Starting phenix.real_space_refine on Sun Jun 22 03:15:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsh_61773/06_2025/9jsh_61773.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsh_61773/06_2025/9jsh_61773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jsh_61773/06_2025/9jsh_61773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsh_61773/06_2025/9jsh_61773.map" model { file = "/net/cci-nas-00/data/ceres_data/9jsh_61773/06_2025/9jsh_61773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsh_61773/06_2025/9jsh_61773.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 21 9.91 5 S 37 5.16 5 C 16601 2.51 5 N 4184 2.21 5 O 5355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26198 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3467 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 427} 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: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3464 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 427} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 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: "D" 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: "E" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3851 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 480} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "F" Number of atoms: 3836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3836 Classifications: {'peptide': 499} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 478} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "G" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3852 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 480} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 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: 16.88, per 1000 atoms: 0.64 Number of scatterers: 26198 At special positions: 0 Unit cell: (177.76, 176.88, 95.92, 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 37 16.00 O 5355 8.00 N 4184 7.00 C 16601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.81 Conformation dependent library (CDL) restraints added in 3.7 seconds 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6370 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 71 sheets defined 16.8% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.24 Creating SS restraints... Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.519A pdb=" N ASN A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 removed outlier: 3.996A pdb=" N ALA A 249 " --> pdb=" O ASP A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 501 through 504 removed outlier: 3.864A pdb=" N ASN A 504 " --> pdb=" O SER A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 501 through 504' Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 545 through 555 Processing helix chain 'A' and resid 571 through 575 removed outlier: 3.648A pdb=" N VAL A 575 " --> pdb=" O GLU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 593 removed outlier: 3.691A pdb=" N TYR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.971A pdb=" N ALA B 249 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 250 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 285 through 290 removed outlier: 3.680A pdb=" N ASP B 290 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 501 through 504 removed outlier: 3.505A pdb=" N ASN B 504 " --> pdb=" O SER B 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 501 through 504' Processing helix chain 'B' and resid 505 through 512 Processing helix chain 'B' and resid 545 through 555 Processing helix chain 'B' and resid 580 through 592 Processing helix chain 'B' and resid 598 through 602 Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 247 through 252 removed outlier: 4.341A pdb=" N GLN C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 252 " --> pdb=" O PHE C 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 247 through 252' Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 285 through 290 removed outlier: 3.581A pdb=" N ASP C 290 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 338 removed outlier: 4.078A pdb=" N GLY C 337 " --> pdb=" O ASN C 334 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL C 338 " --> pdb=" O THR C 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 334 through 338' Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 501 through 504 removed outlier: 3.810A pdb=" N ASN C 504 " --> pdb=" O SER C 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 501 through 504' Processing helix chain 'C' and resid 505 through 511 Processing helix chain 'C' and resid 545 through 555 Processing helix chain 'C' and resid 571 through 575 removed outlier: 3.950A pdb=" N VAL C 575 " --> pdb=" O GLU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 592 removed outlier: 3.758A pdb=" N LYS C 592 " --> pdb=" O LYS C 588 " (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 249 removed outlier: 3.734A pdb=" N ALA D 249 " --> pdb=" O ASP D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 278 Processing helix chain 'D' and resid 285 through 290 removed outlier: 3.863A pdb=" N ASP D 290 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 336 removed outlier: 4.026A pdb=" N THR D 335 " --> pdb=" O THR D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 470 Processing helix chain 'D' and resid 505 through 511 Processing helix chain 'D' and resid 545 through 555 Processing helix chain 'D' and resid 580 through 594 removed outlier: 3.865A pdb=" N LYS D 592 " --> pdb=" O LYS D 588 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR D 593 " --> pdb=" O GLU D 589 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 594 " --> pdb=" O GLN D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 602 Processing helix chain 'D' and resid 658 through 662 Processing helix chain 'E' and resid 226 through 232 removed outlier: 3.595A pdb=" N ASN E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 250 removed outlier: 3.860A pdb=" N ALA E 249 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU E 250 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 277 Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 505 through 511 Processing helix chain 'E' and resid 545 through 555 Processing helix chain 'E' and resid 580 through 592 removed outlier: 3.928A pdb=" N LYS E 592 " --> pdb=" O LYS E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 602 Processing helix chain 'F' and resid 226 through 233 Processing helix chain 'F' and resid 245 through 249 Processing helix chain 'F' and resid 271 through 278 Processing helix chain 'F' and resid 285 through 290 removed outlier: 3.623A pdb=" N ASP F 290 " --> pdb=" O GLU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 416 removed outlier: 3.823A pdb=" N GLU F 416 " --> pdb=" O LEU F 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 413 through 416' Processing helix chain 'F' and resid 462 through 471 Processing helix chain 'F' and resid 501 through 504 removed outlier: 3.701A pdb=" N ASN F 504 " --> pdb=" O SER F 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 501 through 504' Processing helix chain 'F' and resid 505 through 511 Processing helix chain 'F' and resid 545 through 555 Processing helix chain 'F' and resid 580 through 592 removed outlier: 4.061A pdb=" N LYS F 592 " --> pdb=" O LYS F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 602 removed outlier: 3.516A pdb=" N ASN F 601 " --> pdb=" O LYS F 598 " (cutoff:3.500A) 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 removed outlier: 3.528A pdb=" N ALA G 249 " --> pdb=" O ASP G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 277 Processing helix chain 'G' and resid 285 through 289 Processing helix chain 'G' and resid 332 through 337 removed outlier: 4.458A pdb=" N GLY G 337 " --> pdb=" O ALA G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 472 removed outlier: 3.502A pdb=" N LEU G 466 " --> pdb=" O ASN G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 511 Processing helix chain 'G' and resid 545 through 555 Processing helix chain 'G' and resid 580 through 592 removed outlier: 3.777A 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: 5.562A pdb=" N VAL A 301 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR A 395 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N MET A 303 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG A 393 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN A 305 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 391 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 309 " --> pdb=" O TYR A 387 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 309 removed outlier: 5.562A pdb=" N VAL A 301 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR A 395 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N MET A 303 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG A 393 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN A 305 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 391 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 309 " --> pdb=" O TYR A 387 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 417 through 422 removed outlier: 6.595A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A 422 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS A 404 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY A 484 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR A 406 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL A 482 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR A 408 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 3.527A 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 removed outlier: 9.804A pdb=" N ILE A 610 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER A 515 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ILE A 612 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE A 517 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 559 Processing sheet with id=AA8, first strand: chain 'A' and resid 617 through 618 removed outlier: 3.693A pdb=" N THR A 723 " --> pdb=" O ASN A 686 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN A 686 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR A 725 " --> pdb=" O THR A 684 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 683 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 693 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 647 through 657 removed outlier: 4.793A pdb=" N GLY A 728 " --> pdb=" O GLY A 651 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR A 653 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N SER A 726 " --> pdb=" O THR A 653 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 655 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 724 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 657 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE A 722 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU A 732 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LYS A 675 " --> pdb=" O LEU A 732 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASN A 734 " --> pdb=" O TYR A 673 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR A 673 " --> pdb=" O ASN A 734 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 666 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 712 " --> pdb=" O LYS A 666 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 670 " --> pdb=" O TYR A 708 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A 708 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 672 " --> pdb=" O PHE A 706 " (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 301 removed outlier: 3.771A pdb=" N GLU B 436 " --> pdb=" O ASN B 396 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 305 through 309 removed outlier: 3.625A pdb=" N ASN B 305 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 417 through 422 removed outlier: 7.012A pdb=" N LEU B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR B 420 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR B 409 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR B 408 " --> pdb=" O THR B 480 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AB6, first strand: chain 'B' and resid 524 through 530 removed outlier: 9.649A pdb=" N ILE B 610 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SER B 515 " --> pdb=" O ILE B 610 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ILE B 612 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 517 " --> pdb=" O ILE B 612 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 557 through 559 removed outlier: 3.881A pdb=" N LEU B 562 " --> pdb=" O ASN B 559 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 617 through 619 Processing sheet with id=AB9, first strand: chain 'B' and resid 617 through 619 removed outlier: 6.281A pdb=" N ASN B 734 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR B 673 " --> pdb=" O ASN B 734 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 653 through 657 removed outlier: 4.036A pdb=" N THR B 653 " --> pdb=" O LEU B 724 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 724 " --> pdb=" O THR B 653 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE B 655 " --> pdb=" O ILE B 722 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE B 722 " --> pdb=" O ILE B 655 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE B 657 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE B 720 " --> pdb=" O ILE B 657 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 721 " --> pdb=" O LYS B 688 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 234 through 237 Processing sheet with id=AC3, first strand: chain 'C' and resid 299 through 305 removed outlier: 7.027A pdb=" N ASN C 391 " --> pdb=" O GLU C 304 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 299 through 305 removed outlier: 7.027A pdb=" N ASN C 391 " --> pdb=" O GLU C 304 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 326 through 329 removed outlier: 4.109A pdb=" N ASN C 362 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU C 477 " --> pdb=" O ASN C 362 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYS C 476 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL C 412 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU C 478 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR C 408 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N VAL C 482 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR C 406 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY C 484 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS C 404 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR C 409 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N THR C 420 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU C 411 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 416 " --> pdb=" O LEU C 413 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 326 through 329 removed outlier: 4.109A pdb=" N ASN C 362 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU C 477 " --> pdb=" O ASN C 362 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYS C 476 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL C 412 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU C 478 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR C 408 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N VAL C 482 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR C 406 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY C 484 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS C 404 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR C 403 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN C 431 " --> pdb=" O TYR C 403 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 351 through 352 removed outlier: 6.908A pdb=" N ASN C 351 " --> pdb=" O PHE C 579 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 613 " --> pdb=" O GLU C 576 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 557 through 559 removed outlier: 3.805A 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: 8.052A pdb=" N ASP C 733 " --> pdb=" O LYS C 675 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LYS C 675 " --> pdb=" O ASP C 733 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU C 735 " --> pdb=" O TYR C 673 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N TYR C 673 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ILE C 737 " --> pdb=" O SER C 671 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER C 671 " --> pdb=" O ILE C 737 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLU C 739 " --> pdb=" O VAL C 669 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL C 669 " --> pdb=" O GLU C 739 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASN C 741 " --> pdb=" O ARG C 667 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS C 666 " --> pdb=" O THR C 712 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR C 712 " --> pdb=" O LYS C 666 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY C 672 " --> pdb=" O PHE C 706 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 652 through 657 removed outlier: 3.758A pdb=" N ILE C 722 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C 693 " --> pdb=" O ILE C 687 " (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 306 removed outlier: 6.544A 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 306 removed outlier: 6.544A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 327 through 329 removed outlier: 4.186A pdb=" N ASN D 362 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 477 " --> pdb=" O ASN D 362 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N THR D 479 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASN D 410 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN D 481 " --> pdb=" O THR D 408 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 351 through 352 removed outlier: 9.413A pdb=" N ILE D 610 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER D 515 " --> pdb=" O ILE D 610 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE D 612 " --> pdb=" O SER D 515 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE D 517 " --> pdb=" O ILE D 612 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 402 through 405 removed outlier: 6.628A pdb=" N TYR D 403 " --> pdb=" O ASN D 431 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN D 431 " --> pdb=" O TYR D 403 " (cutoff:3.500A) 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: 3.650A 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 Processing sheet with id=AE3, first strand: chain 'D' and resid 647 through 657 removed outlier: 4.085A pdb=" N GLY D 651 " --> pdb=" O GLY D 728 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY D 728 " --> pdb=" O GLY D 651 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N THR D 653 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N SER D 726 " --> pdb=" O THR D 653 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N ILE D 655 " --> pdb=" O LEU D 724 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LEU D 724 " --> pdb=" O ILE D 655 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE D 657 " --> pdb=" O ILE D 722 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ILE D 722 " --> pdb=" O ILE D 657 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ASP D 733 " --> pdb=" O LYS D 675 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LYS D 675 " --> pdb=" O ASP D 733 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU D 735 " --> pdb=" O TYR D 673 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N TYR D 673 " --> pdb=" O LEU D 735 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ILE D 737 " --> pdb=" O SER D 671 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N SER D 671 " --> pdb=" O ILE D 737 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLU D 739 " --> pdb=" O VAL D 669 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 669 " --> pdb=" O GLU D 739 " (cutoff:3.500A) removed outlier: 4.239A 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 236 Processing sheet with id=AE5, first strand: chain 'E' and resid 299 through 305 removed outlier: 3.593A pdb=" N GLU E 304 " --> pdb=" O ASN E 391 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 299 through 305 removed outlier: 3.593A pdb=" N GLU E 304 " --> pdb=" O ASN E 391 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 327 through 329 removed outlier: 4.422A pdb=" N ASN E 362 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU E 477 " --> pdb=" O ASN E 362 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU E 477 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU E 411 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THR E 479 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR E 409 " --> pdb=" O THR E 479 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLN E 481 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER E 483 " --> pdb=" O VAL E 405 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL E 405 " --> pdb=" O SER E 483 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS E 422 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR E 409 " --> pdb=" O THR E 420 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N THR E 420 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU E 411 " --> pdb=" O LEU E 418 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 350 through 352 removed outlier: 6.370A pdb=" N ASN E 351 " --> pdb=" O PHE E 579 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N ILE E 610 " --> pdb=" O SER E 513 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER E 515 " --> pdb=" O ILE E 610 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE E 612 " --> pdb=" O SER E 515 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE E 517 " --> pdb=" O ILE E 612 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 488 through 489 Processing sheet with id=AF1, first strand: chain 'E' and resid 557 through 558 Processing sheet with id=AF2, first strand: chain 'E' and resid 617 through 619 removed outlier: 3.572A pdb=" N LEU E 732 " --> pdb=" O ASN E 647 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 617 through 619 removed outlier: 8.130A pdb=" N ASP E 733 " --> pdb=" O LYS E 675 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LYS E 675 " --> pdb=" O ASP E 733 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU E 735 " --> pdb=" O TYR E 673 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N TYR E 673 " --> pdb=" O LEU E 735 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE E 737 " --> pdb=" O SER E 671 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER E 671 " --> pdb=" O ILE E 737 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU E 739 " --> pdb=" O VAL E 669 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL E 669 " --> pdb=" O GLU E 739 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN E 741 " --> pdb=" O ARG E 667 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 652 through 657 removed outlier: 3.569A pdb=" N ASN E 686 " --> pdb=" O THR E 723 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR E 684 " --> pdb=" O THR E 725 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS E 693 " --> pdb=" O ILE E 687 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 234 through 236 Processing sheet with id=AF6, first strand: chain 'F' and resid 299 through 305 removed outlier: 6.664A pdb=" N ASN F 391 " --> pdb=" O GLU F 304 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU F 436 " --> pdb=" O ASN F 396 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 299 through 305 removed outlier: 6.664A pdb=" N ASN F 391 " --> pdb=" O GLU F 304 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 326 through 329 Processing sheet with id=AF9, first strand: chain 'F' and resid 350 through 352 removed outlier: 6.095A pdb=" N ASN F 351 " --> pdb=" O PHE F 579 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS F 613 " --> pdb=" O GLU F 576 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 420 through 422 removed outlier: 6.671A pdb=" N TYR F 403 " --> pdb=" O ASN F 431 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN F 431 " --> pdb=" O TYR F 403 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 420 through 422 removed outlier: 4.229A pdb=" N VAL F 405 " --> pdb=" O SER F 483 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER F 483 " --> pdb=" O VAL F 405 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLN F 481 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR F 409 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR F 479 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU F 411 " --> pdb=" O LEU F 477 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N LEU F 477 " --> pdb=" O LEU F 411 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 488 through 489 Processing sheet with id=AG4, first strand: chain 'F' and resid 557 through 559 removed outlier: 4.144A pdb=" N LEU F 562 " --> pdb=" O ASN F 559 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 617 through 619 Processing sheet with id=AG6, first strand: chain 'F' and resid 617 through 619 removed outlier: 5.856A pdb=" N LEU F 732 " --> pdb=" O LYS F 675 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LYS F 675 " --> pdb=" O LEU F 732 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ASN F 734 " --> pdb=" O TYR F 673 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR F 673 " --> pdb=" O ASN F 734 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG F 667 " --> pdb=" O LEU F 740 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 652 through 657 removed outlier: 3.558A pdb=" N ASN F 686 " --> pdb=" O THR F 723 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS F 693 " --> pdb=" O ILE F 687 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 234 through 237 Processing sheet with id=AG9, first strand: chain 'G' and resid 299 through 306 removed outlier: 5.540A pdb=" N VAL G 301 " --> pdb=" O TYR G 395 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR G 395 " --> pdb=" O VAL G 301 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N MET G 303 " --> pdb=" O ARG G 393 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG G 393 " --> pdb=" O MET G 303 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 299 through 306 removed outlier: 5.540A pdb=" N VAL G 301 " --> pdb=" O TYR G 395 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR G 395 " --> pdb=" O VAL G 301 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N MET G 303 " --> pdb=" O ARG G 393 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG G 393 " --> pdb=" O MET G 303 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 328 through 329 removed outlier: 4.069A pdb=" N SER G 363 " --> pdb=" O SER G 329 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN G 362 " --> pdb=" O LEU G 477 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU G 477 " --> pdb=" O ASN G 362 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR G 479 " --> pdb=" O ASN G 410 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN G 410 " --> pdb=" O THR G 479 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN G 481 " --> pdb=" O THR G 408 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN G 485 " --> pdb=" O LYS G 404 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LYS G 404 " --> pdb=" O ASN G 485 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 351 through 352 removed outlier: 9.411A pdb=" N ILE G 610 " --> pdb=" O SER G 513 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER G 515 " --> pdb=" O ILE G 610 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ILE G 612 " --> pdb=" O SER G 515 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE G 517 " --> pdb=" O ILE G 612 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 488 through 489 Processing sheet with id=AH5, first strand: chain 'G' and resid 557 through 559 removed outlier: 3.683A pdb=" N ASN G 559 " --> pdb=" O LEU G 562 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU G 562 " --> pdb=" O ASN G 559 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 617 through 619 Processing sheet with id=AH7, first strand: chain 'G' and resid 617 through 619 removed outlier: 5.451A pdb=" N LEU G 732 " --> pdb=" O LYS G 675 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LYS G 675 " --> pdb=" O LEU G 732 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASN G 734 " --> pdb=" O TYR G 673 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR G 673 " --> pdb=" O ASN G 734 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 652 through 657 removed outlier: 3.506A pdb=" N ILE G 722 " --> pdb=" O ILE G 655 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU G 721 " --> pdb=" O LYS G 688 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS G 688 " --> pdb=" O GLU G 721 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 1920 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: 11.96 Time building geometry restraints manager: 8.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8544 1.34 - 1.46: 5725 1.46 - 1.58: 12271 1.58 - 1.70: 1 1.70 - 1.82: 67 Bond restraints: 26608 Sorted by residual: bond pdb=" CD2 TRP D 374 " pdb=" CE2 TRP D 374 " ideal model delta sigma weight residual 1.409 1.447 -0.038 1.70e-02 3.46e+03 4.93e+00 bond pdb=" CD2 TRP D 631 " pdb=" CE2 TRP D 631 " ideal model delta sigma weight residual 1.409 1.447 -0.038 1.70e-02 3.46e+03 4.91e+00 bond pdb=" CD2 TRP B 631 " pdb=" CE2 TRP B 631 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.81e+00 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 4.80e+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 4.78e+00 ... (remaining 26603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 35010 1.40 - 2.80: 714 2.80 - 4.21: 159 4.21 - 5.61: 45 5.61 - 7.01: 6 Bond angle restraints: 35934 Sorted by residual: angle pdb=" CA PRO A 297 " pdb=" N PRO A 297 " pdb=" CD PRO A 297 " ideal model delta sigma weight residual 112.00 105.34 6.66 1.40e+00 5.10e-01 2.26e+01 angle pdb=" CD2 TRP E 631 " pdb=" CE3 TRP E 631 " pdb=" CZ3 TRP E 631 " ideal model delta sigma weight residual 118.60 124.03 -5.43 1.30e+00 5.92e-01 1.74e+01 angle pdb=" CD2 TRP C 631 " pdb=" CE3 TRP C 631 " pdb=" CZ3 TRP C 631 " ideal model delta sigma weight residual 118.60 124.02 -5.42 1.30e+00 5.92e-01 1.74e+01 angle pdb=" CD2 TRP E 374 " pdb=" CE3 TRP E 374 " pdb=" CZ3 TRP E 374 " ideal model delta sigma weight residual 118.60 124.01 -5.41 1.30e+00 5.92e-01 1.73e+01 angle pdb=" CD2 TRP C 374 " pdb=" CE3 TRP C 374 " pdb=" CZ3 TRP C 374 " ideal model delta sigma weight residual 118.60 124.00 -5.40 1.30e+00 5.92e-01 1.73e+01 ... (remaining 35929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14564 17.94 - 35.88: 1295 35.88 - 53.82: 209 53.82 - 71.76: 40 71.76 - 89.70: 24 Dihedral angle restraints: 16132 sinusoidal: 6391 harmonic: 9741 Sorted by residual: dihedral pdb=" CA GLU C 533 " pdb=" C GLU C 533 " pdb=" N GLN C 534 " pdb=" CA GLN C 534 " ideal model delta harmonic sigma weight residual -180.00 -160.60 -19.40 0 5.00e+00 4.00e-02 1.51e+01 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 -160.89 -19.11 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ASP G 571 " pdb=" CB ASP G 571 " pdb=" CG ASP G 571 " pdb=" OD1 ASP G 571 " ideal model delta sinusoidal sigma weight residual -30.00 -88.29 58.29 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 16129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2966 0.041 - 0.083: 812 0.083 - 0.124: 341 0.124 - 0.166: 39 0.166 - 0.207: 4 Chirality restraints: 4162 Sorted by residual: chirality pdb=" CB THR D 406 " pdb=" CA THR D 406 " pdb=" OG1 THR D 406 " pdb=" CG2 THR D 406 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB THR B 406 " pdb=" CA THR B 406 " pdb=" OG1 THR B 406 " pdb=" CG2 THR B 406 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL A 512 " pdb=" CA VAL A 512 " pdb=" CG1 VAL A 512 " pdb=" CG2 VAL A 512 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 4159 not shown) Planarity restraints: 4681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 296 " 0.058 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO A 297 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 297 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 297 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 444 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO D 445 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 445 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 445 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR G 296 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO G 297 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO G 297 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 297 " -0.030 5.00e-02 4.00e+02 ... (remaining 4678 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1700 2.73 - 3.27: 25940 3.27 - 3.82: 40903 3.82 - 4.36: 50350 4.36 - 4.90: 88737 Nonbonded interactions: 207630 Sorted by model distance: nonbonded pdb=" OG1 THR D 364 " pdb=" O ILE D 475 " model vdw 2.191 3.040 nonbonded pdb=" OG SER D 444 " pdb=" OG1 THR E 417 " model vdw 2.201 3.040 nonbonded pdb=" OD1 ASP A 581 " pdb=" N ASN A 582 " model vdw 2.206 3.120 nonbonded pdb=" OE2 GLU A 287 " pdb=" NE ARG A 527 " model vdw 2.207 3.120 nonbonded pdb=" OG1 THR F 331 " pdb=" OD2 ASP F 519 " model vdw 2.208 3.040 ... (remaining 207625 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 388 thro \ ugh 449 or resid 460 through 740 or resid 901 through 903)) selection = (chain 'B' and (resid 216 through 308 or resid 310 through 386 or resid 388 thro \ ugh 449 or resid 460 through 740 or resid 901 through 903)) selection = (chain 'C' and (resid 216 through 308 or resid 326 or resid 341 through 342 or r \ esid 388 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 740 or resi \ d 901 through 903)) selection = (chain 'D' and (resid 216 through 308 or resid 354 through 355 or resid 365 or r \ esid 380 through 381 or resid 390 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 resi \ d 616 through 740 or resid 901 through 903)) selection = (chain 'E' and (resid 216 through 308 or resid 354 through 355 or resid 365 or r \ esid 388 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 740 or resi \ d 901 through 903)) selection = (chain 'F' and (resid 216 through 307 or resid 340 or resid 354 through 355 or r \ esid 365 or resid 380 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 740 or resid 901 through 903)) selection = (chain 'G' and (resid 216 through 308 or resid 354 through 355 or resid 365 or r \ esid 380 through 381 or resid 390 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 resi \ d 616 through 740 or resid 901 through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 1.230 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 64.590 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 0.096 26608 Z= 0.151 Angle : 0.546 7.012 35934 Z= 0.313 Chirality : 0.045 0.207 4162 Planarity : 0.004 0.084 4681 Dihedral : 14.252 89.695 9762 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.07 % Allowed : 0.60 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3345 helix: -0.56 (0.25), residues: 432 sheet: 0.94 (0.21), residues: 696 loop : -0.99 (0.12), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 502 HIS 0.002 0.001 HIS G 358 PHE 0.010 0.001 PHE C 710 TYR 0.012 0.001 TYR G 486 ARG 0.000 0.000 ARG G 667 Details of bonding type rmsd hydrogen bonds : bond 0.23673 ( 730) hydrogen bonds : angle 9.35516 ( 1920) covalent geometry : bond 0.00330 (26608) covalent geometry : angle 0.54583 (35934) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 312 time to evaluate : 2.939 Fit side-chains Corrupt residue: chain: A residue: PRO 615 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 GLU cc_start: 0.6563 (tp30) cc_final: 0.6031 (tp30) REVERT: D 716 ASP cc_start: 0.6877 (p0) cc_final: 0.6467 (p0) REVERT: G 339 SER cc_start: 0.6880 (t) cc_final: 0.6636 (p) outliers start: 3 outliers final: 3 residues processed: 315 average time/residue: 0.3754 time to fit residues: 188.8804 Evaluate side-chains 171 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 168 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 PRO Chi-restraints excluded: chain B residue 463 TYR Chi-restraints excluded: chain C residue 289 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 20.0000 chunk 255 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 87 optimal weight: 50.0000 chunk 172 optimal weight: 9.9990 chunk 136 optimal weight: 50.0000 chunk 264 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 160 optimal weight: 20.0000 chunk 196 optimal weight: 1.9990 chunk 306 optimal weight: 8.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 GLN B 633 ASN ** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN D 430 ASN D 500 ASN ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 500 ASN G 391 ASN G 643 GLN ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.081268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.055312 restraints weight = 83761.487| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.67 r_work: 0.2757 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 26608 Z= 0.248 Angle : 0.618 8.268 35934 Z= 0.344 Chirality : 0.047 0.194 4162 Planarity : 0.004 0.044 4681 Dihedral : 4.635 42.812 3378 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.10 % Allowed : 7.88 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3345 helix: -0.43 (0.24), residues: 445 sheet: 0.63 (0.20), residues: 734 loop : -0.95 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 374 HIS 0.001 0.000 HIS G 358 PHE 0.010 0.001 PHE G 348 TYR 0.013 0.001 TYR C 486 ARG 0.000 0.000 ARG E 527 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 730) hydrogen bonds : angle 6.10704 ( 1920) covalent geometry : bond 0.00554 (26608) covalent geometry : angle 0.61755 (35934) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 2.958 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: B 305 ASN cc_start: 0.8749 (t0) cc_final: 0.8425 (t0) REVERT: B 594 LEU cc_start: 0.8822 (tp) cc_final: 0.8595 (tp) REVERT: C 332 ASP cc_start: 0.8185 (m-30) cc_final: 0.7662 (t0) REVERT: F 332 ASP cc_start: 0.8341 (t70) cc_final: 0.8080 (t70) REVERT: G 339 SER cc_start: 0.8592 (t) cc_final: 0.8284 (p) REVERT: G 375 ASN cc_start: 0.8671 (m-40) cc_final: 0.8404 (t0) outliers start: 33 outliers final: 24 residues processed: 198 average time/residue: 0.3440 time to fit residues: 114.0903 Evaluate side-chains 173 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 463 TYR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain E residue 630 SER Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain G residue 743 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 253 optimal weight: 0.7980 chunk 297 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 250 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 303 optimal weight: 10.0000 chunk 231 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 256 optimal weight: 9.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN B 534 GLN F 362 ASN ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.081468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.055875 restraints weight = 82565.775| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.55 r_work: 0.2800 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26608 Z= 0.189 Angle : 0.552 8.272 35934 Z= 0.310 Chirality : 0.045 0.149 4162 Planarity : 0.003 0.039 4681 Dihedral : 4.366 40.421 3373 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.20 % Allowed : 9.91 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3345 helix: -0.30 (0.25), residues: 446 sheet: 0.71 (0.20), residues: 721 loop : -0.89 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 374 HIS 0.001 0.000 HIS G 358 PHE 0.010 0.001 PHE C 710 TYR 0.011 0.001 TYR A 668 ARG 0.000 0.000 ARG C 457 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 730) hydrogen bonds : angle 5.57657 ( 1920) covalent geometry : bond 0.00417 (26608) covalent geometry : angle 0.55163 (35934) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 3.372 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 615 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 ASN cc_start: 0.8899 (t0) cc_final: 0.8555 (t0) REVERT: B 594 LEU cc_start: 0.8788 (tp) cc_final: 0.8425 (tp) REVERT: C 332 ASP cc_start: 0.8180 (m-30) cc_final: 0.7764 (t0) REVERT: E 476 LYS cc_start: 0.7089 (tppt) cc_final: 0.6745 (mppt) REVERT: F 332 ASP cc_start: 0.8267 (t70) cc_final: 0.8003 (t70) REVERT: F 490 ASN cc_start: 0.9074 (t0) cc_final: 0.8811 (t0) REVERT: F 738 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.7949 (p) REVERT: G 339 SER cc_start: 0.8651 (t) cc_final: 0.8350 (p) REVERT: G 375 ASN cc_start: 0.8589 (m-40) cc_final: 0.8348 (t0) REVERT: G 659 MET cc_start: 0.8532 (tpt) cc_final: 0.8052 (tpp) outliers start: 37 outliers final: 25 residues processed: 192 average time/residue: 0.3372 time to fit residues: 109.0496 Evaluate side-chains 171 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 615 PRO Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 463 TYR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain E residue 630 SER Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 636 THR Chi-restraints excluded: chain G residue 649 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 50 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 270 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 323 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 102 optimal weight: 50.0000 chunk 116 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 ASN C 391 ASN ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN ** E 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.080287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.054613 restraints weight = 83607.292| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.59 r_work: 0.2745 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26608 Z= 0.195 Angle : 0.544 7.353 35934 Z= 0.306 Chirality : 0.045 0.156 4162 Planarity : 0.003 0.039 4681 Dihedral : 4.361 37.981 3373 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.53 % Allowed : 11.14 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3345 helix: -0.26 (0.24), residues: 447 sheet: 0.70 (0.20), residues: 719 loop : -0.83 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 374 HIS 0.001 0.000 HIS G 358 PHE 0.010 0.001 PHE C 710 TYR 0.012 0.001 TYR A 668 ARG 0.000 0.000 ARG E 527 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 730) hydrogen bonds : angle 5.34476 ( 1920) covalent geometry : bond 0.00432 (26608) covalent geometry : angle 0.54379 (35934) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 3.372 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 615 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 ASN cc_start: 0.8988 (t0) cc_final: 0.8545 (t0) REVERT: B 594 LEU cc_start: 0.8810 (tp) cc_final: 0.8373 (tp) REVERT: C 332 ASP cc_start: 0.8244 (m-30) cc_final: 0.7860 (t0) REVERT: E 476 LYS cc_start: 0.7181 (tppt) cc_final: 0.6883 (mppt) REVERT: F 332 ASP cc_start: 0.8337 (t70) cc_final: 0.8054 (t70) REVERT: F 490 ASN cc_start: 0.9095 (t0) cc_final: 0.8814 (t0) REVERT: G 339 SER cc_start: 0.8716 (t) cc_final: 0.8423 (p) REVERT: G 375 ASN cc_start: 0.8485 (m-40) cc_final: 0.8279 (t0) REVERT: G 659 MET cc_start: 0.8536 (tpt) cc_final: 0.8052 (tpp) outliers start: 47 outliers final: 31 residues processed: 194 average time/residue: 0.3302 time to fit residues: 108.6446 Evaluate side-chains 168 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 615 PRO Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 463 TYR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 630 SER Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 636 THR Chi-restraints excluded: chain G residue 649 LEU Chi-restraints excluded: chain G residue 650 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 97 optimal weight: 0.0050 chunk 12 optimal weight: 5.9990 chunk 323 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 238 optimal weight: 20.0000 chunk 274 optimal weight: 10.0000 chunk 279 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 167 optimal weight: 0.4980 overall best weight: 3.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 643 GLN G 741 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.082744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.056850 restraints weight = 84376.834| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.68 r_work: 0.2879 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26608 Z= 0.139 Angle : 0.510 7.922 35934 Z= 0.288 Chirality : 0.044 0.148 4162 Planarity : 0.003 0.039 4681 Dihedral : 4.112 35.845 3373 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.36 % Allowed : 12.21 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3345 helix: -0.11 (0.25), residues: 445 sheet: 0.76 (0.19), residues: 762 loop : -0.75 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 374 HIS 0.001 0.000 HIS G 358 PHE 0.010 0.001 PHE C 710 TYR 0.009 0.001 TYR A 668 ARG 0.000 0.000 ARG E 527 Details of bonding type rmsd hydrogen bonds : bond 0.02831 ( 730) hydrogen bonds : angle 5.11680 ( 1920) covalent geometry : bond 0.00298 (26608) covalent geometry : angle 0.50979 (35934) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 3.175 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 615 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 ASN cc_start: 0.8999 (t0) cc_final: 0.8532 (t0) REVERT: B 594 LEU cc_start: 0.8842 (tp) cc_final: 0.8403 (tp) REVERT: C 332 ASP cc_start: 0.8199 (m-30) cc_final: 0.7774 (t0) REVERT: E 476 LYS cc_start: 0.7281 (tppt) cc_final: 0.7063 (mppt) REVERT: E 697 LEU cc_start: 0.9137 (tt) cc_final: 0.8917 (pp) REVERT: F 332 ASP cc_start: 0.8286 (t70) cc_final: 0.7969 (t70) REVERT: F 490 ASN cc_start: 0.9097 (t0) cc_final: 0.8823 (t0) REVERT: F 519 ASP cc_start: 0.8616 (t0) cc_final: 0.8324 (t0) REVERT: G 339 SER cc_start: 0.8731 (t) cc_final: 0.8442 (p) REVERT: G 659 MET cc_start: 0.8531 (tpt) cc_final: 0.8136 (tpp) outliers start: 42 outliers final: 30 residues processed: 184 average time/residue: 0.3271 time to fit residues: 103.0794 Evaluate side-chains 170 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 615 PRO Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 463 TYR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 630 SER Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 737 ILE Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 649 LEU Chi-restraints excluded: chain G residue 650 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 323 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 330 optimal weight: 0.7980 chunk 297 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 213 optimal weight: 20.0000 chunk 326 optimal weight: 30.0000 chunk 301 optimal weight: 6.9990 chunk 208 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 435 ASN C 465 GLN ** C 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 609 ASN ** F 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.083305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.056366 restraints weight = 85826.060| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.80 r_work: 0.2876 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26608 Z= 0.136 Angle : 0.506 8.101 35934 Z= 0.286 Chirality : 0.044 0.147 4162 Planarity : 0.003 0.039 4681 Dihedral : 4.013 34.187 3373 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.10 % Allowed : 13.54 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3345 helix: -0.07 (0.25), residues: 447 sheet: 0.84 (0.19), residues: 754 loop : -0.69 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 374 HIS 0.001 0.000 HIS G 358 PHE 0.010 0.001 PHE C 710 TYR 0.009 0.001 TYR A 668 ARG 0.000 0.000 ARG E 527 Details of bonding type rmsd hydrogen bonds : bond 0.02704 ( 730) hydrogen bonds : angle 4.97546 ( 1920) covalent geometry : bond 0.00291 (26608) covalent geometry : angle 0.50556 (35934) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 3.274 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 615 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 ASN cc_start: 0.9028 (t0) cc_final: 0.8560 (t0) REVERT: B 702 ASP cc_start: 0.7822 (m-30) cc_final: 0.7240 (p0) REVERT: C 332 ASP cc_start: 0.8210 (m-30) cc_final: 0.7806 (t0) REVERT: E 476 LYS cc_start: 0.7315 (tppt) cc_final: 0.7096 (mppt) REVERT: F 332 ASP cc_start: 0.8333 (t70) cc_final: 0.7986 (t70) REVERT: F 490 ASN cc_start: 0.9092 (t0) cc_final: 0.8829 (t0) REVERT: G 339 SER cc_start: 0.8726 (t) cc_final: 0.8441 (p) REVERT: G 659 MET cc_start: 0.8566 (tpt) cc_final: 0.8191 (tpp) outliers start: 34 outliers final: 30 residues processed: 174 average time/residue: 0.3311 time to fit residues: 99.2023 Evaluate side-chains 168 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 615 PRO Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 630 SER Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 649 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 318 optimal weight: 0.0470 chunk 144 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 236 optimal weight: 40.0000 chunk 203 optimal weight: 20.0000 chunk 239 optimal weight: 7.9990 chunk 258 optimal weight: 0.4980 chunk 222 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 overall best weight: 3.9084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 GLN ** C 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 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 = 0.3579 r_free = 0.3579 target = 0.083081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.056138 restraints weight = 85990.757| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.79 r_work: 0.2871 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26608 Z= 0.145 Angle : 0.510 7.449 35934 Z= 0.289 Chirality : 0.044 0.294 4162 Planarity : 0.003 0.039 4681 Dihedral : 3.957 17.320 3371 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.33 % Allowed : 13.71 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3345 helix: -0.05 (0.25), residues: 447 sheet: 0.77 (0.19), residues: 781 loop : -0.67 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 374 HIS 0.001 0.000 HIS G 358 PHE 0.009 0.001 PHE C 710 TYR 0.009 0.001 TYR C 486 ARG 0.000 0.000 ARG G 667 Details of bonding type rmsd hydrogen bonds : bond 0.02706 ( 730) hydrogen bonds : angle 4.91590 ( 1920) covalent geometry : bond 0.00315 (26608) covalent geometry : angle 0.50976 (35934) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 2.952 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 615 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 ASN cc_start: 0.9031 (t0) cc_final: 0.8543 (t0) REVERT: B 702 ASP cc_start: 0.7880 (m-30) cc_final: 0.7359 (p0) REVERT: C 332 ASP cc_start: 0.8198 (m-30) cc_final: 0.7805 (t0) REVERT: D 659 MET cc_start: 0.7999 (tpp) cc_final: 0.7318 (mmm) REVERT: F 332 ASP cc_start: 0.8349 (t70) cc_final: 0.8001 (t70) REVERT: F 490 ASN cc_start: 0.9095 (t0) cc_final: 0.8811 (t0) REVERT: G 339 SER cc_start: 0.8726 (t) cc_final: 0.8442 (p) REVERT: G 659 MET cc_start: 0.8602 (tpt) cc_final: 0.8219 (tpp) outliers start: 41 outliers final: 35 residues processed: 176 average time/residue: 0.3231 time to fit residues: 97.3073 Evaluate side-chains 172 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 615 PRO Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 630 SER Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 737 ILE Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 649 LEU Chi-restraints excluded: chain G residue 650 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 167 optimal weight: 7.9990 chunk 149 optimal weight: 0.0030 chunk 312 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 271 optimal weight: 3.9990 chunk 254 optimal weight: 8.9990 chunk 306 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 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 = 0.3583 r_free = 0.3583 target = 0.083215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.056370 restraints weight = 85919.919| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.79 r_work: 0.2875 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26608 Z= 0.137 Angle : 0.509 9.062 35934 Z= 0.287 Chirality : 0.044 0.270 4162 Planarity : 0.003 0.039 4681 Dihedral : 3.895 16.953 3371 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.56 % Allowed : 13.64 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3345 helix: -0.00 (0.25), residues: 447 sheet: 0.80 (0.19), residues: 782 loop : -0.64 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 374 HIS 0.001 0.000 HIS F 358 PHE 0.010 0.001 PHE C 710 TYR 0.010 0.001 TYR C 486 ARG 0.000 0.000 ARG E 324 Details of bonding type rmsd hydrogen bonds : bond 0.02616 ( 730) hydrogen bonds : angle 4.85684 ( 1920) covalent geometry : bond 0.00295 (26608) covalent geometry : angle 0.50932 (35934) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 3.076 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 615 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 ASN cc_start: 0.9064 (t0) cc_final: 0.8586 (t0) REVERT: B 702 ASP cc_start: 0.7894 (m-30) cc_final: 0.7388 (p0) REVERT: C 332 ASP cc_start: 0.8215 (m-30) cc_final: 0.7802 (t0) REVERT: D 659 MET cc_start: 0.7999 (tpp) cc_final: 0.7126 (mmm) REVERT: E 427 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8513 (pm20) REVERT: F 332 ASP cc_start: 0.8360 (t70) cc_final: 0.7995 (t70) REVERT: G 330 LYS cc_start: 0.8221 (mptt) cc_final: 0.7976 (mmtp) REVERT: G 339 SER cc_start: 0.8722 (t) cc_final: 0.8437 (p) REVERT: G 659 MET cc_start: 0.8586 (tpt) cc_final: 0.8203 (tpp) outliers start: 48 outliers final: 40 residues processed: 192 average time/residue: 0.3328 time to fit residues: 109.3230 Evaluate side-chains 184 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 615 PRO Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 630 SER Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 737 ILE Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 649 LEU Chi-restraints excluded: chain G residue 650 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 5 optimal weight: 5.9990 chunk 287 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 97 optimal weight: 0.0270 chunk 86 optimal weight: 40.0000 chunk 180 optimal weight: 8.9990 chunk 290 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 235 optimal weight: 40.0000 chunk 202 optimal weight: 10.0000 overall best weight: 6.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 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 = 0.3590 r_free = 0.3590 target = 0.081549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.055558 restraints weight = 84656.693| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.68 r_work: 0.2852 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26608 Z= 0.190 Angle : 0.550 9.688 35934 Z= 0.307 Chirality : 0.045 0.251 4162 Planarity : 0.003 0.038 4681 Dihedral : 4.125 17.380 3371 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.53 % Allowed : 14.11 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3345 helix: -0.07 (0.24), residues: 448 sheet: 0.75 (0.19), residues: 775 loop : -0.67 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 374 HIS 0.001 0.000 HIS G 358 PHE 0.009 0.001 PHE C 710 TYR 0.013 0.001 TYR C 486 ARG 0.000 0.000 ARG F 289 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 730) hydrogen bonds : angle 4.94857 ( 1920) covalent geometry : bond 0.00423 (26608) covalent geometry : angle 0.55001 (35934) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 4.330 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 615 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 ASN cc_start: 0.9060 (t0) cc_final: 0.8607 (t0) REVERT: B 702 ASP cc_start: 0.7874 (m-30) cc_final: 0.7369 (p0) REVERT: C 332 ASP cc_start: 0.8234 (m-30) cc_final: 0.7811 (t0) REVERT: D 659 MET cc_start: 0.8076 (tpp) cc_final: 0.7328 (mmm) REVERT: E 427 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8640 (pm20) REVERT: F 332 ASP cc_start: 0.8362 (t70) cc_final: 0.8046 (t70) REVERT: G 339 SER cc_start: 0.8749 (t) cc_final: 0.8465 (p) REVERT: G 659 MET cc_start: 0.8633 (tpt) cc_final: 0.8259 (tpp) outliers start: 47 outliers final: 40 residues processed: 183 average time/residue: 0.5664 time to fit residues: 174.4312 Evaluate side-chains 176 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 5.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 615 PRO Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 630 SER Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 650 SER Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 737 ILE Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 649 LEU Chi-restraints excluded: chain G residue 650 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 314 optimal weight: 9.9990 chunk 274 optimal weight: 7.9990 chunk 327 optimal weight: 10.0000 chunk 315 optimal weight: 6.9990 chunk 38 optimal weight: 30.0000 chunk 308 optimal weight: 9.9990 chunk 252 optimal weight: 30.0000 chunk 191 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 chunk 97 optimal weight: 0.0050 overall best weight: 6.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 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 = 0.3476 r_free = 0.3476 target = 0.079619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.054208 restraints weight = 82909.112| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.54 r_work: 0.2737 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26608 Z= 0.199 Angle : 0.563 11.501 35934 Z= 0.313 Chirality : 0.045 0.246 4162 Planarity : 0.003 0.038 4681 Dihedral : 4.243 17.899 3371 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.43 % Allowed : 14.30 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3345 helix: -0.10 (0.24), residues: 448 sheet: 0.77 (0.19), residues: 761 loop : -0.69 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 374 HIS 0.001 0.000 HIS G 358 PHE 0.009 0.001 PHE C 710 TYR 0.013 0.001 TYR C 486 ARG 0.000 0.000 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.02956 ( 730) hydrogen bonds : angle 5.00094 ( 1920) covalent geometry : bond 0.00444 (26608) covalent geometry : angle 0.56349 (35934) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6690 Ramachandran restraints generated. 3345 Oldfield, 0 Emsley, 3345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 3.272 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 615 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 MET cc_start: 0.6476 (tmm) cc_final: 0.5803 (tpp) REVERT: B 305 ASN cc_start: 0.9107 (t0) cc_final: 0.8651 (t0) REVERT: B 702 ASP cc_start: 0.7900 (m-30) cc_final: 0.7444 (p0) REVERT: C 332 ASP cc_start: 0.8244 (m-30) cc_final: 0.7886 (t0) REVERT: D 477 LEU cc_start: 0.9196 (tp) cc_final: 0.8970 (tp) REVERT: D 659 MET cc_start: 0.8052 (tpp) cc_final: 0.7299 (mmm) REVERT: E 427 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8618 (pm20) REVERT: F 332 ASP cc_start: 0.8388 (t70) cc_final: 0.8058 (t70) REVERT: G 339 SER cc_start: 0.8768 (t) cc_final: 0.8490 (p) REVERT: G 375 ASN cc_start: 0.8155 (t0) cc_final: 0.7542 (m-40) REVERT: G 418 LEU cc_start: 0.8483 (mp) cc_final: 0.8245 (mt) REVERT: G 659 MET cc_start: 0.8643 (tpt) cc_final: 0.8280 (tpp) outliers start: 44 outliers final: 40 residues processed: 176 average time/residue: 0.3362 time to fit residues: 101.6805 Evaluate side-chains 175 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 615 PRO Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 630 SER Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 650 SER Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 737 ILE Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 649 LEU Chi-restraints excluded: chain G residue 650 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 111 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 269 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 321 optimal weight: 8.9990 chunk 311 optimal weight: 8.9990 chunk 235 optimal weight: 30.0000 chunk 1 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 287 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 ASN ** C 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 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 = 0.3473 r_free = 0.3473 target = 0.079458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.054121 restraints weight = 83235.268| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.54 r_work: 0.2737 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26608 Z= 0.200 Angle : 0.566 11.252 35934 Z= 0.315 Chirality : 0.045 0.240 4162 Planarity : 0.003 0.039 4681 Dihedral : 4.275 18.324 3371 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.43 % Allowed : 14.47 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3345 helix: -0.11 (0.24), residues: 448 sheet: 0.73 (0.19), residues: 766 loop : -0.71 (0.13), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 374 HIS 0.001 0.000 HIS G 358 PHE 0.009 0.001 PHE C 710 TYR 0.013 0.001 TYR C 486 ARG 0.000 0.000 ARG E 527 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 730) hydrogen bonds : angle 5.01587 ( 1920) covalent geometry : bond 0.00445 (26608) covalent geometry : angle 0.56594 (35934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12108.74 seconds wall clock time: 214 minutes 0.33 seconds (12840.33 seconds total)