Starting phenix.real_space_refine on Sun Jul 5 05:13:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsi_61774/07_2026/9jsi_61774.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsi_61774/07_2026/9jsi_61774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jsi_61774/07_2026/9jsi_61774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsi_61774/07_2026/9jsi_61774.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jsi_61774/07_2026/9jsi_61774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsi_61774/07_2026/9jsi_61774.map" } resolution = 3.35 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= 0.094 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 36 5.16 5 C 16835 2.51 5 N 4254 2.21 5 O 5449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26595 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3486 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: "B" 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: 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: "C" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3860 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} 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: "D" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3812 Classifications: {'peptide': 496} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 475} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 3912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3912 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 488} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 46 Chain: "F" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3845 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 479} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "G" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3812 Classifications: {'peptide': 496} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 475} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Time building chain proxies: 6.55, per 1000 atoms: 0.25 Number of scatterers: 26595 At special positions: 0 Unit cell: (177.76, 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 36 16.00 O 5449 8.00 N 4254 7.00 C 16835 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: 2.20 Conformation dependent library (CDL) restraints added in 3.8 seconds 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6468 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 68 sheets defined 18.4% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.734A 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 Processing helix chain 'A' and resid 424 through 428 removed outlier: 4.068A pdb=" N ILE A 428 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 470 removed outlier: 4.249A pdb=" N ASP A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 removed outlier: 4.786A pdb=" N SER A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLN A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 Processing helix chain 'A' and resid 580 through 592 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 232 Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.366A pdb=" N GLN B 251 " --> 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: 3.544A pdb=" N ASP B 290 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 removed outlier: 3.872A pdb=" N THR B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 502 through 512 removed outlier: 4.772A pdb=" N SER B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLN B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 555 Processing helix chain 'B' and resid 571 through 575 removed outlier: 3.999A pdb=" N VAL B 575 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 592 removed outlier: 3.872A 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 'B' and resid 658 through 662 Processing helix chain 'C' and resid 226 through 233 Processing helix chain 'C' and resid 245 through 252 removed outlier: 4.080A pdb=" N GLU C 250 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY C 252 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 285 through 290 removed outlier: 3.657A pdb=" N ASP C 290 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 337 removed outlier: 3.889A pdb=" N THR C 335 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.595A pdb=" N LEU C 378 " --> pdb=" O TRP C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 416 removed outlier: 3.838A pdb=" N GLU C 416 " --> pdb=" O LEU C 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 416' Processing helix chain 'C' and resid 462 through 471 Processing helix chain 'C' and resid 502 through 511 removed outlier: 4.817A pdb=" N SER C 507 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLN C 508 " --> pdb=" O ASN C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 555 Processing helix chain 'C' and resid 580 through 594 removed outlier: 3.828A pdb=" N LYS C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR C 593 " --> pdb=" O GLU C 589 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 594 " --> pdb=" O GLN C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 602 Processing helix chain 'C' and resid 658 through 662 Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 245 through 252 removed outlier: 3.548A pdb=" N ALA D 249 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU D 250 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY D 252 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 278 Processing helix chain 'D' and resid 285 through 290 removed outlier: 3.711A pdb=" N ASP D 290 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 337 removed outlier: 4.011A pdb=" N THR D 335 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 416 removed outlier: 3.605A pdb=" N GLU D 416 " --> pdb=" O LEU D 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 413 through 416' Processing helix chain 'D' and resid 462 through 472 removed outlier: 3.780A pdb=" N LYS D 468 " --> pdb=" O ASP D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 511 removed outlier: 4.734A pdb=" N SER D 507 " --> pdb=" O SER D 503 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLN D 508 " --> pdb=" O ASN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 555 Processing helix chain 'D' and resid 580 through 592 removed outlier: 3.710A pdb=" N LYS D 592 " --> pdb=" O LYS D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 602 Processing helix chain 'D' and resid 658 through 662 Processing helix chain 'E' and resid 226 through 233 Processing helix chain 'E' and resid 245 through 250 removed outlier: 3.523A pdb=" N ALA E 249 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 250 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 278 Processing helix chain 'E' and resid 285 through 290 removed outlier: 3.619A pdb=" N ASP E 290 " --> pdb=" O GLU E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 337 removed outlier: 4.282A pdb=" N GLY E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 470 Processing helix chain 'E' and resid 502 through 511 removed outlier: 4.680A pdb=" N SER E 507 " --> pdb=" O SER E 503 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN E 508 " --> pdb=" O ASN E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 555 Processing helix chain 'E' and resid 580 through 593 removed outlier: 3.731A pdb=" N LYS E 592 " --> pdb=" O LYS E 588 " (cutoff:3.500A) removed outlier: 4.403A 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 'E' and resid 658 through 662 Processing helix chain 'F' and resid 226 through 233 Processing helix chain 'F' and resid 245 through 252 removed outlier: 4.211A 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 290 Processing helix chain 'F' and resid 331 through 337 removed outlier: 3.878A pdb=" N THR F 335 " --> pdb=" O THR F 331 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY F 337 " --> pdb=" O ALA F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 470 Processing helix chain 'F' and resid 502 through 511 removed outlier: 4.783A pdb=" N SER F 507 " --> pdb=" O SER F 503 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLN F 508 " --> pdb=" O ASN F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 555 Processing helix chain 'F' and resid 580 through 592 removed outlier: 3.895A pdb=" N LYS F 592 " --> pdb=" O LYS F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 602 Processing helix chain 'F' and resid 658 through 662 Processing helix chain 'G' and resid 226 through 233 Processing helix chain 'G' and resid 245 through 249 Processing helix chain 'G' and resid 271 through 278 Processing helix chain 'G' and resid 285 through 290 Processing helix chain 'G' and resid 331 through 336 Processing helix chain 'G' and resid 462 through 472 removed outlier: 3.807A pdb=" N GLY G 472 " --> pdb=" O LYS G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 511 removed outlier: 4.688A pdb=" N SER G 507 " --> pdb=" O SER G 503 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLN G 508 " --> pdb=" O ASN G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 555 Processing helix chain 'G' and resid 580 through 592 removed outlier: 3.736A pdb=" N LYS G 592 " --> pdb=" O LYS G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 602 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: 5.659A pdb=" N VAL A 301 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 395 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N MET A 303 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG A 393 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 390 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 417 through 422 removed outlier: 6.869A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS A 422 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR A 403 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A 431 " --> pdb=" O TYR A 403 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 417 through 422 removed outlier: 6.869A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS A 422 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS A 404 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY A 484 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR A 406 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL A 482 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 408 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 478 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 530 Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 559 removed outlier: 4.108A pdb=" N LEU A 562 " --> pdb=" O ASN A 559 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 617 through 619 removed outlier: 3.795A pdb=" N GLU A 721 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP A 695 " --> pdb=" O VAL A 685 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 647 through 656 removed outlier: 5.505A pdb=" N GLY A 728 " --> pdb=" O GLY A 651 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR A 653 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER A 726 " --> pdb=" O THR A 653 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE A 655 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU A 724 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU A 735 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER A 671 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE A 737 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 669 " --> pdb=" O ILE A 737 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB2, first strand: chain 'B' and resid 299 through 305 removed outlier: 6.828A pdb=" N ASN B 391 " --> pdb=" O GLU B 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 299 through 305 removed outlier: 6.828A pdb=" N ASN B 391 " --> pdb=" O GLU B 304 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 326 through 329 removed outlier: 3.508A pdb=" N SER B 363 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASN B 362 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS B 476 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 412 " --> pdb=" O LYS B 476 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR B 408 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL B 482 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR B 406 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY B 484 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS B 404 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 419 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 326 through 329 removed outlier: 3.508A pdb=" N SER B 363 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASN B 362 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS B 476 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 412 " --> pdb=" O LYS B 476 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR B 408 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL B 482 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR B 406 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY B 484 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS B 404 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR B 403 " --> pdb=" O ASN B 431 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN B 431 " --> pdb=" O TYR B 403 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 351 through 352 removed outlier: 4.105A pdb=" N GLN B 523 " --> pdb=" O THR B 520 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AB8, first strand: chain 'B' and resid 557 through 559 removed outlier: 4.032A 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 Processing sheet with id=AC1, first strand: chain 'B' and resid 617 through 619 removed outlier: 5.462A pdb=" N LEU B 732 " --> pdb=" O LYS B 675 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LYS B 675 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASN B 734 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR B 673 " --> pdb=" O ASN B 734 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 674 " --> pdb=" O THR B 704 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 652 through 657 removed outlier: 3.873A pdb=" N ILE B 722 " --> pdb=" O ILE B 655 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 721 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN B 686 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 695 " --> pdb=" O VAL B 685 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 687 " --> pdb=" O LYS B 693 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS B 693 " --> pdb=" O ILE B 687 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 234 through 237 Processing sheet with id=AC4, first strand: chain 'C' and resid 420 through 422 removed outlier: 7.000A pdb=" N LYS C 404 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY C 484 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR C 406 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL C 482 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR C 408 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN C 362 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG C 324 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 306 " --> pdb=" O ARG C 324 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU C 304 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ASN C 328 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N GLY C 302 " --> pdb=" O ASN C 328 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN C 391 " --> pdb=" O GLU C 304 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 429 through 432 removed outlier: 6.440A pdb=" N ASN C 431 " --> pdb=" O TYR C 403 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TYR C 403 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS C 404 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY C 484 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR C 406 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL C 482 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR C 408 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN C 362 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG C 324 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 306 " --> pdb=" O ARG C 324 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU C 304 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ASN C 328 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N GLY C 302 " --> pdb=" O ASN C 328 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN C 391 " --> pdb=" O GLU C 304 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 351 through 352 removed outlier: 3.578A pdb=" N GLU C 576 " --> pdb=" O LYS C 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC8, first strand: chain 'C' and resid 557 through 559 removed outlier: 3.657A pdb=" N LEU C 562 " --> pdb=" O ASN C 559 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 617 through 619 Processing sheet with id=AD1, first strand: chain 'C' and resid 617 through 619 removed outlier: 5.426A pdb=" N LEU C 732 " --> pdb=" O LYS C 675 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LYS C 675 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASN C 734 " --> pdb=" O TYR C 673 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR C 673 " --> pdb=" O ASN C 734 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG C 667 " --> pdb=" O LEU C 740 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 652 through 657 removed outlier: 3.726A pdb=" N GLU C 721 " --> pdb=" O LYS C 688 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 234 through 237 Processing sheet with id=AD4, first strand: chain 'D' and resid 299 through 305 removed outlier: 6.600A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 299 through 305 removed outlier: 6.600A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 326 through 329 removed outlier: 3.571A pdb=" N SER D 363 " --> pdb=" O SER D 329 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N THR D 479 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN D 410 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN D 481 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASN D 485 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LYS D 404 " --> pdb=" O ASN D 485 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 326 through 329 removed outlier: 3.571A pdb=" N SER D 363 " --> pdb=" O SER D 329 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N THR D 479 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN D 410 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN D 481 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASN D 485 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LYS D 404 " --> pdb=" O ASN D 485 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR D 403 " --> pdb=" O ASN D 431 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN D 431 " --> pdb=" O TYR D 403 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 351 through 352 Processing sheet with id=AD9, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AE1, first strand: chain 'D' and resid 557 through 559 removed outlier: 3.506A pdb=" N ASN D 559 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU D 562 " --> pdb=" O ASN D 559 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 617 through 619 removed outlier: 3.879A pdb=" N GLU D 721 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR D 723 " --> pdb=" O ASN D 686 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN D 686 " --> pdb=" O THR D 723 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS D 693 " --> pdb=" O ILE D 687 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 647 through 657 removed outlier: 5.832A 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: 6.254A pdb=" N LEU D 649 " --> pdb=" O GLY D 728 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLY D 728 " --> pdb=" O LEU D 649 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY D 651 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ASP D 733 " --> pdb=" O LYS D 675 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LYS D 675 " --> pdb=" O ASP D 733 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU D 735 " --> pdb=" O TYR D 673 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N TYR D 673 " --> pdb=" O LEU D 735 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE D 737 " --> pdb=" O SER D 671 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N SER D 671 " --> pdb=" O ILE D 737 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU D 739 " --> pdb=" O VAL D 669 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL D 669 " --> pdb=" O GLU D 739 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN D 741 " --> pdb=" O ARG D 667 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 234 through 237 Processing sheet with id=AE5, first strand: chain 'E' and resid 420 through 422 removed outlier: 4.298A pdb=" N VAL E 405 " --> pdb=" O SER E 483 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER E 483 " --> pdb=" O VAL E 405 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLN E 481 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR E 409 " --> pdb=" O THR E 479 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR E 479 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU E 411 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU E 477 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN E 362 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER E 363 " --> pdb=" O SER E 329 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLU E 304 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASN E 328 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N GLY E 302 " --> pdb=" O ASN E 328 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU E 306 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN E 389 " --> pdb=" O LEU E 306 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 429 through 432 removed outlier: 6.471A pdb=" N ASN E 431 " --> pdb=" O TYR E 403 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR E 403 " --> pdb=" O ASN E 431 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL E 405 " --> pdb=" O SER E 483 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER E 483 " --> pdb=" O VAL E 405 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLN E 481 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR E 409 " --> pdb=" O THR E 479 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR E 479 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU E 411 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU E 477 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN E 362 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER E 363 " --> pdb=" O SER E 329 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLU E 304 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASN E 328 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N GLY E 302 " --> pdb=" O ASN E 328 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU E 306 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN E 389 " --> pdb=" O LEU E 306 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 351 through 352 removed outlier: 6.098A pdb=" N ASN E 351 " --> pdb=" O PHE E 579 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ILE E 610 " --> pdb=" O SER E 513 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N SER E 515 " --> pdb=" O ILE E 610 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ILE E 612 " --> pdb=" O SER E 515 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE E 517 " --> pdb=" O ILE E 612 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 488 through 489 Processing sheet with id=AE9, first strand: chain 'E' and resid 557 through 559 removed outlier: 4.251A pdb=" N LEU E 562 " --> pdb=" O ASN E 559 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 617 through 619 Processing sheet with id=AF2, first strand: chain 'E' and resid 617 through 619 removed outlier: 5.466A pdb=" N LEU E 732 " --> pdb=" O LYS E 675 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LYS E 675 " --> pdb=" O LEU E 732 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASN E 734 " --> pdb=" O TYR E 673 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR E 673 " --> pdb=" O ASN E 734 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 652 through 657 removed outlier: 3.517A pdb=" N ILE E 655 " --> pdb=" O ILE E 722 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE E 722 " --> pdb=" O ILE E 655 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE E 687 " --> pdb=" O LYS E 693 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS E 693 " --> pdb=" O ILE E 687 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 234 through 237 Processing sheet with id=AF5, first strand: chain 'F' and resid 420 through 422 removed outlier: 5.989A pdb=" N LYS F 404 " --> pdb=" O ASN F 485 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASN F 485 " --> pdb=" O LYS F 404 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN F 481 " --> pdb=" O THR F 408 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN F 410 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR F 479 " --> pdb=" O ASN F 410 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN F 362 " --> pdb=" O LEU F 477 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG F 324 " --> pdb=" O LEU F 306 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU F 306 " --> pdb=" O ARG F 324 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLU F 304 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASN F 328 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY F 302 " --> pdb=" O ASN F 328 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY F 302 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN F 391 " --> pdb=" O GLU F 304 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 429 through 432 removed outlier: 6.415A pdb=" N ASN F 431 " --> pdb=" O TYR F 403 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR F 403 " --> pdb=" O ASN F 431 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LYS F 404 " --> pdb=" O ASN F 485 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASN F 485 " --> pdb=" O LYS F 404 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN F 481 " --> pdb=" O THR F 408 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN F 410 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR F 479 " --> pdb=" O ASN F 410 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN F 362 " --> pdb=" O LEU F 477 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG F 324 " --> pdb=" O LEU F 306 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU F 306 " --> pdb=" O ARG F 324 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLU F 304 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASN F 328 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY F 302 " --> pdb=" O ASN F 328 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY F 302 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN F 391 " --> pdb=" O GLU F 304 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 351 through 352 removed outlier: 6.039A pdb=" N ASN F 351 " --> pdb=" O PHE F 579 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N ILE F 610 " --> pdb=" O SER F 513 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER F 515 " --> pdb=" O ILE F 610 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ILE F 612 " --> pdb=" O SER F 515 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE F 517 " --> pdb=" O ILE F 612 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 488 through 489 Processing sheet with id=AF9, first strand: chain 'F' and resid 557 through 558 Processing sheet with id=AG1, first strand: chain 'F' and resid 617 through 619 removed outlier: 3.613A pdb=" N TYR F 617 " --> pdb=" O ILE F 737 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 732 " --> pdb=" O ASN F 647 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 617 through 619 removed outlier: 3.613A pdb=" N TYR F 617 " --> pdb=" O ILE F 737 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU F 732 " --> pdb=" O LYS F 675 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LYS F 675 " --> pdb=" O LEU F 732 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASN F 734 " --> pdb=" O TYR F 673 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR F 673 " --> pdb=" O ASN F 734 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG F 667 " --> pdb=" O LEU F 740 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 652 through 657 removed outlier: 3.739A pdb=" N GLU F 721 " --> pdb=" O LYS F 688 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN F 686 " --> pdb=" O THR F 723 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR F 725 " --> pdb=" O THR F 684 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 687 " --> pdb=" O LYS F 693 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS F 693 " --> pdb=" O ILE F 687 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 234 through 237 Processing sheet with id=AG5, first strand: chain 'G' and resid 363 through 366 removed outlier: 4.455A pdb=" N ARG G 324 " --> pdb=" O LEU G 306 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU G 306 " --> pdb=" O ARG G 324 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR G 326 " --> pdb=" O GLU G 304 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU G 304 " --> pdb=" O THR G 326 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASN G 328 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N GLY G 302 " --> pdb=" O ASN G 328 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL G 301 " --> pdb=" O TYR G 395 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR G 395 " --> pdb=" O VAL G 301 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N MET G 303 " --> pdb=" O ARG G 393 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG G 393 " --> pdb=" O MET G 303 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN G 305 " --> pdb=" O ASN G 391 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 363 through 366 removed outlier: 4.455A pdb=" N ARG G 324 " --> pdb=" O LEU G 306 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU G 306 " --> pdb=" O ARG G 324 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR G 326 " --> pdb=" O GLU G 304 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU G 304 " --> pdb=" O THR G 326 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASN G 328 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N GLY G 302 " --> pdb=" O ASN G 328 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL G 301 " --> pdb=" O TYR G 395 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR G 395 " --> pdb=" O VAL G 301 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N MET G 303 " --> pdb=" O ARG G 393 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG G 393 " --> pdb=" O MET G 303 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN G 305 " --> pdb=" O ASN G 391 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA G 390 " --> pdb=" O LEU G 448 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 448 " --> pdb=" O ALA G 390 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 351 through 352 Processing sheet with id=AG8, first strand: chain 'G' and resid 417 through 422 removed outlier: 5.317A pdb=" N ALA G 419 " --> pdb=" O LEU G 411 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU G 411 " --> pdb=" O ALA G 419 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR G 403 " --> pdb=" O ASN G 431 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN G 431 " --> pdb=" O TYR G 403 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 417 through 422 removed outlier: 5.317A pdb=" N ALA G 419 " --> pdb=" O LEU G 411 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU G 411 " --> pdb=" O ALA G 419 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL G 405 " --> pdb=" O SER G 483 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER G 483 " --> pdb=" O VAL G 405 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLN G 481 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR G 409 " --> pdb=" O THR G 479 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR G 479 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU G 411 " --> pdb=" O LEU G 477 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU G 477 " --> pdb=" O LEU G 411 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 488 through 489 Processing sheet with id=AH2, first strand: chain 'G' and resid 557 through 559 removed outlier: 3.500A pdb=" N ASN G 559 " --> pdb=" O LEU G 562 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU G 562 " --> pdb=" O ASN G 559 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 617 through 619 Processing sheet with id=AH4, first strand: chain 'G' and resid 617 through 619 removed outlier: 5.211A pdb=" N LEU G 732 " --> pdb=" O LYS G 675 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS G 675 " --> pdb=" O LEU G 732 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASN G 734 " --> pdb=" O TYR G 673 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR G 673 " --> pdb=" O ASN G 734 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG G 667 " --> pdb=" O LEU G 740 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 652 through 657 removed outlier: 3.803A pdb=" N ILE G 722 " --> pdb=" O ILE G 655 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU G 721 " --> pdb=" O LYS G 688 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE G 687 " --> pdb=" O LYS G 693 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS G 693 " --> pdb=" O ILE G 687 " (cutoff:3.500A) 920 hydrogen bonds defined for protein. 2280 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: 6.01 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8684 1.34 - 1.46: 4899 1.46 - 1.57: 13364 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 27012 Sorted by residual: bond pdb=" CD2 TRP F 374 " pdb=" CE2 TRP F 374 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.81e+00 bond pdb=" CD2 TRP G 374 " pdb=" CE2 TRP G 374 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.77e+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 4.75e+00 bond pdb=" CD2 TRP B 374 " pdb=" CE2 TRP B 374 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.72e+00 bond pdb=" CD2 TRP C 374 " pdb=" CE2 TRP C 374 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.62e+00 ... (remaining 27007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 35499 1.32 - 2.64: 797 2.64 - 3.96: 146 3.96 - 5.28: 19 5.28 - 6.60: 24 Bond angle restraints: 36485 Sorted by residual: angle pdb=" CD2 TRP F 374 " pdb=" CE3 TRP F 374 " pdb=" CZ3 TRP F 374 " ideal model delta sigma weight residual 118.60 124.04 -5.44 1.30e+00 5.92e-01 1.75e+01 angle pdb=" CD2 TRP B 631 " pdb=" CE3 TRP B 631 " pdb=" CZ3 TRP B 631 " ideal model delta sigma weight residual 118.60 124.01 -5.41 1.30e+00 5.92e-01 1.73e+01 angle pdb=" CD2 TRP A 631 " pdb=" CE3 TRP A 631 " pdb=" CZ3 TRP A 631 " ideal model delta sigma weight residual 118.60 124.00 -5.40 1.30e+00 5.92e-01 1.73e+01 angle pdb=" CD2 TRP B 374 " pdb=" CE3 TRP B 374 " pdb=" CZ3 TRP B 374 " 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 C 631 " pdb=" CE3 TRP C 631 " pdb=" CZ3 TRP C 631 " ideal model delta sigma weight residual 118.60 123.98 -5.38 1.30e+00 5.92e-01 1.71e+01 ... (remaining 36480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 14703 17.81 - 35.62: 1360 35.62 - 53.43: 221 53.43 - 71.24: 50 71.24 - 89.05: 29 Dihedral angle restraints: 16363 sinusoidal: 6468 harmonic: 9895 Sorted by residual: dihedral pdb=" CA GLU F 533 " pdb=" C GLU F 533 " pdb=" N GLN F 534 " pdb=" CA GLN F 534 " ideal model delta harmonic sigma weight residual 180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ALA E 386 " pdb=" C ALA E 386 " pdb=" N TYR E 387 " pdb=" CA TYR E 387 " ideal model delta harmonic sigma weight residual 180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLU D 533 " pdb=" C GLU D 533 " pdb=" N GLN D 534 " pdb=" CA GLN D 534 " ideal model delta harmonic sigma weight residual -180.00 -161.35 -18.65 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 16360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2539 0.031 - 0.063: 1107 0.063 - 0.094: 303 0.094 - 0.126: 264 0.126 - 0.157: 12 Chirality restraints: 4225 Sorted by residual: chirality pdb=" CB ILE A 657 " pdb=" CA ILE A 657 " pdb=" CG1 ILE A 657 " pdb=" CG2 ILE A 657 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CB ILE E 656 " pdb=" CA ILE E 656 " pdb=" CG1 ILE E 656 " pdb=" CG2 ILE E 656 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ILE D 352 " pdb=" N ILE D 352 " pdb=" C ILE D 352 " pdb=" CB ILE D 352 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 4222 not shown) Planarity restraints: 4756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 698 " -0.046 5.00e-02 4.00e+02 6.96e-02 7.75e+00 pdb=" N PRO F 699 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO F 699 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 699 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 698 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO G 699 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO G 699 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 699 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 743 " -0.028 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO E 744 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 744 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 744 " -0.024 5.00e-02 4.00e+02 ... (remaining 4753 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4582 2.77 - 3.31: 24158 3.31 - 3.84: 41920 3.84 - 4.37: 51070 4.37 - 4.90: 89406 Nonbonded interactions: 211136 Sorted by model distance: nonbonded pdb=" O GLY A 651 " pdb=" OG SER A 726 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR G 331 " pdb=" OD2 ASP G 519 " model vdw 2.254 3.040 nonbonded pdb=" OE2 GLU C 230 " pdb="CA CA C 901 " model vdw 2.266 3.250 nonbonded pdb=" O SER E 632 " pdb=" OG1 THR E 653 " model vdw 2.268 3.040 nonbonded pdb=" OE2 GLU E 230 " pdb="CA CA E 901 " model vdw 2.270 3.250 ... (remaining 211131 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 308 or resid 310 through 386 or resid 389 thro \ ugh 449 or resid 460 through 903)) selection = (chain 'B' and (resid 216 through 308 or resid 326 or resid 341 through 342 or r \ esid 389 through 449 or resid 460 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 742 or resi \ d 901 through 903)) selection = (chain 'C' and (resid 216 through 308 or resid 354 through 355 or resid 365 or r \ esid 381 or resid 390 through 449 or resid 460 through 614 or (resid 615 and (na \ me N or name CA or name C or name O or name CB or name CG )) or resid 616 throug \ h 742 or resid 901 through 903)) selection = (chain 'D' and (resid 216 through 308 or resid 335 or resid 341 through 342 or r \ esid 346 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 742 or resid 901 throug \ h 903)) selection = (chain 'E' and (resid 216 through 308 or resid 354 through 355 or resid 386 or r \ esid 389 through 449 or resid 460 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 742 or resi \ d 901 through 903)) selection = (chain 'F' and (resid 216 through 308 or resid 354 through 355 or resid 365 or r \ esid 381 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 742 or resid 901 through 903)) selection = (chain 'G' and (resid 216 through 307 or resid 340 or resid 354 through 355 or r \ esid 365 or resid 389 through 614 or (resid 615 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 616 through 742 or resid 901 throug \ h 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 26.270 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 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 : 0.003 0.037 27012 Z= 0.142 Angle : 0.528 6.602 36485 Z= 0.321 Chirality : 0.044 0.157 4225 Planarity : 0.004 0.070 4756 Dihedral : 14.504 89.055 9895 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.13 % Allowed : 0.33 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.13 (0.14), residues: 3401 helix: -0.38 (0.24), residues: 474 sheet: 1.38 (0.19), residues: 742 loop : -0.55 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 324 TYR 0.023 0.001 TYR F 463 PHE 0.012 0.001 PHE C 579 TRP 0.009 0.001 TRP B 374 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (27012) covalent geometry : angle 0.52841 / 0.32 (36485) hydrogen bonds : bond 0.23184 / 14.93 ( 827) hydrogen bonds : angle 8.60302 / 5.94 ( 2280) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 418 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 570 ILE cc_start: 0.7189 (pt) cc_final: 0.6943 (pt) outliers start: 4 outliers final: 0 residues processed: 422 average time/residue: 0.1790 time to fit residues: 119.3755 Evaluate side-chains 175 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 0.0050 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 6.9990 overall best weight: 4.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 485 ASN B 431 ASN B 474 GLN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 ASN ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 ASN D 500 ASN E 391 ASN F 391 ASN F 435 ASN F 500 ASN F 590 GLN G 334 ASN G 500 ASN G 647 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.077197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.056011 restraints weight = 87889.453| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.63 r_work: 0.2808 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27012 Z= 0.163 Angle : 0.570 7.805 36485 Z= 0.324 Chirality : 0.045 0.215 4225 Planarity : 0.004 0.048 4756 Dihedral : 4.134 24.295 3427 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.05 % Allowed : 6.75 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: 0.02 (0.14), residues: 3401 helix: -0.19 (0.24), residues: 471 sheet: 1.40 (0.19), residues: 729 loop : -0.41 (0.13), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 324 TYR 0.012 0.001 TYR D 229 PHE 0.019 0.001 PHE G 670 TRP 0.010 0.001 TRP F 502 HIS 0.002 0.001 HIS E 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (27012) covalent geometry : angle 0.57002 / 0.32 (36485) hydrogen bonds : bond 0.03681 / 2.34 ( 827) hydrogen bonds : angle 5.57757 / 3.83 ( 2280) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 625 ASN cc_start: 0.9146 (t0) cc_final: 0.8712 (m-40) REVERT: B 475 ILE cc_start: 0.5128 (tp) cc_final: 0.4859 (tp) REVERT: B 476 LYS cc_start: 0.6715 (mmtt) cc_final: 0.6336 (mmtt) REVERT: B 492 GLN cc_start: 0.8807 (mp10) cc_final: 0.8591 (mp10) REVERT: B 659 MET cc_start: 0.6961 (tpp) cc_final: 0.6512 (tpp) REVERT: C 303 MET cc_start: 0.7726 (ppp) cc_final: 0.7319 (ppp) REVERT: C 332 ASP cc_start: 0.8936 (m-30) cc_final: 0.8728 (m-30) REVERT: D 305 ASN cc_start: 0.8988 (t0) cc_final: 0.8729 (t0) REVERT: E 723 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8878 (p) REVERT: G 303 MET cc_start: 0.8914 (tpp) cc_final: 0.8557 (tpp) outliers start: 32 outliers final: 19 residues processed: 199 average time/residue: 0.1602 time to fit residues: 52.9550 Evaluate side-chains 157 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 555 SER Chi-restraints excluded: chain D residue 716 ASP Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 647 ASN Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 209 optimal weight: 0.0980 chunk 89 optimal weight: 30.0000 chunk 80 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 280 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 overall best weight: 6.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN B 465 GLN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 ASN E 474 GLN E 500 ASN ** G 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 590 GLN G 647 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.073495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.052128 restraints weight = 89521.456| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.69 r_work: 0.2713 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 27012 Z= 0.211 Angle : 0.570 11.099 36485 Z= 0.325 Chirality : 0.045 0.175 4225 Planarity : 0.004 0.043 4756 Dihedral : 4.237 23.259 3427 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.15 % Allowed : 9.11 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.05 (0.14), residues: 3401 helix: -0.19 (0.24), residues: 482 sheet: 1.28 (0.18), residues: 753 loop : -0.46 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 527 TYR 0.013 0.001 TYR E 296 PHE 0.012 0.001 PHE G 670 TRP 0.010 0.001 TRP F 502 HIS 0.004 0.002 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 (27012) covalent geometry : angle 0.57046 / 0.33 (36485) hydrogen bonds : bond 0.03843 / 2.47 ( 827) hydrogen bonds : angle 5.21387 / 3.60 ( 2280) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 647 ASN cc_start: 0.8505 (p0) cc_final: 0.8071 (p0) REVERT: B 358 HIS cc_start: 0.8852 (m-70) cc_final: 0.8652 (m-70) REVERT: B 492 GLN cc_start: 0.9010 (mp10) cc_final: 0.8727 (mp10) REVERT: B 659 MET cc_start: 0.7495 (tpp) cc_final: 0.6897 (tpp) REVERT: C 303 MET cc_start: 0.7861 (ppp) cc_final: 0.7512 (ppp) REVERT: C 332 ASP cc_start: 0.8961 (m-30) cc_final: 0.8679 (m-30) REVERT: C 697 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8945 (pp) REVERT: D 468 LYS cc_start: 0.9473 (OUTLIER) cc_final: 0.9249 (tttt) REVERT: E 723 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.9012 (p) REVERT: G 719 ASP cc_start: 0.8812 (m-30) cc_final: 0.8548 (m-30) outliers start: 35 outliers final: 18 residues processed: 182 average time/residue: 0.1546 time to fit residues: 47.6877 Evaluate side-chains 148 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 555 SER Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 725 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 630 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 239 optimal weight: 30.0000 chunk 164 optimal weight: 0.9990 chunk 108 optimal weight: 30.0000 chunk 211 optimal weight: 8.9990 chunk 259 optimal weight: 20.0000 chunk 232 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 chunk 260 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 391 ASN B 465 GLN B 500 ASN B 566 ASN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 ASN F 351 ASN F 492 GLN ** F 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.051297 restraints weight = 89313.515| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.68 r_work: 0.2694 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 27012 Z= 0.206 Angle : 0.555 10.294 36485 Z= 0.316 Chirality : 0.045 0.158 4225 Planarity : 0.003 0.046 4756 Dihedral : 4.237 21.824 3427 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.21 % Allowed : 10.65 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.08 (0.14), residues: 3401 helix: -0.14 (0.24), residues: 481 sheet: 1.21 (0.18), residues: 765 loop : -0.49 (0.13), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 527 TYR 0.011 0.001 TYR F 296 PHE 0.011 0.001 PHE C 710 TRP 0.010 0.001 TRP F 502 HIS 0.003 0.001 HIS C 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (27012) covalent geometry : angle 0.55526 / 0.32 (36485) hydrogen bonds : bond 0.03305 / 2.11 ( 827) hydrogen bonds : angle 5.06152 / 3.49 ( 2280) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 492 GLN cc_start: 0.9103 (mp10) cc_final: 0.8831 (mp10) REVERT: B 659 MET cc_start: 0.7599 (tpp) cc_final: 0.7058 (tpp) REVERT: C 303 MET cc_start: 0.8043 (ppp) cc_final: 0.7682 (ppp) REVERT: C 332 ASP cc_start: 0.8992 (m-30) cc_final: 0.8700 (m-30) REVERT: C 697 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9030 (pp) REVERT: D 468 LYS cc_start: 0.9490 (OUTLIER) cc_final: 0.9280 (tttt) REVERT: F 361 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8434 (p0) REVERT: F 657 ILE cc_start: 0.9392 (mm) cc_final: 0.9178 (tp) REVERT: F 659 MET cc_start: 0.8124 (tpp) cc_final: 0.7880 (tpp) REVERT: G 303 MET cc_start: 0.9384 (ttt) cc_final: 0.9069 (tpp) REVERT: G 719 ASP cc_start: 0.8925 (m-30) cc_final: 0.8603 (m-30) outliers start: 37 outliers final: 19 residues processed: 171 average time/residue: 0.1502 time to fit residues: 44.1125 Evaluate side-chains 137 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 716 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 723 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 263 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 330 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 295 optimal weight: 20.0000 chunk 42 optimal weight: 50.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 465 GLN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 ASN E 686 ASN F 492 GLN ** F 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.072387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.051242 restraints weight = 89197.522| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.68 r_work: 0.2694 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27012 Z= 0.183 Angle : 0.535 9.720 36485 Z= 0.306 Chirality : 0.044 0.157 4225 Planarity : 0.003 0.047 4756 Dihedral : 4.155 20.583 3427 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.25 % Allowed : 11.53 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.04 (0.14), residues: 3401 helix: -0.05 (0.24), residues: 482 sheet: 1.20 (0.18), residues: 769 loop : -0.47 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 527 TYR 0.010 0.001 TYR F 296 PHE 0.012 0.001 PHE C 710 TRP 0.007 0.001 TRP C 374 HIS 0.003 0.001 HIS C 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (27012) covalent geometry : angle 0.53453 / 0.31 (36485) hydrogen bonds : bond 0.03210 / 2.04 ( 827) hydrogen bonds : angle 4.97710 / 3.43 ( 2280) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 666 LYS cc_start: 0.8174 (mttm) cc_final: 0.7679 (mtmm) REVERT: B 492 GLN cc_start: 0.9109 (mp10) cc_final: 0.8839 (mp10) REVERT: B 654 LYS cc_start: 0.8565 (mmmt) cc_final: 0.8270 (mmmt) REVERT: B 659 MET cc_start: 0.7594 (tpp) cc_final: 0.7075 (tpp) REVERT: C 303 MET cc_start: 0.8091 (ppp) cc_final: 0.7707 (ppp) REVERT: C 332 ASP cc_start: 0.9011 (m-30) cc_final: 0.8695 (m-30) REVERT: D 468 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.9230 (tttt) REVERT: F 361 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8489 (p0) REVERT: F 659 MET cc_start: 0.8157 (tpp) cc_final: 0.7858 (tpp) REVERT: G 719 ASP cc_start: 0.8957 (m-30) cc_final: 0.8670 (m-30) outliers start: 38 outliers final: 25 residues processed: 168 average time/residue: 0.1437 time to fit residues: 41.5772 Evaluate side-chains 142 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 716 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 725 THR Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 645 VAL Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 736 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 201 optimal weight: 6.9990 chunk 255 optimal weight: 0.7980 chunk 59 optimal weight: 40.0000 chunk 240 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 148 optimal weight: 0.0000 chunk 233 optimal weight: 7.9990 chunk 324 optimal weight: 6.9990 overall best weight: 3.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 391 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 492 GLN ** F 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.073791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.052915 restraints weight = 88529.080| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.64 r_work: 0.2746 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27012 Z= 0.131 Angle : 0.507 11.024 36485 Z= 0.290 Chirality : 0.044 0.254 4225 Planarity : 0.003 0.046 4756 Dihedral : 3.927 19.294 3427 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.18 % Allowed : 12.39 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: 0.11 (0.14), residues: 3401 helix: 0.16 (0.24), residues: 482 sheet: 1.28 (0.18), residues: 770 loop : -0.39 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 667 TYR 0.008 0.001 TYR F 260 PHE 0.010 0.001 PHE C 710 TRP 0.007 0.001 TRP C 631 HIS 0.002 0.001 HIS C 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (27012) covalent geometry : angle 0.50685 / 0.29 (36485) hydrogen bonds : bond 0.02853 / 1.83 ( 827) hydrogen bonds : angle 4.79251 / 3.30 ( 2280) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 666 LYS cc_start: 0.8214 (mttm) cc_final: 0.7703 (mtmm) REVERT: B 492 GLN cc_start: 0.9128 (mp10) cc_final: 0.8913 (mp10) REVERT: B 654 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8108 (mmmm) REVERT: B 659 MET cc_start: 0.7612 (tpp) cc_final: 0.7117 (tpp) REVERT: C 303 MET cc_start: 0.8150 (ppp) cc_final: 0.7813 (ppp) REVERT: C 332 ASP cc_start: 0.8961 (m-30) cc_final: 0.8650 (m-30) REVERT: D 468 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.9256 (tttt) REVERT: E 389 ASN cc_start: 0.8375 (t0) cc_final: 0.7926 (t0) REVERT: F 254 LYS cc_start: 0.9037 (mmtp) cc_final: 0.8693 (mtmt) REVERT: F 361 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8569 (p0) REVERT: F 659 MET cc_start: 0.8206 (tpp) cc_final: 0.7893 (tpp) REVERT: F 697 LEU cc_start: 0.9063 (mt) cc_final: 0.8735 (mp) REVERT: G 719 ASP cc_start: 0.8947 (m-30) cc_final: 0.8679 (m-30) outliers start: 36 outliers final: 25 residues processed: 164 average time/residue: 0.1509 time to fit residues: 42.9830 Evaluate side-chains 141 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 716 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 645 VAL Chi-restraints excluded: chain G residue 716 ASP Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 738 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 213 optimal weight: 10.0000 chunk 193 optimal weight: 30.0000 chunk 330 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 262 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 217 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 431 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 ASN ** F 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.071828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.050752 restraints weight = 89466.290| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.67 r_work: 0.2682 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 27012 Z= 0.203 Angle : 0.549 10.584 36485 Z= 0.312 Chirality : 0.045 0.344 4225 Planarity : 0.003 0.046 4756 Dihedral : 4.162 21.171 3427 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.47 % Allowed : 13.11 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.01 (0.14), residues: 3401 helix: 0.05 (0.24), residues: 479 sheet: 1.24 (0.18), residues: 766 loop : -0.48 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 289 TYR 0.011 0.001 TYR F 296 PHE 0.010 0.001 PHE A 621 TRP 0.008 0.001 TRP F 502 HIS 0.003 0.001 HIS C 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (27012) covalent geometry : angle 0.54944 / 0.31 (36485) hydrogen bonds : bond 0.03238 / 2.06 ( 827) hydrogen bonds : angle 4.89447 / 3.37 ( 2280) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 666 LYS cc_start: 0.8271 (mttm) cc_final: 0.7783 (mtmm) REVERT: B 492 GLN cc_start: 0.9159 (mp10) cc_final: 0.8887 (mp10) REVERT: B 654 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8094 (mmmm) REVERT: B 659 MET cc_start: 0.7554 (tpp) cc_final: 0.7096 (tpp) REVERT: C 303 MET cc_start: 0.8098 (ppp) cc_final: 0.7726 (ppp) REVERT: C 332 ASP cc_start: 0.8998 (m-30) cc_final: 0.8674 (m-30) REVERT: C 352 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9018 (mm) REVERT: D 468 LYS cc_start: 0.9502 (OUTLIER) cc_final: 0.9247 (tttt) REVERT: D 533 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8388 (pt0) REVERT: F 361 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8587 (p0) REVERT: F 657 ILE cc_start: 0.9412 (mm) cc_final: 0.9202 (tp) REVERT: F 659 MET cc_start: 0.8167 (tpp) cc_final: 0.7836 (tpp) REVERT: G 719 ASP cc_start: 0.8983 (m-30) cc_final: 0.8689 (m-30) outliers start: 45 outliers final: 31 residues processed: 156 average time/residue: 0.1532 time to fit residues: 41.6787 Evaluate side-chains 143 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 716 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 725 THR Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 645 VAL Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 736 SER Chi-restraints excluded: chain G residue 738 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 329 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 230 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 chunk 170 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 43 optimal weight: 50.0000 chunk 7 optimal weight: 6.9990 chunk 269 optimal weight: 8.9990 chunk 280 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 692 GLN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 ASN ** F 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.072233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.051717 restraints weight = 88630.822| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.56 r_work: 0.2712 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27012 Z= 0.190 Angle : 0.538 9.685 36485 Z= 0.306 Chirality : 0.045 0.260 4225 Planarity : 0.003 0.047 4756 Dihedral : 4.143 20.656 3427 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.41 % Allowed : 13.43 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.00 (0.14), residues: 3401 helix: 0.03 (0.24), residues: 482 sheet: 1.25 (0.18), residues: 782 loop : -0.48 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 289 TYR 0.010 0.001 TYR F 296 PHE 0.010 0.001 PHE A 621 TRP 0.006 0.001 TRP F 502 HIS 0.003 0.001 HIS C 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (27012) covalent geometry : angle 0.53773 / 0.31 (36485) hydrogen bonds : bond 0.03072 / 1.97 ( 827) hydrogen bonds : angle 4.87346 / 3.36 ( 2280) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.8987 (ttm) cc_final: 0.8784 (mtp) REVERT: A 666 LYS cc_start: 0.8248 (mttm) cc_final: 0.7745 (mtmm) REVERT: B 492 GLN cc_start: 0.9159 (mp10) cc_final: 0.8905 (mp10) REVERT: B 654 LYS cc_start: 0.8583 (mmmt) cc_final: 0.7962 (mmmm) REVERT: B 659 MET cc_start: 0.7461 (tpp) cc_final: 0.7021 (tpp) REVERT: C 303 MET cc_start: 0.8241 (ppp) cc_final: 0.7976 (ppp) REVERT: C 332 ASP cc_start: 0.8979 (m-30) cc_final: 0.8661 (m-30) REVERT: C 352 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9051 (mm) REVERT: C 464 ASP cc_start: 0.8814 (m-30) cc_final: 0.8548 (t0) REVERT: C 478 GLU cc_start: 0.8374 (pm20) cc_final: 0.7816 (pm20) REVERT: D 468 LYS cc_start: 0.9497 (OUTLIER) cc_final: 0.9245 (tttt) REVERT: D 533 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8405 (pt0) REVERT: F 361 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8659 (p0) REVERT: F 657 ILE cc_start: 0.9420 (mm) cc_final: 0.9212 (tp) REVERT: F 659 MET cc_start: 0.8202 (tpp) cc_final: 0.7885 (tpp) REVERT: G 719 ASP cc_start: 0.8993 (m-30) cc_final: 0.8695 (m-30) outliers start: 43 outliers final: 30 residues processed: 160 average time/residue: 0.1569 time to fit residues: 43.2750 Evaluate side-chains 149 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 716 ASP Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 736 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 165 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 265 optimal weight: 0.0370 chunk 48 optimal weight: 9.9990 chunk 189 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 221 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** D 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 ASN ** F 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.072961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.052146 restraints weight = 89003.992| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.62 r_work: 0.2727 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27012 Z= 0.150 Angle : 0.521 9.260 36485 Z= 0.297 Chirality : 0.044 0.224 4225 Planarity : 0.003 0.046 4756 Dihedral : 4.018 19.770 3427 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.25 % Allowed : 13.89 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: 0.07 (0.14), residues: 3401 helix: 0.08 (0.24), residues: 481 sheet: 1.36 (0.18), residues: 775 loop : -0.46 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 324 TYR 0.009 0.001 TYR F 260 PHE 0.010 0.001 PHE A 621 TRP 0.006 0.001 TRP C 631 HIS 0.002 0.001 HIS C 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (27012) covalent geometry : angle 0.52079 / 0.30 (36485) hydrogen bonds : bond 0.02920 / 1.88 ( 827) hydrogen bonds : angle 4.77319 / 3.30 ( 2280) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 666 LYS cc_start: 0.8218 (mttm) cc_final: 0.7692 (mtmm) REVERT: B 492 GLN cc_start: 0.9144 (mp10) cc_final: 0.8920 (mp10) REVERT: B 654 LYS cc_start: 0.8592 (mmmt) cc_final: 0.7953 (mmmm) REVERT: B 659 MET cc_start: 0.7515 (tpp) cc_final: 0.7104 (tpp) REVERT: C 303 MET cc_start: 0.8242 (ppp) cc_final: 0.8020 (ppp) REVERT: C 332 ASP cc_start: 0.8978 (m-30) cc_final: 0.8648 (m-30) REVERT: C 352 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9075 (mm) REVERT: C 430 ASN cc_start: 0.9184 (OUTLIER) cc_final: 0.8963 (m110) REVERT: C 464 ASP cc_start: 0.8843 (m-30) cc_final: 0.8570 (t0) REVERT: C 478 GLU cc_start: 0.8400 (pm20) cc_final: 0.7861 (pm20) REVERT: D 468 LYS cc_start: 0.9497 (OUTLIER) cc_final: 0.9263 (tttt) REVERT: D 533 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8380 (pt0) REVERT: E 389 ASN cc_start: 0.8349 (t0) cc_final: 0.8033 (t0) REVERT: F 254 LYS cc_start: 0.9043 (mmtp) cc_final: 0.8692 (mtmt) REVERT: F 361 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8686 (p0) REVERT: F 657 ILE cc_start: 0.9404 (mm) cc_final: 0.9193 (tp) REVERT: F 659 MET cc_start: 0.8197 (tpp) cc_final: 0.7883 (tpp) REVERT: G 719 ASP cc_start: 0.8989 (m-30) cc_final: 0.8705 (m-30) outliers start: 38 outliers final: 25 residues processed: 149 average time/residue: 0.1595 time to fit residues: 40.8656 Evaluate side-chains 140 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 716 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 523 GLN Chi-restraints excluded: chain G residue 723 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 61 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 247 optimal weight: 0.0170 chunk 327 optimal weight: 6.9990 chunk 278 optimal weight: 9.9990 chunk 79 optimal weight: 0.0870 chunk 296 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 chunk 221 optimal weight: 9.9990 overall best weight: 2.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.073799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.053009 restraints weight = 88426.828| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.62 r_work: 0.2749 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27012 Z= 0.126 Angle : 0.513 13.105 36485 Z= 0.291 Chirality : 0.044 0.221 4225 Planarity : 0.003 0.045 4756 Dihedral : 3.853 19.128 3427 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.95 % Allowed : 14.12 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: 0.20 (0.14), residues: 3401 helix: 0.21 (0.24), residues: 482 sheet: 1.47 (0.18), residues: 775 loop : -0.38 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 667 TYR 0.008 0.001 TYR E 260 PHE 0.010 0.001 PHE C 710 TRP 0.007 0.001 TRP C 631 HIS 0.002 0.001 HIS C 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (27012) covalent geometry : angle 0.51326 / 0.29 (36485) hydrogen bonds : bond 0.02690 / 1.74 ( 827) hydrogen bonds : angle 4.66208 / 3.23 ( 2280) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 666 LYS cc_start: 0.8188 (mttm) cc_final: 0.7654 (mtmm) REVERT: B 492 GLN cc_start: 0.9147 (mp10) cc_final: 0.8929 (mp10) REVERT: B 654 LYS cc_start: 0.8580 (mmmt) cc_final: 0.7935 (mmmm) REVERT: B 659 MET cc_start: 0.7570 (tpp) cc_final: 0.7171 (tpp) REVERT: C 303 MET cc_start: 0.8215 (ppp) cc_final: 0.7981 (ppp) REVERT: C 332 ASP cc_start: 0.8960 (m-30) cc_final: 0.8601 (m-30) REVERT: C 352 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9108 (mm) REVERT: C 430 ASN cc_start: 0.9152 (OUTLIER) cc_final: 0.8920 (m110) REVERT: C 464 ASP cc_start: 0.8846 (m-30) cc_final: 0.8574 (t0) REVERT: C 478 GLU cc_start: 0.8462 (pm20) cc_final: 0.7938 (pm20) REVERT: D 468 LYS cc_start: 0.9500 (OUTLIER) cc_final: 0.9204 (tttt) REVERT: D 533 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8325 (pt0) REVERT: E 389 ASN cc_start: 0.8305 (t0) cc_final: 0.7989 (t0) REVERT: F 254 LYS cc_start: 0.9032 (mmtp) cc_final: 0.8688 (mtmt) REVERT: F 657 ILE cc_start: 0.9381 (mm) cc_final: 0.9154 (tp) REVERT: F 659 MET cc_start: 0.8167 (tpp) cc_final: 0.7885 (tpp) REVERT: G 303 MET cc_start: 0.9363 (ttt) cc_final: 0.8950 (tpp) REVERT: G 659 MET cc_start: 0.7834 (tpp) cc_final: 0.7634 (tpp) REVERT: G 719 ASP cc_start: 0.9027 (m-30) cc_final: 0.8782 (m-30) outliers start: 29 outliers final: 23 residues processed: 151 average time/residue: 0.1620 time to fit residues: 41.9482 Evaluate side-chains 144 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 716 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 523 GLN Chi-restraints excluded: chain G residue 716 ASP Chi-restraints excluded: chain G residue 723 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 221 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 330 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 329 optimal weight: 6.9990 chunk 243 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN ** F 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.071486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.050457 restraints weight = 89599.835| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.66 r_work: 0.2677 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 27012 Z= 0.211 Angle : 0.561 12.779 36485 Z= 0.316 Chirality : 0.045 0.215 4225 Planarity : 0.003 0.046 4756 Dihedral : 4.151 21.134 3427 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.08 % Allowed : 14.19 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: 0.00 (0.14), residues: 3401 helix: -0.01 (0.24), residues: 482 sheet: 1.30 (0.18), residues: 782 loop : -0.49 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 527 TYR 0.011 0.001 TYR F 260 PHE 0.009 0.001 PHE C 710 TRP 0.008 0.001 TRP F 502 HIS 0.003 0.001 HIS C 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (27012) covalent geometry : angle 0.56072 / 0.32 (36485) hydrogen bonds : bond 0.03186 / 2.05 ( 827) hydrogen bonds : angle 4.82886 / 3.34 ( 2280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5067.79 seconds wall clock time: 88 minutes 30.84 seconds (5310.84 seconds total)