS B 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 557 through 559 removed outlier: 4.321A pdb=" N LEU B 562 " --> pdb=" O ASN B 559 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 617 through 619 removed outlier: 3.512A pdb=" N THR B 684 " --> pdb=" O THR B 725 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 647 through 657 removed outlier: 5.802A pdb=" N ASN B 647 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE B 730 " --> pdb=" O ASN B 647 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 649 " --> pdb=" O GLY B 728 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY B 728 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY B 651 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 722 " --> pdb=" O ILE B 655 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE B 657 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE B 720 " --> pdb=" O ILE B 657 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU B 732 " --> pdb=" O LYS B 675 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LYS B 675 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASN B 734 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR B 673 " --> pdb=" O ASN B 734 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR B 738 " --> pdb=" O VAL B 669 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 672 " --> pdb=" O PHE B 706 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 234 through 237 Processing sheet with id=AC3, first strand: chain 'C' and resid 299 through 309 removed outlier: 5.178A pdb=" N VAL C 301 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR C 395 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N MET C 303 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG C 393 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 305 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 417 through 422 removed outlier: 6.619A pdb=" N LEU C 411 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR C 420 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N THR C 409 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS C 422 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS C 404 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY C 484 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR C 406 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL C 482 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N THR C 408 " --> pdb=" O THR C 480 " (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: 8.938A pdb=" N ILE C 610 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER C 515 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE C 612 " --> pdb=" O SER C 515 " (cutoff:3.500A) removed outlier: 6.298A 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: 4.163A 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 618 Processing sheet with id=AC9, first strand: chain 'C' and resid 647 through 656 removed outlier: 5.830A pdb=" N ASN C 647 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE C 730 " --> pdb=" O ASN C 647 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU C 649 " --> pdb=" O GLY C 728 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY C 728 " --> pdb=" O LEU C 649 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY C 651 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 722 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU C 732 " --> pdb=" O LYS C 675 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LYS C 675 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASN C 734 " --> pdb=" O TYR C 673 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR C 673 " --> pdb=" O ASN C 734 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE C 670 " --> pdb=" O TYR C 708 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR C 708 " --> pdb=" O PHE C 670 " (cutoff:3.500A) removed outlier: 3.548A 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 293 through 294 removed outlier: 4.864A pdb=" N ARG D 528 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS D 613 " --> pdb=" O GLU D 576 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU D 576 " --> pdb=" O LYS D 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 299 through 309 removed outlier: 5.231A pdb=" N VAL D 301 " --> pdb=" O TYR D 395 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TYR D 395 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N MET D 303 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG D 393 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 305 " --> pdb=" O ASN D 391 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 402 through 405 removed outlier: 6.730A pdb=" N ASN D 430 " --> pdb=" O LYS D 404 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 417 through 422 removed outlier: 6.545A pdb=" N LEU D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR D 420 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR D 409 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS D 422 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR D 408 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 478 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 450 through 452 removed outlier: 7.026A pdb=" N ALA D 456 " --> pdb=" O MET D 451 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AD8, first strand: chain 'D' and resid 557 through 558 Processing sheet with id=AD9, first strand: chain 'D' and resid 617 through 619 removed outlier: 3.614A pdb=" N THR D 684 " --> pdb=" O THR D 725 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 647 through 657 removed outlier: 5.839A pdb=" N ASN D 647 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE D 730 " --> pdb=" O ASN D 647 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU D 649 " --> pdb=" O GLY D 728 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY D 728 " --> pdb=" O LEU D 649 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY D 651 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 722 " --> pdb=" O ILE D 655 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE D 657 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE D 720 " --> pdb=" O ILE D 657 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU D 732 " --> pdb=" O LYS D 675 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LYS D 675 " --> pdb=" O LEU D 732 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASN D 734 " --> pdb=" O TYR D 673 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR D 673 " --> pdb=" O ASN D 734 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR D 738 " --> pdb=" O VAL D 669 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 234 through 237 Processing sheet with id=AE3, first strand: chain 'E' and resid 299 through 309 removed outlier: 5.316A pdb=" N VAL E 301 " --> pdb=" O TYR E 395 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR E 395 " --> pdb=" O VAL E 301 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N MET E 303 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG E 393 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN E 305 " --> pdb=" O ASN E 391 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 299 through 309 removed outlier: 5.316A pdb=" N VAL E 301 " --> pdb=" O TYR E 395 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR E 395 " --> pdb=" O VAL E 301 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N MET E 303 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG E 393 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN E 305 " --> pdb=" O ASN E 391 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU E 446 " --> pdb=" O VAL E 392 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 417 through 422 removed outlier: 4.151A pdb=" N ALA E 419 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR E 408 " --> pdb=" O THR E 480 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU E 478 " --> pdb=" O ASN E 410 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL E 412 " --> pdb=" O LYS E 476 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 488 through 489 removed outlier: 3.579A pdb=" N THR E 488 " --> pdb=" O ILE E 496 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 524 through 530 Processing sheet with id=AE8, first strand: chain 'E' and resid 557 through 559 removed outlier: 4.325A pdb=" N LEU E 562 " --> pdb=" O ASN E 559 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 617 through 619 removed outlier: 3.601A pdb=" N THR E 725 " --> pdb=" O THR E 684 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR E 684 " --> pdb=" O THR E 725 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP E 695 " --> pdb=" O VAL E 685 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE E 687 " --> pdb=" O LYS E 693 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 647 through 656 removed outlier: 5.694A pdb=" N ASN E 647 " --> pdb=" O ILE E 730 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE E 730 " --> pdb=" O ASN E 647 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU E 649 " --> pdb=" O GLY E 728 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLY E 728 " --> pdb=" O LEU E 649 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY E 651 " --> pdb=" O SER E 726 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU E 732 " --> pdb=" O LYS E 675 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LYS E 675 " --> pdb=" O LEU E 732 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ASN E 734 " --> pdb=" O TYR E 673 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR E 673 " --> pdb=" O ASN E 734 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG E 667 " --> pdb=" O LEU E 740 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE E 670 " --> pdb=" O TYR E 708 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR E 708 " --> pdb=" O PHE E 670 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY E 672 " --> pdb=" O PHE E 706 " (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 299 through 303 removed outlier: 3.753A pdb=" N GLU F 436 " --> pdb=" O ASN F 396 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 299 through 303 Processing sheet with id=AF5, first strand: chain 'F' and resid 326 through 329 removed outlier: 3.669A pdb=" N THR F 327 " --> pdb=" O ALA F 365 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER F 329 " --> pdb=" O SER F 363 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER F 363 " --> pdb=" O SER F 329 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 351 through 353 removed outlier: 3.569A pdb=" N PHE F 579 " --> pdb=" O ASN F 351 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN F 609 " --> pdb=" O ASP F 580 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N ILE F 610 " --> pdb=" O SER F 513 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER F 515 " --> pdb=" O ILE F 610 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE F 612 " --> pdb=" O SER F 515 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE F 517 " --> pdb=" O ILE F 612 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 416 through 422 removed outlier: 7.220A pdb=" N LEU F 411 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR F 420 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR F 409 " --> pdb=" O THR F 420 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYS F 422 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS F 404 " --> pdb=" O GLY F 484 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY F 484 " --> pdb=" O LYS F 404 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR F 406 " --> pdb=" O VAL F 482 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N VAL F 482 " --> pdb=" O THR F 406 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR F 408 " --> pdb=" O THR F 480 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 557 through 559 Processing sheet with id=AF9, first strand: chain 'F' and resid 617 through 619 removed outlier: 3.906A pdb=" N LEU F 732 " --> pdb=" O ASN F 647 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN F 647 " --> pdb=" O LEU F 732 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 617 through 619 removed outlier: 8.120A pdb=" N ASP F 733 " --> pdb=" O LYS F 675 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LYS F 675 " --> pdb=" O ASP F 733 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU F 735 " --> pdb=" O TYR F 673 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N TYR F 673 " --> pdb=" O LEU F 735 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE F 737 " --> pdb=" O SER F 671 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N SER F 671 " --> pdb=" O ILE F 737 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLU F 739 " --> pdb=" O VAL F 669 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL F 669 " --> pdb=" O GLU F 739 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN F 741 " --> pdb=" O ARG F 667 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY F 672 " --> pdb=" O PHE F 706 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 652 through 653 removed outlier: 3.534A pdb=" N ILE F 657 " --> pdb=" O ILE F 720 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 652 through 653 removed outlier: 3.509A pdb=" N GLU F 721 " --> pdb=" O LYS F 688 " (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 293 through 294 removed outlier: 4.720A pdb=" N ARG G 528 " --> pdb=" O ALA G 294 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N ILE G 610 " --> pdb=" O SER G 513 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER G 515 " --> pdb=" O ILE G 610 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ILE G 612 " --> pdb=" O SER G 515 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE G 517 " --> pdb=" O ILE G 612 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU G 611 " --> pdb=" O ILE G 578 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE G 352 " --> pdb=" O SER G 339 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 363 through 366 removed outlier: 4.948A pdb=" N GLU G 304 " --> pdb=" O THR G 326 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASN G 328 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N GLY G 302 " --> pdb=" O ASN G 328 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN G 391 " --> pdb=" O GLU G 304 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 363 through 366 removed outlier: 4.948A pdb=" N GLU G 304 " --> pdb=" O THR G 326 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASN G 328 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N GLY G 302 " --> pdb=" O ASN G 328 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN G 391 " --> pdb=" O GLU G 304 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA G 390 " --> pdb=" O LEU G 448 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 429 through 432 removed outlier: 6.429A pdb=" N ASN G 431 " --> pdb=" O TYR G 403 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR G 403 " --> pdb=" O ASN G 431 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LYS G 404 " --> pdb=" O ASN G 485 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN G 485 " --> pdb=" O LYS G 404 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER G 483 " --> pdb=" O THR G 406 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN G 481 " --> pdb=" O THR G 408 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 557 through 559 removed outlier: 3.569A pdb=" N LEU G 562 " --> pdb=" O ASN G 559 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 617 through 619 Processing sheet with id=AH2, first strand: chain 'G' and resid 617 through 619 removed outlier: 4.536A pdb=" N LEU G 735 " --> pdb=" O SER G 671 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER G 671 " --> pdb=" O LEU G 735 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE G 737 " --> pdb=" O VAL G 669 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL G 669 " --> pdb=" O ILE G 737 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLU G 739 " --> pdb=" O ARG G 667 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ARG G 667 " --> pdb=" O GLU G 739 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE G 710 " --> pdb=" O TYR G 668 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY G 672 " --> pdb=" O PHE G 706 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR G 704 " --> pdb=" O SER G 674 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 652 through 657 removed outlier: 3.525A pdb=" N LEU G 724 " --> pdb=" O THR G 653 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE G 655 " --> pdb=" O ILE G 722 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE G 720 " --> pdb=" O ILE G 657 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN G 686 " --> pdb=" O THR G 723 " (cutoff:3.500A) 746 hydrogen bonds defined for protein. 1824 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: 4.41 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 4529 1.27 - 1.41: 5509 1.41 - 1.54: 15398 1.54 - 1.68: 100 1.68 - 1.81: 73 Bond restraints: 25609 Sorted by residual: bond pdb=" C ASN D 485 " pdb=" O ASN D 485 " ideal model delta sigma weight residual 1.233 1.140 0.094 1.31e-02 5.83e+03 5.10e+01 bond pdb=" CD2 TRP D 631 " pdb=" CE2 TRP D 631 " ideal model delta sigma weight residual 1.409 1.447 -0.038 1.70e-02 3.46e+03 4.91e+00 bond pdb=" CD2 TRP B 631 " pdb=" CE2 TRP B 631 " ideal model delta sigma weight residual 1.409 1.447 -0.038 1.70e-02 3.46e+03 4.89e+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 4.74e+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 4.63e+00 ... (remaining 25604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 33453 1.40 - 2.80: 912 2.80 - 4.20: 160 4.20 - 5.60: 38 5.60 - 7.01: 4 Bond angle restraints: 34567 Sorted by residual: angle pdb=" CD2 TRP C 631 " pdb=" CE3 TRP C 631 " pdb=" CZ3 TRP C 631 " ideal model delta sigma weight residual 118.60 124.08 -5.48 1.30e+00 5.92e-01 1.78e+01 angle pdb=" CD2 TRP D 631 " pdb=" CE3 TRP D 631 " pdb=" CZ3 TRP D 631 " ideal model delta sigma weight residual 118.60 124.00 -5.40 1.30e+00 5.92e-01 1.72e+01 angle pdb=" CD2 TRP G 631 " pdb=" CE3 TRP G 631 " pdb=" CZ3 TRP G 631 " ideal model delta sigma weight residual 118.60 123.99 -5.39 1.30e+00 5.92e-01 1.72e+01 angle pdb=" CD2 TRP G 374 " pdb=" CE3 TRP G 374 " pdb=" CZ3 TRP G 374 " ideal model delta sigma weight residual 118.60 123.99 -5.39 1.30e+00 5.92e-01 1.72e+01 angle pdb=" N VAL B 512 " pdb=" CA VAL B 512 " pdb=" C VAL B 512 " ideal model delta sigma weight residual 113.20 109.22 3.98 9.60e-01 1.09e+00 1.72e+01 ... (remaining 34562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14040 17.95 - 35.91: 1240 35.91 - 53.86: 202 53.86 - 71.82: 40 71.82 - 89.77: 39 Dihedral angle restraints: 15561 sinusoidal: 6201 harmonic: 9360 Sorted by residual: dihedral pdb=" CA ASN D 566 " pdb=" C ASN D 566 " pdb=" N GLY D 567 " pdb=" CA GLY D 567 " ideal model delta harmonic sigma weight residual 180.00 -162.22 -17.78 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ARG A 606 " pdb=" C ARG A 606 " pdb=" N GLY A 607 " pdb=" CA GLY A 607 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA GLN B 453 " pdb=" C GLN B 453 " pdb=" N PHE B 454 " pdb=" CA PHE B 454 " ideal model delta harmonic sigma weight residual -180.00 -163.42 -16.58 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 15558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2847 0.043 - 0.087: 814 0.087 - 0.130: 309 0.130 - 0.173: 16 0.173 - 0.216: 3 Chirality restraints: 3989 Sorted by residual: chirality pdb=" CB THR G 406 " pdb=" CA THR G 406 " pdb=" OG1 THR G 406 " pdb=" CG2 THR G 406 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB VAL G 512 " pdb=" CA VAL G 512 " pdb=" CG1 VAL G 512 " pdb=" CG2 VAL G 512 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ASP G 414 " pdb=" N ASP G 414 " pdb=" C ASP G 414 " pdb=" CB ASP G 414 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 3986 not shown) Planarity restraints: 4502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 536 " -0.068 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO D 537 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO D 537 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 537 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 698 " -0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO F 699 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO F 699 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 699 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 268 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.26e+00 pdb=" N PRO D 269 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 269 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 269 " -0.034 5.00e-02 4.00e+02 ... (remaining 4499 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2460 2.74 - 3.28: 24904 3.28 - 3.82: 39509 3.82 - 4.36: 47494 4.36 - 4.90: 82866 Nonbonded interactions: 197233 Sorted by model distance: nonbonded pdb=" OD1 ASN A 430 " pdb=" OG SER B 483 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR F 364 " pdb=" O ILE F 475 " model vdw 2.215 3.040 nonbonded pdb=" OE2 GLU E 721 " pdb=" OG1 THR E 723 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR B 265 " pdb=" OD2 ASP B 272 " model vdw 2.233 3.040 nonbonded pdb=" OG SER B 309 " pdb=" ND2 ASN C 462 " model vdw 2.244 3.120 ... (remaining 197228 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 295 or resid 297 through 308 or resid 310 thro \ ugh 386 or resid 388 through 449 or resid 459 through 741 or resid 801 through 8 \ 03)) selection = (chain 'B' and (resid 216 through 295 or resid 297 through 308 or resid 310 thro \ ugh 386 or resid 388 through 449 or resid 459 through 741 or resid 801 through 8 \ 03)) selection = (chain 'C' and (resid 216 through 295 or resid 297 through 308 or resid 310 thro \ ugh 386 or resid 388 through 449 or resid 459 through 803)) selection = (chain 'D' and (resid 216 through 295 or resid 297 through 308 or resid 310 thro \ ugh 386 or resid 388 through 449 or resid 459 through 741 or resid 801 through 8 \ 03)) selection = (chain 'E' and (resid 216 through 295 or resid 297 through 308 or resid 310 thro \ ugh 386 or resid 388 through 449 or resid 459 through 741 or resid 801 through 8 \ 03)) selection = (chain 'F' and (resid 216 through 295 or resid 297 through 308 or resid 326 or r \ esid 341 through 342 or resid 388 through 449 or resid 459 through 614 or (resid \ 615 and (name N or name CA or name C or name O or name CB or name CG )) or resi \ d 616 through 741 or resid 801 through 803)) selection = (chain 'G' and (resid 216 through 295 or resid 297 through 307 or resid 340 or r \ esid 354 through 355 or resid 365 or resid 380 through 381 or resid 390 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 801 through 803)) } 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.300 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 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 : 0.004 0.094 25609 Z= 0.185 Angle : 0.576 7.006 34567 Z= 0.335 Chirality : 0.045 0.216 3989 Planarity : 0.004 0.103 4502 Dihedral : 14.621 89.771 9437 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.17 % Allowed : 0.52 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: -0.94 (0.14), residues: 3216 helix: -1.34 (0.24), residues: 410 sheet: 0.45 (0.19), residues: 811 loop : -0.94 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 606 TYR 0.019 0.001 TYR G 356 PHE 0.021 0.001 PHE D 454 TRP 0.010 0.001 TRP F 244 HIS 0.001 0.001 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (25609) covalent geometry : angle 0.57640 / 0.33 (34567) hydrogen bonds : bond 0.28450 / 18.28 ( 709) hydrogen bonds : angle 10.05731 / 6.96 ( 1824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 302 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 552 LYS cc_start: 0.7208 (mtmm) cc_final: 0.6743 (mtmm) outliers start: 5 outliers final: 2 residues processed: 307 average time/residue: 0.1389 time to fit residues: 70.0470 Evaluate side-chains 174 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain F residue 528 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 508 GLN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 ASN D 601 ASN D 692 GLN E 453 GLN F 435 ASN F 492 GLN G 351 ASN G 435 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.068238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.051528 restraints weight = 130550.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.052894 restraints weight = 73000.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.053798 restraints weight = 49584.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.054414 restraints weight = 38081.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.054793 restraints weight = 31881.774| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25609 Z= 0.181 Angle : 0.600 6.995 34567 Z= 0.338 Chirality : 0.045 0.255 3989 Planarity : 0.004 0.068 4502 Dihedral : 4.682 59.235 3242 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.21 % Allowed : 7.55 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3216 helix: -0.82 (0.23), residues: 444 sheet: 0.51 (0.18), residues: 831 loop : -0.86 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 457 TYR 0.018 0.001 TYR G 463 PHE 0.017 0.001 PHE B 670 TRP 0.006 0.001 TRP F 502 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (25609) covalent geometry : angle 0.60024 / 0.34 (34567) hydrogen bonds : bond 0.04228 / 2.77 ( 709) hydrogen bonds : angle 6.44653 / 4.51 ( 1824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 691 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7756 (tm-30) REVERT: C 519 ASP cc_start: 0.8569 (t0) cc_final: 0.8353 (t0) REVERT: C 562 LEU cc_start: 0.8693 (tp) cc_final: 0.8389 (tt) REVERT: D 517 ILE cc_start: 0.9063 (mt) cc_final: 0.8791 (tt) REVERT: D 642 LEU cc_start: 0.7000 (mp) cc_final: 0.6719 (tp) REVERT: E 489 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7929 (tmtt) REVERT: E 548 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8792 (pt0) outliers start: 35 outliers final: 21 residues processed: 202 average time/residue: 0.1358 time to fit residues: 46.0917 Evaluate side-chains 175 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 601 ASN Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 489 LYS Chi-restraints excluded: chain E residue 548 GLU Chi-restraints excluded: chain E residue 570 ILE Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain F residue 528 ARG Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 143 optimal weight: 10.0000 chunk 271 optimal weight: 30.0000 chunk 73 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 176 optimal weight: 30.0000 chunk 276 optimal weight: 9.9990 chunk 295 optimal weight: 8.9990 chunk 213 optimal weight: 30.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 ASN A 647 ASN B 435 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.066163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.049707 restraints weight = 132682.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.051060 restraints weight = 74530.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.051947 restraints weight = 50357.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.052546 restraints weight = 38621.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.052896 restraints weight = 32341.477| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25609 Z= 0.208 Angle : 0.596 10.469 34567 Z= 0.330 Chirality : 0.045 0.273 3989 Planarity : 0.004 0.056 4502 Dihedral : 4.763 59.539 3242 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.39 % Allowed : 10.29 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: -0.65 (0.14), residues: 3216 helix: -0.52 (0.24), residues: 428 sheet: 0.46 (0.18), residues: 850 loop : -0.82 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 457 TYR 0.016 0.001 TYR E 708 PHE 0.011 0.001 PHE G 565 TRP 0.008 0.001 TRP F 244 HIS 0.003 0.001 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (25609) covalent geometry : angle 0.59610 / 0.33 (34567) hydrogen bonds : bond 0.03728 / 2.43 ( 709) hydrogen bonds : angle 5.85804 / 4.12 ( 1824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8545 (tp) REVERT: C 519 ASP cc_start: 0.8693 (t0) cc_final: 0.8491 (t0) REVERT: C 591 LEU cc_start: 0.8943 (pp) cc_final: 0.8402 (mt) REVERT: C 594 LEU cc_start: 0.8600 (tp) cc_final: 0.8362 (tp) REVERT: D 517 ILE cc_start: 0.9150 (mt) cc_final: 0.8807 (tt) REVERT: D 642 LEU cc_start: 0.7027 (mp) cc_final: 0.6784 (tp) REVERT: E 436 GLU cc_start: 0.8106 (tp30) cc_final: 0.7692 (tp30) REVERT: E 519 ASP cc_start: 0.8857 (t0) cc_final: 0.8642 (t0) REVERT: E 548 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8785 (pt0) outliers start: 40 outliers final: 26 residues processed: 191 average time/residue: 0.1274 time to fit residues: 41.8788 Evaluate side-chains 177 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 453 GLN Chi-restraints excluded: chain E residue 548 GLU Chi-restraints excluded: chain E residue 570 ILE Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain F residue 528 ARG Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 201 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 279 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 ASN B 465 GLN C 485 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.066609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.050259 restraints weight = 130842.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.051631 restraints weight = 72996.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.052509 restraints weight = 49231.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.053105 restraints weight = 37759.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.053498 restraints weight = 31648.675| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25609 Z= 0.141 Angle : 0.538 8.749 34567 Z= 0.300 Chirality : 0.044 0.171 3989 Planarity : 0.003 0.054 4502 Dihedral : 4.467 54.455 3242 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.39 % Allowed : 11.54 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: -0.47 (0.14), residues: 3216 helix: -0.15 (0.26), residues: 422 sheet: 0.50 (0.18), residues: 847 loop : -0.71 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 457 TYR 0.012 0.001 TYR C 708 PHE 0.010 0.001 PHE G 565 TRP 0.008 0.001 TRP A 631 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (25609) covalent geometry : angle 0.53848 / 0.30 (34567) hydrogen bonds : bond 0.03046 / 1.98 ( 709) hydrogen bonds : angle 5.41699 / 3.79 ( 1824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8474 (tp) REVERT: A 691 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7758 (tm-30) REVERT: B 451 MET cc_start: 0.7626 (tpp) cc_final: 0.7374 (mmm) REVERT: B 670 PHE cc_start: 0.8435 (t80) cc_final: 0.8103 (t80) REVERT: C 519 ASP cc_start: 0.8642 (t0) cc_final: 0.8380 (t0) REVERT: C 591 LEU cc_start: 0.8939 (pp) cc_final: 0.8387 (mt) REVERT: C 594 LEU cc_start: 0.8556 (tp) cc_final: 0.8340 (tp) REVERT: C 661 LYS cc_start: 0.8950 (tptp) cc_final: 0.8191 (mptt) REVERT: C 705 LYS cc_start: 0.8321 (tptp) cc_final: 0.8029 (tptp) REVERT: D 451 MET cc_start: 0.8207 (ppp) cc_final: 0.7975 (ppp) REVERT: D 517 ILE cc_start: 0.9172 (mt) cc_final: 0.8828 (tt) REVERT: D 642 LEU cc_start: 0.6941 (mp) cc_final: 0.6715 (tp) REVERT: F 340 ILE cc_start: 0.9206 (mp) cc_final: 0.8968 (mm) REVERT: F 709 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8115 (mp0) outliers start: 40 outliers final: 21 residues processed: 186 average time/residue: 0.1289 time to fit residues: 40.9947 Evaluate side-chains 167 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain F residue 528 ARG Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 266 optimal weight: 10.0000 chunk 112 optimal weight: 30.0000 chunk 118 optimal weight: 6.9990 chunk 264 optimal weight: 50.0000 chunk 205 optimal weight: 10.0000 chunk 256 optimal weight: 20.0000 chunk 115 optimal weight: 0.0070 chunk 96 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 overall best weight: 4.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 GLN D 686 ASN E 734 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.066367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.050119 restraints weight = 131794.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.051468 restraints weight = 73432.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.052332 restraints weight = 49515.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.052942 restraints weight = 38054.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.053318 restraints weight = 31840.848| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25609 Z= 0.140 Angle : 0.533 9.540 34567 Z= 0.297 Chirality : 0.044 0.295 3989 Planarity : 0.003 0.053 4502 Dihedral : 4.371 54.508 3242 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.56 % Allowed : 12.79 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: -0.36 (0.15), residues: 3216 helix: -0.02 (0.26), residues: 423 sheet: 0.47 (0.17), residues: 885 loop : -0.61 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 457 TYR 0.012 0.001 TYR C 708 PHE 0.010 0.001 PHE F 670 TRP 0.009 0.001 TRP A 631 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (25609) covalent geometry : angle 0.53326 / 0.30 (34567) hydrogen bonds : bond 0.02902 / 1.89 ( 709) hydrogen bonds : angle 5.24719 / 3.67 ( 1824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8464 (tp) REVERT: A 414 ASP cc_start: 0.8160 (t0) cc_final: 0.7559 (p0) REVERT: B 594 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8502 (tt) REVERT: B 670 PHE cc_start: 0.8499 (t80) cc_final: 0.8299 (t80) REVERT: C 451 MET cc_start: 0.8043 (ttt) cc_final: 0.7743 (ttp) REVERT: C 591 LEU cc_start: 0.8957 (pp) cc_final: 0.8400 (mt) REVERT: C 594 LEU cc_start: 0.8515 (tp) cc_final: 0.8299 (tp) REVERT: C 705 LYS cc_start: 0.8343 (tptp) cc_final: 0.8084 (tptp) REVERT: D 517 ILE cc_start: 0.9195 (mt) cc_final: 0.8834 (tt) REVERT: D 642 LEU cc_start: 0.6946 (mp) cc_final: 0.6678 (tp) REVERT: G 659 MET cc_start: 0.8107 (tpt) cc_final: 0.7881 (tpt) outliers start: 45 outliers final: 29 residues processed: 188 average time/residue: 0.1270 time to fit residues: 41.6308 Evaluate side-chains 176 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 454 PHE Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 570 ILE Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 194 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 321 optimal weight: 10.0000 chunk 165 optimal weight: 0.0970 chunk 70 optimal weight: 10.0000 chunk 285 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 chunk 145 optimal weight: 30.0000 chunk 52 optimal weight: 20.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 633 ASN D 427 GLN ** G 465 GLN ** 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 = 0.3525 r_free = 0.3525 target = 0.066394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.050128 restraints weight = 132791.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.051483 restraints weight = 74323.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.052372 restraints weight = 50122.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.052973 restraints weight = 38400.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.053334 restraints weight = 32096.190| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25609 Z= 0.135 Angle : 0.537 8.632 34567 Z= 0.299 Chirality : 0.044 0.200 3989 Planarity : 0.003 0.052 4502 Dihedral : 4.177 37.314 3238 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.49 % Allowed : 13.34 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: -0.30 (0.15), residues: 3216 helix: 0.07 (0.26), residues: 429 sheet: 0.52 (0.18), residues: 878 loop : -0.58 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 289 TYR 0.010 0.001 TYR E 486 PHE 0.015 0.001 PHE F 670 TRP 0.008 0.001 TRP A 631 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (25609) covalent geometry : angle 0.53657 / 0.30 (34567) hydrogen bonds : bond 0.02844 / 1.86 ( 709) hydrogen bonds : angle 5.13583 / 3.60 ( 1824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8540 (tp) REVERT: A 414 ASP cc_start: 0.8218 (t0) cc_final: 0.7567 (p0) REVERT: A 691 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7698 (tm-30) REVERT: A 732 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7850 (mt) REVERT: B 454 PHE cc_start: 0.6728 (m-80) cc_final: 0.6464 (m-80) REVERT: B 594 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8465 (tt) REVERT: C 451 MET cc_start: 0.8099 (ttt) cc_final: 0.7808 (ttp) REVERT: C 591 LEU cc_start: 0.8970 (pp) cc_final: 0.8434 (mt) REVERT: C 594 LEU cc_start: 0.8517 (tp) cc_final: 0.8285 (tp) REVERT: C 661 LYS cc_start: 0.8687 (tptp) cc_final: 0.7990 (mptt) REVERT: C 705 LYS cc_start: 0.8215 (tptp) cc_final: 0.7998 (tptp) REVERT: D 517 ILE cc_start: 0.9167 (mt) cc_final: 0.8829 (tt) REVERT: D 642 LEU cc_start: 0.6986 (mp) cc_final: 0.6714 (tp) REVERT: F 352 ILE cc_start: 0.8921 (mm) cc_final: 0.8534 (mm) REVERT: F 709 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8220 (mp0) REVERT: G 402 MET cc_start: 0.8847 (tpp) cc_final: 0.8517 (ttt) REVERT: G 498 GLU cc_start: 0.8296 (tp30) cc_final: 0.7948 (tp30) outliers start: 43 outliers final: 29 residues processed: 184 average time/residue: 0.1260 time to fit residues: 40.2455 Evaluate side-chains 176 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 570 ILE Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 645 VAL Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 111 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 chunk 304 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 229 optimal weight: 30.0000 chunk 249 optimal weight: 8.9990 chunk 274 optimal weight: 30.0000 chunk 207 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 504 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.065165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.049236 restraints weight = 133192.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.050541 restraints weight = 74765.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.051379 restraints weight = 50857.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.051968 restraints weight = 39255.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.052333 restraints weight = 33004.629| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25609 Z= 0.185 Angle : 0.577 10.801 34567 Z= 0.318 Chirality : 0.044 0.166 3989 Planarity : 0.003 0.054 4502 Dihedral : 4.436 37.084 3238 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.52 % Allowed : 14.24 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: -0.43 (0.15), residues: 3216 helix: 0.03 (0.26), residues: 430 sheet: 0.48 (0.18), residues: 834 loop : -0.69 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 527 TYR 0.014 0.001 TYR E 708 PHE 0.010 0.001 PHE D 618 TRP 0.008 0.001 TRP A 631 HIS 0.002 0.001 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (25609) covalent geometry : angle 0.57651 / 0.32 (34567) hydrogen bonds : bond 0.03015 / 1.95 ( 709) hydrogen bonds : angle 5.22965 / 3.66 ( 1824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 307 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8452 (tp) REVERT: A 414 ASP cc_start: 0.8131 (t0) cc_final: 0.7599 (p0) REVERT: A 732 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7839 (mt) REVERT: B 454 PHE cc_start: 0.6786 (m-80) cc_final: 0.6552 (m-80) REVERT: B 594 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8512 (tt) REVERT: C 594 LEU cc_start: 0.8527 (tp) cc_final: 0.8281 (tp) REVERT: C 661 LYS cc_start: 0.8741 (tptp) cc_final: 0.8162 (tttt) REVERT: D 517 ILE cc_start: 0.9171 (mt) cc_final: 0.8848 (tt) REVERT: D 642 LEU cc_start: 0.7110 (mp) cc_final: 0.6825 (tp) REVERT: D 740 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6557 (mp) REVERT: F 709 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8217 (mp0) REVERT: G 402 MET cc_start: 0.8903 (tpp) cc_final: 0.8605 (ttt) REVERT: G 498 GLU cc_start: 0.8393 (tp30) cc_final: 0.8086 (tp30) outliers start: 44 outliers final: 32 residues processed: 183 average time/residue: 0.1277 time to fit residues: 40.5880 Evaluate side-chains 172 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 645 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 570 ILE Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 645 VAL Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 312 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 245 optimal weight: 20.0000 chunk 291 optimal weight: 10.0000 chunk 307 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 590 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.065485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.049405 restraints weight = 132861.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.050739 restraints weight = 74129.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.051626 restraints weight = 50028.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.052192 restraints weight = 38345.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.052591 restraints weight = 32258.944| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25609 Z= 0.141 Angle : 0.555 12.258 34567 Z= 0.305 Chirality : 0.044 0.192 3989 Planarity : 0.003 0.055 4502 Dihedral : 4.260 37.182 3238 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.52 % Allowed : 14.66 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: -0.35 (0.15), residues: 3216 helix: 0.16 (0.26), residues: 429 sheet: 0.51 (0.18), residues: 878 loop : -0.67 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 667 TYR 0.010 0.001 TYR E 486 PHE 0.014 0.001 PHE F 670 TRP 0.007 0.001 TRP A 631 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (25609) covalent geometry : angle 0.55500 / 0.30 (34567) hydrogen bonds : bond 0.02740 / 1.78 ( 709) hydrogen bonds : angle 5.09987 / 3.56 ( 1824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 307 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8492 (tp) REVERT: A 414 ASP cc_start: 0.8110 (t0) cc_final: 0.7563 (p0) REVERT: A 691 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7729 (tm-30) REVERT: A 732 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7884 (mt) REVERT: B 451 MET cc_start: 0.7261 (mmm) cc_final: 0.6945 (mmm) REVERT: B 454 PHE cc_start: 0.6832 (m-80) cc_final: 0.6599 (m-80) REVERT: B 594 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8468 (tt) REVERT: C 594 LEU cc_start: 0.8494 (tp) cc_final: 0.8254 (tp) REVERT: C 661 LYS cc_start: 0.8728 (tptp) cc_final: 0.8028 (mptt) REVERT: D 517 ILE cc_start: 0.9139 (mt) cc_final: 0.8832 (tt) REVERT: D 548 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7970 (tp30) REVERT: D 642 LEU cc_start: 0.7048 (mp) cc_final: 0.6771 (tp) REVERT: D 740 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6633 (mp) REVERT: E 451 MET cc_start: 0.6238 (ppp) cc_final: 0.5766 (tmm) REVERT: F 608 MET cc_start: 0.8931 (mtt) cc_final: 0.8649 (mtt) REVERT: G 402 MET cc_start: 0.8880 (tpp) cc_final: 0.8582 (ttt) REVERT: G 498 GLU cc_start: 0.8367 (tp30) cc_final: 0.8042 (tp30) REVERT: G 659 MET cc_start: 0.8140 (tpp) cc_final: 0.7892 (tpt) outliers start: 44 outliers final: 33 residues processed: 177 average time/residue: 0.1246 time to fit residues: 38.3570 Evaluate side-chains 174 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 548 GLU Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 570 ILE Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 645 VAL Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 22 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 317 optimal weight: 30.0000 chunk 301 optimal weight: 20.0000 chunk 253 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 176 optimal weight: 50.0000 chunk 309 optimal weight: 9.9990 chunk 305 optimal weight: 6.9990 chunk 263 optimal weight: 0.3980 overall best weight: 5.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 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 = 0.3496 r_free = 0.3496 target = 0.065132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.049133 restraints weight = 133598.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.050447 restraints weight = 74970.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.051327 restraints weight = 50722.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.051883 restraints weight = 38896.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.052269 restraints weight = 32748.564| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25609 Z= 0.157 Angle : 0.568 11.935 34567 Z= 0.310 Chirality : 0.044 0.246 3989 Planarity : 0.003 0.057 4502 Dihedral : 4.293 37.132 3238 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.42 % Allowed : 14.80 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: -0.34 (0.15), residues: 3216 helix: 0.25 (0.26), residues: 423 sheet: 0.50 (0.18), residues: 872 loop : -0.67 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 528 TYR 0.013 0.001 TYR G 356 PHE 0.010 0.001 PHE A 621 TRP 0.006 0.001 TRP A 631 HIS 0.000 0.000 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (25609) covalent geometry : angle 0.56788 / 0.31 (34567) hydrogen bonds : bond 0.02778 / 1.80 ( 709) hydrogen bonds : angle 5.10080 / 3.55 ( 1824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8500 (tp) REVERT: A 414 ASP cc_start: 0.8082 (t0) cc_final: 0.7544 (p0) REVERT: A 691 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 732 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7876 (mt) REVERT: B 451 MET cc_start: 0.7329 (mmm) cc_final: 0.7091 (mmm) REVERT: B 454 PHE cc_start: 0.6808 (m-80) cc_final: 0.6566 (m-80) REVERT: B 594 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8494 (tt) REVERT: C 594 LEU cc_start: 0.8514 (tp) cc_final: 0.8266 (tp) REVERT: C 661 LYS cc_start: 0.8695 (tptp) cc_final: 0.7993 (mptt) REVERT: D 517 ILE cc_start: 0.9114 (mt) cc_final: 0.8822 (tt) REVERT: D 548 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8331 (pt0) REVERT: D 642 LEU cc_start: 0.7089 (mp) cc_final: 0.6801 (tp) REVERT: D 740 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6634 (mp) REVERT: E 451 MET cc_start: 0.6284 (ppp) cc_final: 0.5827 (tmm) REVERT: F 709 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8339 (mp0) REVERT: G 402 MET cc_start: 0.8908 (tpp) cc_final: 0.8679 (ttt) REVERT: G 498 GLU cc_start: 0.8460 (tp30) cc_final: 0.8217 (tp30) outliers start: 41 outliers final: 34 residues processed: 168 average time/residue: 0.1248 time to fit residues: 36.4113 Evaluate side-chains 171 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 548 GLU Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 570 ILE Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 645 VAL Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 55 optimal weight: 8.9990 chunk 235 optimal weight: 8.9990 chunk 148 optimal weight: 0.0270 chunk 40 optimal weight: 30.0000 chunk 165 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 221 optimal weight: 20.0000 chunk 173 optimal weight: 50.0000 chunk 65 optimal weight: 10.0000 chunk 265 optimal weight: 9.9990 overall best weight: 6.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.064978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.048859 restraints weight = 133049.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.050188 restraints weight = 75020.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.051019 restraints weight = 50977.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.051630 restraints weight = 39400.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.051985 restraints weight = 33045.303| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25609 Z= 0.161 Angle : 0.570 11.727 34567 Z= 0.312 Chirality : 0.044 0.176 3989 Planarity : 0.003 0.058 4502 Dihedral : 4.337 37.018 3238 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.52 % Allowed : 14.76 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: -0.36 (0.15), residues: 3216 helix: 0.23 (0.26), residues: 426 sheet: 0.49 (0.18), residues: 870 loop : -0.68 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 289 TYR 0.011 0.001 TYR E 486 PHE 0.014 0.001 PHE F 670 TRP 0.006 0.001 TRP A 631 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (25609) covalent geometry : angle 0.57015 / 0.31 (34567) hydrogen bonds : bond 0.02773 / 1.80 ( 709) hydrogen bonds : angle 5.09874 / 3.55 ( 1824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8432 (tp) REVERT: A 414 ASP cc_start: 0.8153 (t0) cc_final: 0.7630 (p0) REVERT: A 691 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7600 (tm-30) REVERT: A 732 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7909 (mt) REVERT: B 451 MET cc_start: 0.7416 (mmm) cc_final: 0.7093 (mmm) REVERT: B 594 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8510 (tt) REVERT: C 594 LEU cc_start: 0.8507 (tp) cc_final: 0.8262 (tp) REVERT: C 661 LYS cc_start: 0.8664 (tptp) cc_final: 0.7947 (mptt) REVERT: D 517 ILE cc_start: 0.9128 (mt) cc_final: 0.8853 (tt) REVERT: D 548 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8337 (pt0) REVERT: D 642 LEU cc_start: 0.7078 (mp) cc_final: 0.6784 (tp) REVERT: D 740 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6716 (mp) REVERT: E 451 MET cc_start: 0.6317 (ppp) cc_final: 0.5880 (tmm) REVERT: E 608 MET cc_start: 0.8826 (ptp) cc_final: 0.8197 (ptt) REVERT: F 659 MET cc_start: 0.8366 (tpt) cc_final: 0.7861 (tpt) REVERT: F 709 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8360 (mp0) outliers start: 44 outliers final: 34 residues processed: 171 average time/residue: 0.1467 time to fit residues: 43.7127 Evaluate side-chains 170 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 548 GLU Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 570 ILE Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 290 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 254 optimal weight: 8.9990 chunk 79 optimal weight: 0.1980 chunk 242 optimal weight: 30.0000 chunk 62 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 125 optimal weight: 40.0000 chunk 280 optimal weight: 0.0070 chunk 26 optimal weight: 20.0000 overall best weight: 4.0404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 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 = 0.3493 r_free = 0.3493 target = 0.065360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.049239 restraints weight = 133458.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.050560 restraints weight = 74861.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.051427 restraints weight = 50746.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.052015 restraints weight = 39069.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.052363 restraints weight = 32790.394| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25609 Z= 0.133 Angle : 0.560 11.787 34567 Z= 0.305 Chirality : 0.044 0.154 3989 Planarity : 0.003 0.055 4502 Dihedral : 4.193 36.824 3238 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.35 % Allowed : 14.97 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.15), residues: 3216 helix: 0.37 (0.26), residues: 423 sheet: 0.51 (0.18), residues: 883 loop : -0.63 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 606 TYR 0.010 0.001 TYR E 486 PHE 0.011 0.001 PHE A 621 TRP 0.006 0.001 TRP A 631 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (25609) covalent geometry : angle 0.55955 / 0.30 (34567) hydrogen bonds : bond 0.02627 / 1.70 ( 709) hydrogen bonds : angle 5.00415 / 3.48 ( 1824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3281.71 seconds wall clock time: 58 minutes 8.05 seconds (3488.05 seconds total)