Starting phenix.real_space_refine on Sun Jun 22 09:57:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsi_61774/06_2025/9jsi_61774.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsi_61774/06_2025/9jsi_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jsi_61774/06_2025/9jsi_61774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsi_61774/06_2025/9jsi_61774.map" model { file = "/net/cci-nas-00/data/ceres_data/9jsi_61774/06_2025/9jsi_61774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsi_61774/06_2025/9jsi_61774.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 15.91, per 1000 atoms: 0.60 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: 6.22 Conformation dependent library (CDL) restraints added in 4.0 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: 4.61 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: 10.93 Time building geometry restraints manager: 7.41 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 2.510 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 2.510 ... (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 742 or resid 901 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.140 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 62.360 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (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 TRP 0.009 0.001 TRP B 374 HIS 0.001 0.000 HIS F 358 PHE 0.012 0.001 PHE C 579 TYR 0.023 0.001 TYR F 463 ARG 0.000 0.000 ARG E 324 Details of bonding type rmsd hydrogen bonds : bond 0.23184 ( 827) hydrogen bonds : angle 8.60302 ( 2280) covalent geometry : bond 0.00280 (27012) covalent geometry : angle 0.52841 (36485) *********************** 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 : 3.350 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: 0.3863 time to fit residues: 256.2975 Evaluate side-chains 174 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 9.9990 chunk 259 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 88 optimal weight: 40.0000 chunk 175 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 268 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 163 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 chunk 311 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN 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 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 ASN E 391 ASN ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.074466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.052987 restraints weight = 89121.356| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.68 r_work: 0.2730 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 27012 Z= 0.237 Angle : 0.614 7.953 36485 Z= 0.347 Chirality : 0.046 0.218 4225 Planarity : 0.004 0.046 4756 Dihedral : 4.324 23.190 3427 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.02 % Allowed : 6.85 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3401 helix: -0.31 (0.24), residues: 468 sheet: 1.28 (0.19), residues: 739 loop : -0.47 (0.13), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 502 HIS 0.003 0.001 HIS F 358 PHE 0.020 0.001 PHE G 670 TYR 0.012 0.001 TYR E 296 ARG 0.000 0.000 ARG C 324 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 827) hydrogen bonds : angle 5.70284 ( 2280) covalent geometry : bond 0.00529 (27012) covalent geometry : angle 0.61397 (36485) *********************** 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 195 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 625 ASN cc_start: 0.9160 (t0) cc_final: 0.8735 (m-40) REVERT: B 492 GLN cc_start: 0.8913 (mp10) cc_final: 0.8651 (mp10) REVERT: B 659 MET cc_start: 0.6998 (tpp) cc_final: 0.6529 (tpp) REVERT: C 303 MET cc_start: 0.7841 (ppp) cc_final: 0.7446 (ppp) REVERT: C 332 ASP cc_start: 0.8976 (m-30) cc_final: 0.8677 (m-30) REVERT: D 305 ASN cc_start: 0.9069 (t0) cc_final: 0.8796 (t0) REVERT: E 262 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8697 (pm20) REVERT: E 723 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9023 (p) REVERT: F 739 GLU cc_start: 0.8449 (pp20) cc_final: 0.8215 (pp20) outliers start: 31 outliers final: 20 residues processed: 192 average time/residue: 0.3500 time to fit residues: 113.5918 Evaluate side-chains 148 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 3.330 ------------------------------------------------------------------------------- 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 411 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 555 SER Chi-restraints excluded: chain E residue 262 GLU 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 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 409 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 335 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 106 optimal weight: 0.0470 chunk 264 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 195 optimal weight: 9.9990 chunk 289 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 overall best weight: 2.6684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN B 500 ASN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 ASN ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 492 GLN ** F 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 734 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 = 0.3408 r_free = 0.3408 target = 0.075721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.054557 restraints weight = 88000.504| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.64 r_work: 0.2785 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2879 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= 0.129 Angle : 0.517 12.313 36485 Z= 0.296 Chirality : 0.044 0.165 4225 Planarity : 0.003 0.042 4756 Dihedral : 3.961 21.470 3427 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.85 % Allowed : 8.45 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3401 helix: -0.15 (0.24), residues: 470 sheet: 1.44 (0.19), residues: 749 loop : -0.39 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 502 HIS 0.002 0.001 HIS C 358 PHE 0.015 0.001 PHE G 670 TYR 0.008 0.001 TYR F 260 ARG 0.000 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 827) hydrogen bonds : angle 5.19457 ( 2280) covalent geometry : bond 0.00269 (27012) covalent geometry : angle 0.51660 (36485) *********************** 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 182 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8444 (tp30) REVERT: A 625 ASN cc_start: 0.9150 (t0) cc_final: 0.8706 (m-40) REVERT: B 492 GLN cc_start: 0.8958 (mp10) cc_final: 0.8666 (mp10) REVERT: B 654 LYS cc_start: 0.8494 (mmmt) cc_final: 0.8283 (mmmt) REVERT: B 659 MET cc_start: 0.7367 (tpp) cc_final: 0.6814 (tpp) REVERT: C 303 MET cc_start: 0.7913 (ppp) cc_final: 0.7586 (ppp) REVERT: C 332 ASP cc_start: 0.8937 (m-30) cc_final: 0.8650 (m-30) REVERT: C 697 LEU cc_start: 0.9171 (tt) cc_final: 0.8946 (pp) REVERT: D 305 ASN cc_start: 0.9085 (t0) cc_final: 0.8870 (t0) REVERT: D 468 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9253 (tttt) REVERT: E 723 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.9006 (p) REVERT: F 659 MET cc_start: 0.7856 (tpp) cc_final: 0.7655 (tpp) REVERT: F 739 GLU cc_start: 0.8534 (pp20) cc_final: 0.8206 (pp20) outliers start: 26 outliers final: 12 residues processed: 178 average time/residue: 0.3523 time to fit residues: 105.7996 Evaluate side-chains 147 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain D residue 468 LYS 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 645 VAL Chi-restraints excluded: chain E residue 649 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 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 342 optimal weight: 30.0000 chunk 312 optimal weight: 9.9990 chunk 331 optimal weight: 3.9990 chunk 275 optimal weight: 0.0870 chunk 158 optimal weight: 20.0000 chunk 258 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 286 optimal weight: 6.9990 chunk 42 optimal weight: 0.0060 chunk 15 optimal weight: 20.0000 chunk 325 optimal weight: 5.9990 overall best weight: 3.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN E 391 ASN E 474 GLN F 351 ASN ** 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 = 0.3394 r_free = 0.3394 target = 0.074948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.053712 restraints weight = 89147.819| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.71 r_work: 0.2766 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.3305 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= 0.137 Angle : 0.506 9.588 36485 Z= 0.290 Chirality : 0.044 0.202 4225 Planarity : 0.003 0.041 4756 Dihedral : 3.852 19.389 3427 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.08 % Allowed : 10.26 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3401 helix: -0.03 (0.24), residues: 477 sheet: 1.48 (0.18), residues: 745 loop : -0.36 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 502 HIS 0.002 0.001 HIS C 358 PHE 0.011 0.001 PHE G 670 TYR 0.008 0.001 TYR F 260 ARG 0.000 0.000 ARG E 667 Details of bonding type rmsd hydrogen bonds : bond 0.02943 ( 827) hydrogen bonds : angle 4.88805 ( 2280) covalent geometry : bond 0.00293 (27012) covalent geometry : angle 0.50639 (36485) *********************** 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 180 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 625 ASN cc_start: 0.9137 (t0) cc_final: 0.8625 (m-40) REVERT: B 492 GLN cc_start: 0.9003 (mp10) cc_final: 0.8735 (mp10) REVERT: B 654 LYS cc_start: 0.8583 (mmmt) cc_final: 0.8222 (mmmm) REVERT: B 659 MET cc_start: 0.7514 (tpp) cc_final: 0.6937 (tpp) REVERT: C 303 MET cc_start: 0.8037 (ppp) cc_final: 0.7679 (ppp) REVERT: C 332 ASP cc_start: 0.8957 (m-30) cc_final: 0.8688 (m-30) REVERT: C 697 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9049 (pp) REVERT: D 468 LYS cc_start: 0.9500 (OUTLIER) cc_final: 0.9278 (tttt) REVERT: E 262 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8771 (pm20) REVERT: E 389 ASN cc_start: 0.8085 (t0) cc_final: 0.7494 (t0) REVERT: E 608 MET cc_start: 0.9580 (mtp) cc_final: 0.9365 (mtm) REVERT: F 657 ILE cc_start: 0.9292 (mm) cc_final: 0.9067 (tp) REVERT: F 659 MET cc_start: 0.8063 (tpp) cc_final: 0.7829 (tpp) REVERT: F 687 ILE cc_start: 0.9398 (mt) cc_final: 0.9179 (mt) REVERT: G 303 MET cc_start: 0.9317 (ttt) cc_final: 0.8876 (tpp) outliers start: 33 outliers final: 17 residues processed: 176 average time/residue: 0.3461 time to fit residues: 103.8142 Evaluate side-chains 143 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 3.010 ------------------------------------------------------------------------------- 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 477 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 716 ASP Chi-restraints excluded: chain E residue 262 GLU 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 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 146 optimal weight: 0.9980 chunk 193 optimal weight: 4.9990 chunk 281 optimal weight: 0.0010 chunk 141 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 237 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 195 optimal weight: 30.0000 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 ASN E 686 ASN F 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.074650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.053550 restraints weight = 88718.334| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.65 r_work: 0.2763 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27012 Z= 0.136 Angle : 0.503 9.396 36485 Z= 0.288 Chirality : 0.044 0.198 4225 Planarity : 0.003 0.041 4756 Dihedral : 3.786 18.463 3427 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.15 % Allowed : 11.04 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3401 helix: 0.08 (0.24), residues: 477 sheet: 1.48 (0.18), residues: 745 loop : -0.34 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 502 HIS 0.002 0.001 HIS C 358 PHE 0.010 0.001 PHE C 710 TYR 0.007 0.001 TYR F 260 ARG 0.000 0.000 ARG E 393 Details of bonding type rmsd hydrogen bonds : bond 0.02886 ( 827) hydrogen bonds : angle 4.78675 ( 2280) covalent geometry : bond 0.00290 (27012) covalent geometry : angle 0.50349 (36485) *********************** 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 174 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 625 ASN cc_start: 0.9142 (t0) cc_final: 0.8623 (m-40) REVERT: B 492 GLN cc_start: 0.9069 (mp10) cc_final: 0.8787 (mp10) REVERT: B 654 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8069 (mmmm) REVERT: B 659 MET cc_start: 0.7529 (tpp) cc_final: 0.6967 (tpp) REVERT: C 303 MET cc_start: 0.8087 (ppp) cc_final: 0.7744 (ppp) REVERT: C 332 ASP cc_start: 0.8948 (m-30) cc_final: 0.8683 (m-30) REVERT: D 468 LYS cc_start: 0.9497 (OUTLIER) cc_final: 0.9238 (tttt) REVERT: E 389 ASN cc_start: 0.8187 (t0) cc_final: 0.7641 (t0) REVERT: E 608 MET cc_start: 0.9562 (mtp) cc_final: 0.9331 (mtm) REVERT: F 659 MET cc_start: 0.8126 (tpp) cc_final: 0.7840 (tpp) REVERT: F 687 ILE cc_start: 0.9372 (mt) cc_final: 0.9158 (mt) REVERT: G 303 MET cc_start: 0.9317 (ttt) cc_final: 0.8894 (tpp) REVERT: G 719 ASP cc_start: 0.8930 (m-30) cc_final: 0.8673 (m-30) outliers start: 35 outliers final: 18 residues processed: 168 average time/residue: 0.3485 time to fit residues: 99.8914 Evaluate side-chains 138 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 3.336 ------------------------------------------------------------------------------- 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 477 LEU 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 D residue 468 LYS Chi-restraints excluded: chain D residue 716 ASP 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 684 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 247 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 320 optimal weight: 9.9990 chunk 271 optimal weight: 10.0000 chunk 8 optimal weight: 0.4980 chunk 186 optimal weight: 7.9990 chunk 48 optimal weight: 0.0670 chunk 173 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 overall best weight: 4.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 GLN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 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 = 0.3373 r_free = 0.3373 target = 0.073841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.052743 restraints weight = 88786.874| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.69 r_work: 0.2747 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.3798 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= 0.148 Angle : 0.513 11.914 36485 Z= 0.292 Chirality : 0.044 0.286 4225 Planarity : 0.003 0.043 4756 Dihedral : 3.820 19.213 3427 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.18 % Allowed : 11.73 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3401 helix: 0.08 (0.24), residues: 477 sheet: 1.46 (0.18), residues: 753 loop : -0.33 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 502 HIS 0.002 0.001 HIS C 358 PHE 0.010 0.001 PHE C 710 TYR 0.008 0.001 TYR F 296 ARG 0.000 0.000 ARG E 324 Details of bonding type rmsd hydrogen bonds : bond 0.02882 ( 827) hydrogen bonds : angle 4.75512 ( 2280) covalent geometry : bond 0.00321 (27012) covalent geometry : angle 0.51278 (36485) *********************** 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 159 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 3.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 625 ASN cc_start: 0.9163 (t0) cc_final: 0.8624 (m-40) REVERT: B 465 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: B 492 GLN cc_start: 0.9099 (mp10) cc_final: 0.8827 (mp10) REVERT: B 659 MET cc_start: 0.7581 (tpp) cc_final: 0.7037 (tpp) REVERT: C 303 MET cc_start: 0.8201 (ppp) cc_final: 0.7854 (ppp) REVERT: C 332 ASP cc_start: 0.8957 (m-30) cc_final: 0.8668 (m-30) REVERT: D 468 LYS cc_start: 0.9499 (OUTLIER) cc_final: 0.9249 (tttt) REVERT: E 389 ASN cc_start: 0.8180 (t0) cc_final: 0.7661 (t0) REVERT: E 608 MET cc_start: 0.9575 (mtp) cc_final: 0.9334 (mtm) REVERT: F 361 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8434 (p0) REVERT: F 659 MET cc_start: 0.8060 (tpp) cc_final: 0.7691 (tpp) REVERT: F 687 ILE cc_start: 0.9360 (mt) cc_final: 0.9074 (mm) REVERT: F 697 LEU cc_start: 0.9070 (mt) cc_final: 0.8715 (mp) REVERT: G 719 ASP cc_start: 0.8960 (m-30) cc_final: 0.8722 (m-30) outliers start: 36 outliers final: 23 residues processed: 155 average time/residue: 0.3324 time to fit residues: 90.3129 Evaluate side-chains 141 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 581 ASP 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 D residue 262 GLU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 716 ASP 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 Chi-restraints excluded: chain G residue 736 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 145 optimal weight: 20.0000 chunk 272 optimal weight: 0.6980 chunk 248 optimal weight: 0.4980 chunk 121 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 329 optimal weight: 7.9990 chunk 212 optimal weight: 0.0670 chunk 105 optimal weight: 5.9990 chunk 202 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 overall best weight: 2.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 ASN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 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 = 0.3384 r_free = 0.3384 target = 0.074414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.053356 restraints weight = 88681.367| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.70 r_work: 0.2756 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.3902 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= 0.124 Angle : 0.498 10.486 36485 Z= 0.284 Chirality : 0.044 0.224 4225 Planarity : 0.003 0.046 4756 Dihedral : 3.719 18.231 3427 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.85 % Allowed : 12.58 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3401 helix: 0.18 (0.24), residues: 477 sheet: 1.54 (0.18), residues: 751 loop : -0.30 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 631 HIS 0.002 0.001 HIS C 358 PHE 0.012 0.001 PHE A 621 TYR 0.007 0.001 TYR F 260 ARG 0.000 0.000 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.02746 ( 827) hydrogen bonds : angle 4.66143 ( 2280) covalent geometry : bond 0.00260 (27012) covalent geometry : angle 0.49776 (36485) *********************** 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 153 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.8945 (ttm) cc_final: 0.8704 (mtp) REVERT: A 625 ASN cc_start: 0.9160 (t0) cc_final: 0.8746 (m-40) REVERT: B 492 GLN cc_start: 0.9128 (mp10) cc_final: 0.8867 (mp10) REVERT: B 654 LYS cc_start: 0.8692 (tptp) cc_final: 0.8201 (mmmt) REVERT: B 659 MET cc_start: 0.7556 (tpp) cc_final: 0.7017 (tpp) REVERT: C 303 MET cc_start: 0.8188 (ppp) cc_final: 0.7848 (ppp) REVERT: C 332 ASP cc_start: 0.8950 (m-30) cc_final: 0.8645 (m-30) REVERT: D 468 LYS cc_start: 0.9504 (OUTLIER) cc_final: 0.9269 (tttt) REVERT: E 389 ASN cc_start: 0.8100 (t0) cc_final: 0.7614 (t0) REVERT: F 361 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8449 (p0) REVERT: F 659 MET cc_start: 0.8027 (tpp) cc_final: 0.7616 (tpp) REVERT: F 687 ILE cc_start: 0.9330 (mt) cc_final: 0.9063 (mm) REVERT: F 697 LEU cc_start: 0.9087 (mt) cc_final: 0.8685 (mp) REVERT: G 719 ASP cc_start: 0.8979 (m-30) cc_final: 0.8739 (m-30) outliers start: 26 outliers final: 19 residues processed: 150 average time/residue: 0.3129 time to fit residues: 82.7587 Evaluate side-chains 138 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 3.411 ------------------------------------------------------------------------------- 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 477 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 644 SER 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 657 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 110 optimal weight: 30.0000 chunk 245 optimal weight: 9.9990 chunk 314 optimal weight: 8.9990 chunk 128 optimal weight: 0.2980 chunk 292 optimal weight: 20.0000 chunk 259 optimal weight: 30.0000 chunk 193 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 289 optimal weight: 20.0000 chunk 315 optimal weight: 0.0970 chunk 299 optimal weight: 9.9990 overall best weight: 5.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.072692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.051634 restraints weight = 89258.653| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.68 r_work: 0.2704 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27012 Z= 0.171 Angle : 0.527 11.998 36485 Z= 0.299 Chirality : 0.044 0.182 4225 Planarity : 0.003 0.043 4756 Dihedral : 3.925 19.660 3427 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.08 % Allowed : 12.78 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3401 helix: 0.08 (0.24), residues: 475 sheet: 1.40 (0.18), residues: 771 loop : -0.35 (0.13), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 502 HIS 0.003 0.001 HIS F 358 PHE 0.010 0.001 PHE C 710 TYR 0.009 0.001 TYR F 296 ARG 0.000 0.000 ARG E 667 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 827) hydrogen bonds : angle 4.72436 ( 2280) covalent geometry : bond 0.00377 (27012) covalent geometry : angle 0.52698 (36485) *********************** 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 145 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 3.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 625 ASN cc_start: 0.9219 (t0) cc_final: 0.8796 (m-40) REVERT: B 492 GLN cc_start: 0.9165 (mp10) cc_final: 0.8844 (mp10) REVERT: B 654 LYS cc_start: 0.8692 (tptp) cc_final: 0.8178 (mmmt) REVERT: B 659 MET cc_start: 0.7524 (tpp) cc_final: 0.7035 (tpp) REVERT: C 303 MET cc_start: 0.8167 (ppp) cc_final: 0.7815 (ppp) REVERT: C 332 ASP cc_start: 0.8986 (m-30) cc_final: 0.8693 (m-30) REVERT: D 468 LYS cc_start: 0.9509 (OUTLIER) cc_final: 0.9272 (tttt) REVERT: F 361 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8502 (p0) REVERT: F 659 MET cc_start: 0.8031 (tpp) cc_final: 0.7607 (tpp) REVERT: F 687 ILE cc_start: 0.9397 (mt) cc_final: 0.9130 (mm) REVERT: F 697 LEU cc_start: 0.9104 (mt) cc_final: 0.8722 (mp) REVERT: G 719 ASP cc_start: 0.8977 (m-30) cc_final: 0.8727 (m-30) outliers start: 33 outliers final: 24 residues processed: 142 average time/residue: 0.3267 time to fit residues: 82.3403 Evaluate side-chains 132 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 648 LYS 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 477 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 644 SER 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 421 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 657 ILE 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 738 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 2 optimal weight: 0.0770 chunk 341 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 276 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 258 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 192 optimal weight: 40.0000 chunk 323 optimal weight: 10.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.073212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.052254 restraints weight = 89237.978| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.64 r_work: 0.2731 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.4181 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= 0.157 Angle : 0.517 11.370 36485 Z= 0.293 Chirality : 0.044 0.164 4225 Planarity : 0.003 0.044 4756 Dihedral : 3.891 19.000 3427 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.95 % Allowed : 13.04 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3401 helix: 0.07 (0.24), residues: 481 sheet: 1.42 (0.18), residues: 779 loop : -0.37 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 374 HIS 0.002 0.001 HIS C 358 PHE 0.010 0.001 PHE C 710 TYR 0.008 0.001 TYR F 296 ARG 0.000 0.000 ARG F 393 Details of bonding type rmsd hydrogen bonds : bond 0.02900 ( 827) hydrogen bonds : angle 4.71391 ( 2280) covalent geometry : bond 0.00343 (27012) covalent geometry : angle 0.51690 (36485) *********************** 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 143 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 4.269 Fit side-chains revert: symmetry clash REVERT: A 402 MET cc_start: 0.8973 (ttm) cc_final: 0.8744 (mtp) REVERT: B 492 GLN cc_start: 0.9164 (mp10) cc_final: 0.8903 (mp10) REVERT: B 654 LYS cc_start: 0.8684 (tptp) cc_final: 0.8219 (mmmt) REVERT: B 659 MET cc_start: 0.7525 (tpp) cc_final: 0.7101 (tpp) REVERT: C 303 MET cc_start: 0.8274 (ppp) cc_final: 0.8068 (ppp) REVERT: C 332 ASP cc_start: 0.8939 (m-30) cc_final: 0.8640 (m-30) REVERT: D 468 LYS cc_start: 0.9505 (OUTLIER) cc_final: 0.9265 (tttt) REVERT: D 533 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8246 (pt0) REVERT: F 361 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8565 (p0) REVERT: F 659 MET cc_start: 0.8054 (tpp) cc_final: 0.7611 (tpp) REVERT: F 687 ILE cc_start: 0.9349 (mt) cc_final: 0.9083 (mm) REVERT: F 697 LEU cc_start: 0.9081 (mt) cc_final: 0.8704 (mp) REVERT: G 719 ASP cc_start: 0.8973 (m-30) cc_final: 0.8720 (m-30) outliers start: 29 outliers final: 24 residues processed: 140 average time/residue: 0.4585 time to fit residues: 113.1393 Evaluate side-chains 137 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 3.085 ------------------------------------------------------------------------------- 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 466 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 262 GLU 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 644 SER 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 421 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 657 ILE 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 738 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 144 optimal weight: 40.0000 chunk 25 optimal weight: 6.9990 chunk 306 optimal weight: 40.0000 chunk 309 optimal weight: 20.0000 chunk 312 optimal weight: 9.9990 chunk 207 optimal weight: 0.0270 chunk 299 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 overall best weight: 5.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.072523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.051680 restraints weight = 88953.031| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.65 r_work: 0.2715 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27012 Z= 0.183 Angle : 0.541 11.498 36485 Z= 0.306 Chirality : 0.044 0.158 4225 Planarity : 0.003 0.044 4756 Dihedral : 4.034 19.912 3427 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.15 % Allowed : 13.01 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3401 helix: 0.01 (0.24), residues: 480 sheet: 1.32 (0.18), residues: 780 loop : -0.42 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 502 HIS 0.003 0.001 HIS F 358 PHE 0.010 0.001 PHE C 710 TYR 0.009 0.001 TYR F 296 ARG 0.000 0.000 ARG E 527 Details of bonding type rmsd hydrogen bonds : bond 0.03099 ( 827) hydrogen bonds : angle 4.79576 ( 2280) covalent geometry : bond 0.00405 (27012) covalent geometry : angle 0.54126 (36485) ********************** 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 153 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.9036 (ttm) cc_final: 0.8803 (mtp) REVERT: A 625 ASN cc_start: 0.9210 (t0) cc_final: 0.8846 (m-40) REVERT: A 666 LYS cc_start: 0.8232 (mttm) cc_final: 0.7726 (mtmm) REVERT: B 492 GLN cc_start: 0.9176 (mp10) cc_final: 0.8908 (mp10) REVERT: B 654 LYS cc_start: 0.8645 (tptp) cc_final: 0.8183 (mmmt) REVERT: B 659 MET cc_start: 0.7576 (tpp) cc_final: 0.7184 (tpp) REVERT: C 303 MET cc_start: 0.8291 (ppp) cc_final: 0.8079 (ppp) REVERT: C 332 ASP cc_start: 0.8988 (m-30) cc_final: 0.8660 (m-30) REVERT: C 352 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9039 (mm) REVERT: C 478 GLU cc_start: 0.8428 (pm20) cc_final: 0.7977 (pm20) REVERT: D 468 LYS cc_start: 0.9510 (OUTLIER) cc_final: 0.9272 (tttt) REVERT: D 533 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8286 (pt0) REVERT: E 389 ASN cc_start: 0.8334 (t0) cc_final: 0.7906 (t0) REVERT: F 361 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8627 (p0) REVERT: F 659 MET cc_start: 0.8115 (tpp) cc_final: 0.7663 (tpp) REVERT: F 687 ILE cc_start: 0.9387 (mt) cc_final: 0.9113 (mm) REVERT: F 697 LEU cc_start: 0.9104 (mt) cc_final: 0.8734 (mp) REVERT: G 719 ASP cc_start: 0.9014 (m-30) cc_final: 0.8722 (m-30) outliers start: 35 outliers final: 26 residues processed: 148 average time/residue: 0.3234 time to fit residues: 83.7552 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 : 3.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 648 LYS 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 581 ASP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 262 GLU 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 644 SER Chi-restraints excluded: chain D residue 716 ASP 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 421 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 657 ILE 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 738 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 324 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 265 optimal weight: 40.0000 chunk 339 optimal weight: 20.0000 chunk 275 optimal weight: 7.9990 chunk 271 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 207 optimal weight: 30.0000 chunk 188 optimal weight: 7.9990 chunk 2 optimal weight: 0.0770 chunk 112 optimal weight: 10.0000 overall best weight: 5.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.051743 restraints weight = 89219.183| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.66 r_work: 0.2717 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27012 Z= 0.174 Angle : 0.537 8.874 36485 Z= 0.304 Chirality : 0.044 0.177 4225 Planarity : 0.003 0.045 4756 Dihedral : 4.027 19.634 3427 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.02 % Allowed : 13.24 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3401 helix: 0.10 (0.24), residues: 475 sheet: 1.30 (0.18), residues: 783 loop : -0.42 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 631 HIS 0.003 0.001 HIS C 358 PHE 0.010 0.001 PHE C 710 TYR 0.009 0.001 TYR F 296 ARG 0.000 0.000 ARG E 527 Details of bonding type rmsd hydrogen bonds : bond 0.02996 ( 827) hydrogen bonds : angle 4.79697 ( 2280) covalent geometry : bond 0.00386 (27012) covalent geometry : angle 0.53742 (36485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11092.26 seconds wall clock time: 196 minutes 20.80 seconds (11780.80 seconds total)