Starting phenix.real_space_refine on Fri Sep 19 12:10:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsi_61774/09_2025/9jsi_61774.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsi_61774/09_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_61774/09_2025/9jsi_61774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsi_61774/09_2025/9jsi_61774.map" model { file = "/net/cci-nas-00/data/ceres_data/9jsi_61774/09_2025/9jsi_61774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsi_61774/09_2025/9jsi_61774.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 21 9.91 5 S 36 5.16 5 C 16835 2.51 5 N 4254 2.21 5 O 5449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26595 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3486 Classifications: {'peptide': 450} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 430} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3847 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 479} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3860 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3812 Classifications: {'peptide': 496} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 475} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 3912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3912 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 488} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 46 Chain: "F" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3845 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 479} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "G" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3812 Classifications: {'peptide': 496} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 475} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 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: 7.21, per 1000 atoms: 0.27 Number of scatterers: 26595 At special positions: 0 Unit cell: (177.76, 176.88, 96.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 21 19.99 S 36 16.00 O 5449 8.00 N 4254 7.00 C 16835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6468 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 68 sheets defined 18.4% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.734A pdb=" N GLU A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 424 through 428 removed outlier: 4.068A pdb=" N ILE A 428 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 470 removed outlier: 4.249A pdb=" N ASP A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 removed outlier: 4.786A pdb=" N SER A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLN A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 Processing helix chain 'A' and resid 580 through 592 removed outlier: 3.729A pdb=" N LYS A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.366A pdb=" N GLN B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 285 through 290 removed outlier: 3.544A pdb=" N ASP B 290 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 removed outlier: 3.872A pdb=" N THR B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 502 through 512 removed outlier: 4.772A pdb=" N SER B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLN B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 555 Processing helix chain 'B' and resid 571 through 575 removed outlier: 3.999A pdb=" N VAL B 575 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 592 removed outlier: 3.872A pdb=" N LYS B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 602 Processing helix chain 'B' and resid 658 through 662 Processing helix chain 'C' and resid 226 through 233 Processing helix chain 'C' and resid 245 through 252 removed outlier: 4.080A pdb=" N GLU C 250 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY C 252 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 285 through 290 removed outlier: 3.657A pdb=" N ASP C 290 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 337 removed outlier: 3.889A pdb=" N THR C 335 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.595A pdb=" N LEU C 378 " --> pdb=" O TRP C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 416 removed outlier: 3.838A pdb=" N GLU C 416 " --> pdb=" O LEU C 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 416' Processing helix chain 'C' and resid 462 through 471 Processing helix chain 'C' and resid 502 through 511 removed outlier: 4.817A pdb=" N SER C 507 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLN C 508 " --> pdb=" O ASN C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 555 Processing helix chain 'C' and resid 580 through 594 removed outlier: 3.828A pdb=" N LYS C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR C 593 " --> pdb=" O GLU C 589 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 594 " --> pdb=" O GLN C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 602 Processing helix chain 'C' and resid 658 through 662 Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 245 through 252 removed outlier: 3.548A pdb=" N ALA D 249 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU D 250 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY D 252 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 278 Processing helix chain 'D' and resid 285 through 290 removed outlier: 3.711A pdb=" N ASP D 290 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 337 removed outlier: 4.011A pdb=" N THR D 335 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 416 removed outlier: 3.605A pdb=" N GLU D 416 " --> pdb=" O LEU D 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 413 through 416' Processing helix chain 'D' and resid 462 through 472 removed outlier: 3.780A pdb=" N LYS D 468 " --> pdb=" O ASP D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 511 removed outlier: 4.734A pdb=" N SER D 507 " --> pdb=" O SER D 503 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLN D 508 " --> pdb=" O ASN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 555 Processing helix chain 'D' and resid 580 through 592 removed outlier: 3.710A pdb=" N LYS D 592 " --> pdb=" O LYS D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 602 Processing helix chain 'D' and resid 658 through 662 Processing helix chain 'E' and resid 226 through 233 Processing helix chain 'E' and resid 245 through 250 removed outlier: 3.523A pdb=" N ALA E 249 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 250 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 278 Processing helix chain 'E' and resid 285 through 290 removed outlier: 3.619A pdb=" N ASP E 290 " --> pdb=" O GLU E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 337 removed outlier: 4.282A pdb=" N GLY E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 470 Processing helix chain 'E' and resid 502 through 511 removed outlier: 4.680A pdb=" N SER E 507 " --> pdb=" O SER E 503 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN E 508 " --> pdb=" O ASN E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 555 Processing helix chain 'E' and resid 580 through 593 removed outlier: 3.731A pdb=" N LYS E 592 " --> pdb=" O LYS E 588 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR E 593 " --> pdb=" O GLU E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 602 Processing helix chain 'E' and resid 658 through 662 Processing helix chain 'F' and resid 226 through 233 Processing helix chain 'F' and resid 245 through 252 removed outlier: 4.211A pdb=" N GLU F 250 " --> pdb=" O SER F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 278 Processing helix chain 'F' and resid 285 through 290 Processing helix chain 'F' and resid 331 through 337 removed outlier: 3.878A pdb=" N THR F 335 " --> pdb=" O THR F 331 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY F 337 " --> pdb=" O ALA F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 470 Processing helix chain 'F' and resid 502 through 511 removed outlier: 4.783A pdb=" N SER F 507 " --> pdb=" O SER F 503 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLN F 508 " --> pdb=" O ASN F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 555 Processing helix chain 'F' and resid 580 through 592 removed outlier: 3.895A pdb=" N LYS F 592 " --> pdb=" O LYS F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 602 Processing helix chain 'F' and resid 658 through 662 Processing helix chain 'G' and resid 226 through 233 Processing helix chain 'G' and resid 245 through 249 Processing helix chain 'G' and resid 271 through 278 Processing helix chain 'G' and resid 285 through 290 Processing helix chain 'G' and resid 331 through 336 Processing helix chain 'G' and resid 462 through 472 removed outlier: 3.807A pdb=" N GLY G 472 " --> pdb=" O LYS G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 511 removed outlier: 4.688A pdb=" N SER G 507 " --> pdb=" O SER G 503 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLN G 508 " --> pdb=" O ASN G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 555 Processing helix chain 'G' and resid 580 through 592 removed outlier: 3.736A pdb=" N LYS G 592 " --> pdb=" O LYS G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 602 Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 237 Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 309 removed outlier: 5.659A pdb=" N VAL A 301 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 395 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N MET A 303 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG A 393 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 390 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 417 through 422 removed outlier: 6.869A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS A 422 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR A 403 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A 431 " --> pdb=" O TYR A 403 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 417 through 422 removed outlier: 6.869A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS A 422 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS A 404 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY A 484 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR A 406 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL A 482 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 408 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 478 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 530 Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 559 removed outlier: 4.108A pdb=" N LEU A 562 " --> pdb=" O ASN A 559 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 617 through 619 removed outlier: 3.795A pdb=" N GLU A 721 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP A 695 " --> pdb=" O VAL A 685 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 647 through 656 removed outlier: 5.505A pdb=" N GLY A 728 " --> pdb=" O GLY A 651 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR A 653 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER A 726 " --> pdb=" O THR A 653 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE A 655 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU A 724 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU A 735 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER A 671 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE A 737 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 669 " --> pdb=" O ILE A 737 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB2, first strand: chain 'B' and resid 299 through 305 removed outlier: 6.828A pdb=" N ASN B 391 " --> pdb=" O GLU B 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 299 through 305 removed outlier: 6.828A pdb=" N ASN B 391 " --> pdb=" O GLU B 304 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 326 through 329 removed outlier: 3.508A pdb=" N SER B 363 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASN B 362 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS B 476 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 412 " --> pdb=" O LYS B 476 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR B 408 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL B 482 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR B 406 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY B 484 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS B 404 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 419 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 326 through 329 removed outlier: 3.508A pdb=" N SER B 363 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASN B 362 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS B 476 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 412 " --> pdb=" O LYS B 476 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR B 408 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL B 482 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR B 406 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY B 484 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS B 404 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR B 403 " --> pdb=" O ASN B 431 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN B 431 " --> pdb=" O TYR B 403 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 351 through 352 removed outlier: 4.105A pdb=" N GLN B 523 " --> pdb=" O THR B 520 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AB8, first strand: chain 'B' and resid 557 through 559 removed outlier: 4.032A pdb=" N LEU B 562 " --> pdb=" O ASN B 559 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 617 through 619 Processing sheet with id=AC1, first strand: chain 'B' and resid 617 through 619 removed outlier: 5.462A pdb=" N LEU B 732 " --> pdb=" O LYS B 675 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LYS B 675 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASN B 734 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR B 673 " --> pdb=" O ASN B 734 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 674 " --> pdb=" O THR B 704 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 652 through 657 removed outlier: 3.873A pdb=" N ILE B 722 " --> pdb=" O ILE B 655 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 721 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN B 686 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 695 " --> pdb=" O VAL B 685 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 687 " --> pdb=" O LYS B 693 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS B 693 " --> pdb=" O ILE B 687 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 234 through 237 Processing sheet with id=AC4, first strand: chain 'C' and resid 420 through 422 removed outlier: 7.000A pdb=" N LYS C 404 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY C 484 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR C 406 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL C 482 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR C 408 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN C 362 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG C 324 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 306 " --> pdb=" O ARG C 324 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU C 304 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ASN C 328 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N GLY C 302 " --> pdb=" O ASN C 328 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN C 391 " --> pdb=" O GLU C 304 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 429 through 432 removed outlier: 6.440A pdb=" N ASN C 431 " --> pdb=" O TYR C 403 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TYR C 403 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS C 404 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY C 484 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR C 406 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL C 482 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR C 408 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN C 362 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG C 324 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 306 " --> pdb=" O ARG C 324 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU C 304 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ASN C 328 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N GLY C 302 " --> pdb=" O ASN C 328 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN C 391 " --> pdb=" O GLU C 304 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 351 through 352 removed outlier: 3.578A pdb=" N GLU C 576 " --> pdb=" O LYS C 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC8, first strand: chain 'C' and resid 557 through 559 removed outlier: 3.657A pdb=" N LEU C 562 " --> pdb=" O ASN C 559 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 617 through 619 Processing sheet with id=AD1, first strand: chain 'C' and resid 617 through 619 removed outlier: 5.426A pdb=" N LEU C 732 " --> pdb=" O LYS C 675 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LYS C 675 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASN C 734 " --> pdb=" O TYR C 673 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR C 673 " --> pdb=" O ASN C 734 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG C 667 " --> pdb=" O LEU C 740 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 652 through 657 removed outlier: 3.726A pdb=" N GLU C 721 " --> pdb=" O LYS C 688 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 234 through 237 Processing sheet with id=AD4, first strand: chain 'D' and resid 299 through 305 removed outlier: 6.600A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 299 through 305 removed outlier: 6.600A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 326 through 329 removed outlier: 3.571A pdb=" N SER D 363 " --> pdb=" O SER D 329 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N THR D 479 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN D 410 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN D 481 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASN D 485 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LYS D 404 " --> pdb=" O ASN D 485 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 326 through 329 removed outlier: 3.571A pdb=" N SER D 363 " --> pdb=" O SER D 329 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N THR D 479 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN D 410 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN D 481 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASN D 485 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LYS D 404 " --> pdb=" O ASN D 485 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR D 403 " --> pdb=" O ASN D 431 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN D 431 " --> pdb=" O TYR D 403 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 351 through 352 Processing sheet with id=AD9, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AE1, first strand: chain 'D' and resid 557 through 559 removed outlier: 3.506A pdb=" N ASN D 559 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU D 562 " --> pdb=" O ASN D 559 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 617 through 619 removed outlier: 3.879A pdb=" N GLU D 721 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR D 723 " --> pdb=" O ASN D 686 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN D 686 " --> pdb=" O THR D 723 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS D 693 " --> pdb=" O ILE D 687 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 647 through 657 removed outlier: 5.832A pdb=" N ASN D 647 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE D 730 " --> pdb=" O ASN D 647 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU D 649 " --> pdb=" O GLY D 728 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLY D 728 " --> pdb=" O LEU D 649 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY D 651 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ASP D 733 " --> pdb=" O LYS D 675 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LYS D 675 " --> pdb=" O ASP D 733 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU D 735 " --> pdb=" O TYR D 673 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N TYR D 673 " --> pdb=" O LEU D 735 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE D 737 " --> pdb=" O SER D 671 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N SER D 671 " --> pdb=" O ILE D 737 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU D 739 " --> pdb=" O VAL D 669 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL D 669 " --> pdb=" O GLU D 739 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN D 741 " --> pdb=" O ARG D 667 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 234 through 237 Processing sheet with id=AE5, first strand: chain 'E' and resid 420 through 422 removed outlier: 4.298A pdb=" N VAL E 405 " --> pdb=" O SER E 483 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER E 483 " --> pdb=" O VAL E 405 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLN E 481 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR E 409 " --> pdb=" O THR E 479 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR E 479 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU E 411 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU E 477 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN E 362 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER E 363 " --> pdb=" O SER E 329 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLU E 304 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASN E 328 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N GLY E 302 " --> pdb=" O ASN E 328 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU E 306 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN E 389 " --> pdb=" O LEU E 306 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 429 through 432 removed outlier: 6.471A pdb=" N ASN E 431 " --> pdb=" O TYR E 403 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR E 403 " --> pdb=" O ASN E 431 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL E 405 " --> pdb=" O SER E 483 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER E 483 " --> pdb=" O VAL E 405 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLN E 481 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR E 409 " --> pdb=" O THR E 479 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR E 479 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU E 411 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU E 477 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN E 362 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER E 363 " --> pdb=" O SER E 329 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLU E 304 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASN E 328 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N GLY E 302 " --> pdb=" O ASN E 328 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU E 306 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN E 389 " --> pdb=" O LEU E 306 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 351 through 352 removed outlier: 6.098A pdb=" N ASN E 351 " --> pdb=" O PHE E 579 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ILE E 610 " --> pdb=" O SER E 513 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N SER E 515 " --> pdb=" O ILE E 610 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ILE E 612 " --> pdb=" O SER E 515 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE E 517 " --> pdb=" O ILE E 612 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 488 through 489 Processing sheet with id=AE9, first strand: chain 'E' and resid 557 through 559 removed outlier: 4.251A pdb=" N LEU E 562 " --> pdb=" O ASN E 559 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 617 through 619 Processing sheet with id=AF2, first strand: chain 'E' and resid 617 through 619 removed outlier: 5.466A pdb=" N LEU E 732 " --> pdb=" O LYS E 675 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LYS E 675 " --> pdb=" O LEU E 732 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASN E 734 " --> pdb=" O TYR E 673 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR E 673 " --> pdb=" O ASN E 734 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 652 through 657 removed outlier: 3.517A pdb=" N ILE E 655 " --> pdb=" O ILE E 722 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE E 722 " --> pdb=" O ILE E 655 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE E 687 " --> pdb=" O LYS E 693 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS E 693 " --> pdb=" O ILE E 687 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 234 through 237 Processing sheet with id=AF5, first strand: chain 'F' and resid 420 through 422 removed outlier: 5.989A pdb=" N LYS F 404 " --> pdb=" O ASN F 485 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASN F 485 " --> pdb=" O LYS F 404 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN F 481 " --> pdb=" O THR F 408 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN F 410 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR F 479 " --> pdb=" O ASN F 410 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN F 362 " --> pdb=" O LEU F 477 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG F 324 " --> pdb=" O LEU F 306 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU F 306 " --> pdb=" O ARG F 324 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLU F 304 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASN F 328 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY F 302 " --> pdb=" O ASN F 328 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY F 302 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN F 391 " --> pdb=" O GLU F 304 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 429 through 432 removed outlier: 6.415A pdb=" N ASN F 431 " --> pdb=" O TYR F 403 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR F 403 " --> pdb=" O ASN F 431 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LYS F 404 " --> pdb=" O ASN F 485 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASN F 485 " --> pdb=" O LYS F 404 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN F 481 " --> pdb=" O THR F 408 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN F 410 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR F 479 " --> pdb=" O ASN F 410 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN F 362 " --> pdb=" O LEU F 477 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG F 324 " --> pdb=" O LEU F 306 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU F 306 " --> pdb=" O ARG F 324 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLU F 304 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASN F 328 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY F 302 " --> pdb=" O ASN F 328 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY F 302 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN F 391 " --> pdb=" O GLU F 304 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 351 through 352 removed outlier: 6.039A pdb=" N ASN F 351 " --> pdb=" O PHE F 579 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N ILE F 610 " --> pdb=" O SER F 513 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER F 515 " --> pdb=" O ILE F 610 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ILE F 612 " --> pdb=" O SER F 515 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE F 517 " --> pdb=" O ILE F 612 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 488 through 489 Processing sheet with id=AF9, first strand: chain 'F' and resid 557 through 558 Processing sheet with id=AG1, first strand: chain 'F' and resid 617 through 619 removed outlier: 3.613A pdb=" N TYR F 617 " --> pdb=" O ILE F 737 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 732 " --> pdb=" O ASN F 647 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 617 through 619 removed outlier: 3.613A pdb=" N TYR F 617 " --> pdb=" O ILE F 737 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU F 732 " --> pdb=" O LYS F 675 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LYS F 675 " --> pdb=" O LEU F 732 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASN F 734 " --> pdb=" O TYR F 673 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR F 673 " --> pdb=" O ASN F 734 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG F 667 " --> pdb=" O LEU F 740 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 652 through 657 removed outlier: 3.739A pdb=" N GLU F 721 " --> pdb=" O LYS F 688 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN F 686 " --> pdb=" O THR F 723 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR F 725 " --> pdb=" O THR F 684 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 687 " --> pdb=" O LYS F 693 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS F 693 " --> pdb=" O ILE F 687 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 234 through 237 Processing sheet with id=AG5, first strand: chain 'G' and resid 363 through 366 removed outlier: 4.455A pdb=" N ARG G 324 " --> pdb=" O LEU G 306 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU G 306 " --> pdb=" O ARG G 324 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR G 326 " --> pdb=" O GLU G 304 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU G 304 " --> pdb=" O THR G 326 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASN G 328 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N GLY G 302 " --> pdb=" O ASN G 328 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL G 301 " --> pdb=" O TYR G 395 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR G 395 " --> pdb=" O VAL G 301 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N MET G 303 " --> pdb=" O ARG G 393 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG G 393 " --> pdb=" O MET G 303 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN G 305 " --> pdb=" O ASN G 391 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 363 through 366 removed outlier: 4.455A pdb=" N ARG G 324 " --> pdb=" O LEU G 306 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU G 306 " --> pdb=" O ARG G 324 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR G 326 " --> pdb=" O GLU G 304 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU G 304 " --> pdb=" O THR G 326 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASN G 328 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N GLY G 302 " --> pdb=" O ASN G 328 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL G 301 " --> pdb=" O TYR G 395 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR G 395 " --> pdb=" O VAL G 301 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N MET G 303 " --> pdb=" O ARG G 393 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG G 393 " --> pdb=" O MET G 303 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN G 305 " --> pdb=" O ASN G 391 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA G 390 " --> pdb=" O LEU G 448 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 448 " --> pdb=" O ALA G 390 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 351 through 352 Processing sheet with id=AG8, first strand: chain 'G' and resid 417 through 422 removed outlier: 5.317A pdb=" N ALA G 419 " --> pdb=" O LEU G 411 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU G 411 " --> pdb=" O ALA G 419 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR G 403 " --> pdb=" O ASN G 431 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN G 431 " --> pdb=" O TYR G 403 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 417 through 422 removed outlier: 5.317A pdb=" N ALA G 419 " --> pdb=" O LEU G 411 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU G 411 " --> pdb=" O ALA G 419 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL G 405 " --> pdb=" O SER G 483 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER G 483 " --> pdb=" O VAL G 405 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLN G 481 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR G 409 " --> pdb=" O THR G 479 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR G 479 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU G 411 " --> pdb=" O LEU G 477 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU G 477 " --> pdb=" O LEU G 411 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 488 through 489 Processing sheet with id=AH2, first strand: chain 'G' and resid 557 through 559 removed outlier: 3.500A pdb=" N ASN G 559 " --> pdb=" O LEU G 562 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU G 562 " --> pdb=" O ASN G 559 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 617 through 619 Processing sheet with id=AH4, first strand: chain 'G' and resid 617 through 619 removed outlier: 5.211A pdb=" N LEU G 732 " --> pdb=" O LYS G 675 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS G 675 " --> pdb=" O LEU G 732 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASN G 734 " --> pdb=" O TYR G 673 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR G 673 " --> pdb=" O ASN G 734 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG G 667 " --> pdb=" O LEU G 740 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 652 through 657 removed outlier: 3.803A pdb=" N ILE G 722 " --> pdb=" O ILE G 655 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU G 721 " --> pdb=" O LYS G 688 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE G 687 " --> pdb=" O LYS G 693 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS G 693 " --> pdb=" O ILE G 687 " (cutoff:3.500A) 920 hydrogen bonds defined for protein. 2280 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 2.99 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 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: 0.010 Normalize map: mean=0, sd=1: 0.700 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: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.870 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.480 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.14), residues: 3401 helix: -0.38 (0.24), residues: 474 sheet: 1.38 (0.19), residues: 742 loop : -0.55 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 324 TYR 0.023 0.001 TYR F 463 PHE 0.012 0.001 PHE C 579 TRP 0.009 0.001 TRP B 374 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00280 (27012) covalent geometry : angle 0.52841 (36485) hydrogen bonds : bond 0.23184 ( 827) hydrogen bonds : angle 8.60302 ( 2280) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 418 time to evaluate : 1.163 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: 0.6944 (pt) outliers start: 4 outliers final: 0 residues processed: 422 average time/residue: 0.1924 time to fit residues: 128.1643 Evaluate side-chains 175 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 0.0050 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 6.9990 overall best weight: 4.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** 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 391 ASN F 435 ASN F 500 ASN F 590 GLN G 334 ASN G 500 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.076153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.054799 restraints weight = 88855.827| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.68 r_work: 0.2780 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27012 Z= 0.178 Angle : 0.574 9.343 36485 Z= 0.326 Chirality : 0.045 0.206 4225 Planarity : 0.004 0.049 4756 Dihedral : 4.147 22.986 3427 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.92 % Allowed : 6.88 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.14), residues: 3401 helix: -0.24 (0.24), residues: 470 sheet: 1.39 (0.19), residues: 730 loop : -0.42 (0.13), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 324 TYR 0.010 0.001 TYR F 438 PHE 0.019 0.001 PHE G 670 TRP 0.011 0.001 TRP F 502 HIS 0.002 0.001 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00389 (27012) covalent geometry : angle 0.57448 (36485) hydrogen bonds : bond 0.03948 ( 827) hydrogen bonds : angle 5.62117 ( 2280) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 625 ASN cc_start: 0.9204 (t0) cc_final: 0.8773 (m-40) REVERT: B 475 ILE cc_start: 0.5148 (tp) cc_final: 0.4786 (tp) REVERT: B 476 LYS cc_start: 0.6762 (mmtt) cc_final: 0.6422 (mmtt) REVERT: B 492 GLN cc_start: 0.8843 (mp10) cc_final: 0.8622 (mp10) REVERT: B 654 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8197 (mmmt) REVERT: B 659 MET cc_start: 0.6974 (tpp) cc_final: 0.6502 (tpp) REVERT: C 303 MET cc_start: 0.7742 (ppp) cc_final: 0.7299 (ppp) REVERT: C 332 ASP cc_start: 0.8966 (m-30) cc_final: 0.8764 (m-30) REVERT: D 305 ASN cc_start: 0.9019 (t0) cc_final: 0.8749 (t0) REVERT: E 262 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8631 (pm20) REVERT: E 723 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.8936 (p) REVERT: F 739 GLU cc_start: 0.8418 (pp20) cc_final: 0.8209 (pp20) REVERT: G 303 MET cc_start: 0.8939 (tpp) cc_final: 0.8587 (tpp) outliers start: 28 outliers final: 16 residues processed: 198 average time/residue: 0.1684 time to fit residues: 55.4917 Evaluate side-chains 153 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 477 LEU Chi-restraints excluded: chain D residue 555 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 443 LEU Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 209 optimal weight: 3.9990 chunk 89 optimal weight: 30.0000 chunk 80 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 280 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 96 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 ASN E 474 GLN ** F 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 590 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.074012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.052668 restraints weight = 89536.163| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.69 r_work: 0.2732 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27012 Z= 0.167 Angle : 0.536 11.270 36485 Z= 0.307 Chirality : 0.045 0.178 4225 Planarity : 0.003 0.044 4756 Dihedral : 4.055 19.779 3427 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.08 % Allowed : 8.81 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.14), residues: 3401 helix: -0.14 (0.24), residues: 482 sheet: 1.38 (0.18), residues: 753 loop : -0.41 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 667 TYR 0.012 0.001 TYR E 463 PHE 0.013 0.001 PHE G 670 TRP 0.009 0.001 TRP F 502 HIS 0.003 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00365 (27012) covalent geometry : angle 0.53649 (36485) hydrogen bonds : bond 0.03519 ( 827) hydrogen bonds : angle 5.08902 ( 2280) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 LYS cc_start: 0.7868 (tttm) cc_final: 0.7604 (tttm) REVERT: B 358 HIS cc_start: 0.8845 (m-70) cc_final: 0.8635 (m-70) REVERT: B 492 GLN cc_start: 0.8983 (mp10) cc_final: 0.8699 (mp10) REVERT: B 654 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8274 (mmmt) REVERT: B 659 MET cc_start: 0.7489 (tpp) cc_final: 0.6844 (tpp) REVERT: C 303 MET cc_start: 0.7847 (ppp) cc_final: 0.7513 (ppp) REVERT: C 332 ASP cc_start: 0.8946 (m-30) cc_final: 0.8644 (m-30) REVERT: C 697 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8987 (pp) REVERT: D 468 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9233 (tttt) REVERT: E 262 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8747 (pm20) REVERT: G 719 ASP cc_start: 0.8873 (m-30) cc_final: 0.8614 (m-30) outliers start: 33 outliers final: 16 residues processed: 182 average time/residue: 0.1588 time to fit residues: 48.1975 Evaluate side-chains 143 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 555 SER Chi-restraints excluded: chain 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 469 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 725 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 630 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 239 optimal weight: 40.0000 chunk 164 optimal weight: 5.9990 chunk 108 optimal weight: 30.0000 chunk 211 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 chunk 232 optimal weight: 20.0000 chunk 261 optimal weight: 8.9990 chunk 253 optimal weight: 20.0000 chunk 260 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 ASN B 566 ASN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN E 686 ASN F 351 ASN ** F 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 647 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.071734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.050400 restraints weight = 89668.645| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.70 r_work: 0.2668 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 27012 Z= 0.238 Angle : 0.580 10.006 36485 Z= 0.328 Chirality : 0.046 0.246 4225 Planarity : 0.003 0.047 4756 Dihedral : 4.365 21.422 3427 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.41 % Allowed : 10.42 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.14), residues: 3401 helix: -0.25 (0.23), residues: 479 sheet: 1.16 (0.18), residues: 762 loop : -0.50 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 667 TYR 0.013 0.001 TYR F 296 PHE 0.012 0.001 PHE B 525 TRP 0.012 0.001 TRP F 502 HIS 0.004 0.002 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00530 (27012) covalent geometry : angle 0.58049 (36485) hydrogen bonds : bond 0.03561 ( 827) hydrogen bonds : angle 5.14365 ( 2280) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 492 GLN cc_start: 0.9091 (mp10) cc_final: 0.8825 (mp10) REVERT: B 654 LYS cc_start: 0.8616 (mmmt) cc_final: 0.8203 (mmmm) REVERT: B 659 MET cc_start: 0.7583 (tpp) cc_final: 0.7024 (tpp) REVERT: C 303 MET cc_start: 0.8053 (ppp) cc_final: 0.7679 (ppp) REVERT: C 332 ASP cc_start: 0.9025 (m-30) cc_final: 0.8728 (m-30) REVERT: C 697 LEU cc_start: 0.9257 (tt) cc_final: 0.8999 (pp) REVERT: D 468 LYS cc_start: 0.9496 (OUTLIER) cc_final: 0.9291 (tttt) REVERT: E 262 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8797 (pm20) REVERT: E 411 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7655 (pt) REVERT: E 608 MET cc_start: 0.9576 (mtp) cc_final: 0.9336 (mtm) REVERT: F 361 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8379 (p0) REVERT: F 659 MET cc_start: 0.8073 (tpp) cc_final: 0.7829 (tpp) REVERT: G 303 MET cc_start: 0.9430 (ttt) cc_final: 0.9044 (tpp) REVERT: G 719 ASP cc_start: 0.8951 (m-30) cc_final: 0.8619 (m-30) outliers start: 43 outliers final: 25 residues processed: 168 average time/residue: 0.1510 time to fit residues: 43.8533 Evaluate side-chains 138 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 B residue 581 ASP Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 431 ASN 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 F residue 361 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 647 ASN Chi-restraints excluded: chain G residue 723 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 263 optimal weight: 6.9990 chunk 309 optimal weight: 8.9990 chunk 210 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 330 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 295 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** 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 = 0.3331 r_free = 0.3331 target = 0.072434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.051345 restraints weight = 89178.652| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.67 r_work: 0.2694 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27012 Z= 0.165 Angle : 0.520 9.545 36485 Z= 0.299 Chirality : 0.044 0.258 4225 Planarity : 0.003 0.047 4756 Dihedral : 4.130 20.247 3427 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.18 % Allowed : 11.50 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.14), residues: 3401 helix: -0.10 (0.23), residues: 480 sheet: 1.18 (0.18), residues: 769 loop : -0.46 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 606 TYR 0.009 0.001 TYR F 260 PHE 0.017 0.001 PHE A 670 TRP 0.006 0.001 TRP C 374 HIS 0.003 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00361 (27012) covalent geometry : angle 0.51977 (36485) hydrogen bonds : bond 0.03142 ( 827) hydrogen bonds : angle 4.97866 ( 2280) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 666 LYS cc_start: 0.8165 (mttm) cc_final: 0.7662 (mtmm) REVERT: B 492 GLN cc_start: 0.9102 (mp10) cc_final: 0.8870 (mp10) REVERT: B 654 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8155 (mmmm) REVERT: B 659 MET cc_start: 0.7609 (tpp) cc_final: 0.7060 (tpp) REVERT: C 303 MET cc_start: 0.8115 (ppp) cc_final: 0.7737 (ppp) REVERT: C 332 ASP cc_start: 0.9014 (m-30) cc_final: 0.8711 (m-30) REVERT: C 697 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9051 (pp) REVERT: D 468 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9242 (tttt) REVERT: E 389 ASN cc_start: 0.8290 (t0) cc_final: 0.7761 (t0) REVERT: F 361 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8443 (p0) REVERT: F 659 MET cc_start: 0.8182 (tpp) cc_final: 0.7872 (tpp) REVERT: G 719 ASP cc_start: 0.8967 (m-30) cc_final: 0.8684 (m-30) outliers start: 36 outliers final: 23 residues processed: 154 average time/residue: 0.1512 time to fit residues: 40.2194 Evaluate side-chains 144 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 697 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 411 LEU 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 725 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 716 ASP Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 738 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 201 optimal weight: 5.9990 chunk 255 optimal weight: 8.9990 chunk 59 optimal weight: 50.0000 chunk 240 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 110 optimal weight: 30.0000 chunk 194 optimal weight: 10.0000 chunk 148 optimal weight: 0.0030 chunk 233 optimal weight: 30.0000 chunk 324 optimal weight: 4.9990 overall best weight: 5.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN ** B 741 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.072101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.051117 restraints weight = 89309.509| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.67 r_work: 0.2689 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27012 Z= 0.174 Angle : 0.522 9.867 36485 Z= 0.300 Chirality : 0.045 0.226 4225 Planarity : 0.003 0.047 4756 Dihedral : 4.086 20.517 3427 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.31 % Allowed : 12.32 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.14), residues: 3401 helix: -0.01 (0.24), residues: 474 sheet: 1.16 (0.18), residues: 773 loop : -0.46 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 324 TYR 0.010 0.001 TYR F 296 PHE 0.010 0.001 PHE A 670 TRP 0.007 0.001 TRP F 502 HIS 0.003 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00383 (27012) covalent geometry : angle 0.52190 (36485) hydrogen bonds : bond 0.03099 ( 827) hydrogen bonds : angle 4.89129 ( 2280) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.9047 (ttm) cc_final: 0.8825 (mtp) REVERT: A 666 LYS cc_start: 0.8214 (mttm) cc_final: 0.7723 (mtmm) REVERT: B 492 GLN cc_start: 0.9116 (mp10) cc_final: 0.8861 (mp10) REVERT: B 654 LYS cc_start: 0.8682 (mmmt) cc_final: 0.8213 (mmmm) REVERT: B 659 MET cc_start: 0.7625 (tpp) cc_final: 0.7109 (tpp) REVERT: B 723 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8064 (p) REVERT: C 303 MET cc_start: 0.8098 (ppp) cc_final: 0.7732 (ppp) REVERT: C 332 ASP cc_start: 0.9018 (m-30) cc_final: 0.8691 (m-30) REVERT: C 352 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9001 (mm) REVERT: D 468 LYS cc_start: 0.9504 (OUTLIER) cc_final: 0.9260 (tttt) REVERT: D 533 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8321 (pt0) REVERT: E 389 ASN cc_start: 0.8287 (t0) cc_final: 0.7768 (t0) REVERT: F 361 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8543 (p0) REVERT: F 659 MET cc_start: 0.8208 (tpp) cc_final: 0.7879 (tpp) REVERT: G 303 MET cc_start: 0.9396 (ttt) cc_final: 0.8951 (tpp) REVERT: G 719 ASP cc_start: 0.8969 (m-30) cc_final: 0.8674 (m-30) outliers start: 40 outliers final: 25 residues processed: 159 average time/residue: 0.1510 time to fit residues: 41.4584 Evaluate side-chains 150 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 340 ILE 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 411 LEU 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 286 LEU Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 716 ASP Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 738 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 213 optimal weight: 0.6980 chunk 193 optimal weight: 8.9990 chunk 330 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 262 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 217 optimal weight: 7.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- 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** ** 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 = 0.3317 r_free = 0.3317 target = 0.071721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.051048 restraints weight = 88622.588| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.58 r_work: 0.2689 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27012 Z= 0.180 Angle : 0.530 10.813 36485 Z= 0.302 Chirality : 0.045 0.229 4225 Planarity : 0.003 0.047 4756 Dihedral : 4.100 20.667 3427 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.28 % Allowed : 12.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.14), residues: 3401 helix: 0.01 (0.24), residues: 474 sheet: 1.21 (0.18), residues: 778 loop : -0.48 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 324 TYR 0.010 0.001 TYR F 296 PHE 0.012 0.001 PHE A 621 TRP 0.006 0.001 TRP F 502 HIS 0.003 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00399 (27012) covalent geometry : angle 0.53019 (36485) hydrogen bonds : bond 0.03097 ( 827) hydrogen bonds : angle 4.88599 ( 2280) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 666 LYS cc_start: 0.8253 (mttm) cc_final: 0.7761 (mtmm) REVERT: B 492 GLN cc_start: 0.9120 (mp10) cc_final: 0.8881 (mp10) REVERT: B 654 LYS cc_start: 0.8699 (mmmt) cc_final: 0.8250 (mmmm) REVERT: B 659 MET cc_start: 0.7585 (tpp) cc_final: 0.7117 (tpp) REVERT: C 303 MET cc_start: 0.8164 (ppp) cc_final: 0.7871 (ppp) REVERT: C 332 ASP cc_start: 0.8987 (m-30) cc_final: 0.8667 (m-30) REVERT: C 352 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9037 (mm) REVERT: D 468 LYS cc_start: 0.9504 (OUTLIER) cc_final: 0.9257 (tttt) REVERT: D 533 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8326 (pt0) REVERT: E 389 ASN cc_start: 0.8182 (t0) cc_final: 0.7701 (t0) REVERT: F 361 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8574 (p0) REVERT: F 657 ILE cc_start: 0.9401 (mm) cc_final: 0.9186 (tp) REVERT: F 659 MET cc_start: 0.8212 (tpp) cc_final: 0.7871 (tpp) REVERT: G 719 ASP cc_start: 0.8947 (m-30) cc_final: 0.8653 (m-30) outliers start: 39 outliers final: 26 residues processed: 158 average time/residue: 0.1418 time to fit residues: 38.6445 Evaluate side-chains 145 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 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 411 LEU 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 725 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 716 ASP Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 736 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 329 optimal weight: 1.9990 chunk 233 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 43 optimal weight: 50.0000 chunk 7 optimal weight: 7.9990 chunk 269 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** 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 = 0.072568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.051768 restraints weight = 89515.046| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.64 r_work: 0.2719 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27012 Z= 0.161 Angle : 0.522 10.078 36485 Z= 0.298 Chirality : 0.044 0.214 4225 Planarity : 0.003 0.046 4756 Dihedral : 4.040 20.227 3427 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.25 % Allowed : 13.17 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.14), residues: 3401 helix: 0.01 (0.24), residues: 480 sheet: 1.29 (0.18), residues: 773 loop : -0.48 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 606 TYR 0.009 0.001 TYR F 260 PHE 0.011 0.001 PHE A 621 TRP 0.005 0.001 TRP C 631 HIS 0.003 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00352 (27012) covalent geometry : angle 0.52250 (36485) hydrogen bonds : bond 0.02999 ( 827) hydrogen bonds : angle 4.83912 ( 2280) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 666 LYS cc_start: 0.8264 (mttm) cc_final: 0.7751 (mtmm) REVERT: B 492 GLN cc_start: 0.9130 (mp10) cc_final: 0.8903 (mp10) REVERT: B 654 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8322 (mmmm) REVERT: B 659 MET cc_start: 0.7603 (tpp) cc_final: 0.7158 (tpp) REVERT: C 303 MET cc_start: 0.8255 (ppp) cc_final: 0.7983 (ppp) REVERT: C 332 ASP cc_start: 0.8982 (m-30) cc_final: 0.8642 (m-30) REVERT: C 352 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9061 (mm) REVERT: C 464 ASP cc_start: 0.8797 (m-30) cc_final: 0.8556 (t0) REVERT: D 303 MET cc_start: 0.9010 (ttp) cc_final: 0.8809 (ptm) REVERT: D 468 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.9268 (tttt) REVERT: D 533 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8318 (pt0) REVERT: E 389 ASN cc_start: 0.8199 (t0) cc_final: 0.7744 (t0) REVERT: F 361 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8628 (p0) REVERT: F 657 ILE cc_start: 0.9409 (mm) cc_final: 0.9183 (tp) REVERT: F 659 MET cc_start: 0.8217 (tpp) cc_final: 0.7913 (tpp) REVERT: G 719 ASP cc_start: 0.8998 (m-30) cc_final: 0.8707 (m-30) outliers start: 38 outliers final: 26 residues processed: 155 average time/residue: 0.1439 time to fit residues: 38.9720 Evaluate side-chains 146 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 352 ILE 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 411 LEU Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 725 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 431 ASN Chi-restraints excluded: chain G residue 523 GLN Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 736 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 165 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 265 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 189 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 221 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 ASN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 ASN ** F 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.071692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.051080 restraints weight = 89090.759| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.59 r_work: 0.2687 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27012 Z= 0.178 Angle : 0.531 9.660 36485 Z= 0.302 Chirality : 0.044 0.207 4225 Planarity : 0.003 0.047 4756 Dihedral : 4.097 20.943 3427 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.28 % Allowed : 13.24 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.14), residues: 3401 helix: -0.03 (0.24), residues: 480 sheet: 1.23 (0.18), residues: 779 loop : -0.49 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 667 TYR 0.009 0.001 TYR F 260 PHE 0.011 0.001 PHE A 621 TRP 0.006 0.001 TRP F 502 HIS 0.003 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00393 (27012) covalent geometry : angle 0.53087 (36485) hydrogen bonds : bond 0.03055 ( 827) hydrogen bonds : angle 4.85612 ( 2280) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 492 GLN cc_start: 0.9148 (mp10) cc_final: 0.8921 (mp10) REVERT: B 654 LYS cc_start: 0.8662 (mmmt) cc_final: 0.8257 (mmmm) REVERT: B 659 MET cc_start: 0.7494 (tpp) cc_final: 0.7074 (tpp) REVERT: C 303 MET cc_start: 0.8232 (ppp) cc_final: 0.8012 (ppp) REVERT: C 332 ASP cc_start: 0.8992 (m-30) cc_final: 0.8666 (m-30) REVERT: C 352 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9069 (mm) REVERT: C 464 ASP cc_start: 0.8820 (m-30) cc_final: 0.8565 (t0) REVERT: D 303 MET cc_start: 0.9004 (ttp) cc_final: 0.8803 (ptm) REVERT: D 468 LYS cc_start: 0.9500 (OUTLIER) cc_final: 0.9268 (tttt) REVERT: D 533 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8340 (pt0) REVERT: E 389 ASN cc_start: 0.8179 (t0) cc_final: 0.7730 (t0) REVERT: F 361 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8640 (p0) REVERT: F 657 ILE cc_start: 0.9419 (mm) cc_final: 0.9192 (tp) REVERT: F 659 MET cc_start: 0.8236 (tpp) cc_final: 0.7923 (tpp) REVERT: G 719 ASP cc_start: 0.9002 (m-30) cc_final: 0.8704 (m-30) outliers start: 39 outliers final: 33 residues processed: 154 average time/residue: 0.1383 time to fit residues: 36.8772 Evaluate side-chains 148 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 364 THR 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 340 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 725 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 431 ASN Chi-restraints excluded: chain G residue 523 GLN Chi-restraints excluded: chain G residue 716 ASP Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 736 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 61 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 chunk 278 optimal weight: 0.0970 chunk 79 optimal weight: 3.9990 chunk 296 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 221 optimal weight: 9.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 ASN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 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 = 0.3361 r_free = 0.3361 target = 0.073267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.052512 restraints weight = 88804.422| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.63 r_work: 0.2737 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.4455 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= 0.127 Angle : 0.510 12.852 36485 Z= 0.291 Chirality : 0.044 0.206 4225 Planarity : 0.003 0.045 4756 Dihedral : 3.895 19.061 3427 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.08 % Allowed : 13.70 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.14), residues: 3401 helix: 0.12 (0.24), residues: 483 sheet: 1.36 (0.18), residues: 773 loop : -0.42 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 457 TYR 0.008 0.001 TYR F 260 PHE 0.010 0.001 PHE C 710 TRP 0.007 0.001 TRP C 631 HIS 0.002 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00270 (27012) covalent geometry : angle 0.50995 (36485) hydrogen bonds : bond 0.02767 ( 827) hydrogen bonds : angle 4.73216 ( 2280) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6802 Ramachandran restraints generated. 3401 Oldfield, 0 Emsley, 3401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 492 GLN cc_start: 0.9149 (mp10) cc_final: 0.8938 (mp10) REVERT: B 654 LYS cc_start: 0.8683 (mmmt) cc_final: 0.8249 (mmmm) REVERT: B 659 MET cc_start: 0.7547 (tpp) cc_final: 0.7156 (tpp) REVERT: C 303 MET cc_start: 0.8252 (ppp) cc_final: 0.8003 (ppp) REVERT: C 332 ASP cc_start: 0.8964 (m-30) cc_final: 0.8619 (m-30) REVERT: C 464 ASP cc_start: 0.8833 (m-30) cc_final: 0.8581 (t0) REVERT: D 303 MET cc_start: 0.8972 (ttp) cc_final: 0.8763 (ptm) REVERT: D 468 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.9207 (tttt) REVERT: D 533 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8276 (pt0) REVERT: E 389 ASN cc_start: 0.8245 (t0) cc_final: 0.7856 (t0) REVERT: F 254 LYS cc_start: 0.9045 (mmtp) cc_final: 0.8662 (mtmt) REVERT: F 361 ASP cc_start: 0.8914 (t70) cc_final: 0.8690 (p0) REVERT: F 657 ILE cc_start: 0.9392 (mm) cc_final: 0.9172 (tp) REVERT: F 659 MET cc_start: 0.8200 (tpp) cc_final: 0.7909 (tpp) REVERT: G 719 ASP cc_start: 0.9006 (m-30) cc_final: 0.8714 (m-30) outliers start: 33 outliers final: 29 residues processed: 163 average time/residue: 0.1486 time to fit residues: 41.6466 Evaluate side-chains 149 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 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 411 LEU Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 431 ASN Chi-restraints excluded: chain G residue 523 GLN Chi-restraints excluded: chain G residue 716 ASP Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 738 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 221 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 330 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 329 optimal weight: 6.9990 chunk 243 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 ASN ** B 741 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.072576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.051828 restraints weight = 89131.488| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.63 r_work: 0.2719 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27012 Z= 0.162 Angle : 0.534 12.440 36485 Z= 0.302 Chirality : 0.045 0.394 4225 Planarity : 0.003 0.045 4756 Dihedral : 3.961 20.404 3427 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.21 % Allowed : 13.93 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.14), residues: 3401 helix: 0.09 (0.24), residues: 479 sheet: 1.33 (0.18), residues: 775 loop : -0.45 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 289 TYR 0.009 0.001 TYR F 260 PHE 0.009 0.001 PHE C 710 TRP 0.006 0.001 TRP F 502 HIS 0.002 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00355 (27012) covalent geometry : angle 0.53424 (36485) hydrogen bonds : bond 0.02924 ( 827) hydrogen bonds : angle 4.75543 ( 2280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5089.57 seconds wall clock time: 88 minutes 41.62 seconds (5321.62 seconds total)