Starting phenix.real_space_refine on Fri Sep 19 11:27:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsh_61773/09_2025/9jsh_61773.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsh_61773/09_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_61773/09_2025/9jsh_61773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsh_61773/09_2025/9jsh_61773.map" model { file = "/net/cci-nas-00/data/ceres_data/9jsh_61773/09_2025/9jsh_61773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsh_61773/09_2025/9jsh_61773.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.087 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.65, per 1000 atoms: 0.25 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: 2.31 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.19 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: 5.34 Time building geometry restraints manager: 3.10 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 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.420 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.900 ------------------------------------------------------------------------------- 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 : 7.20 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (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 ARG 0.000 0.000 ARG G 667 TYR 0.012 0.001 TYR G 486 PHE 0.010 0.001 PHE C 710 TRP 0.008 0.001 TRP G 502 HIS 0.002 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00330 (26608) covalent geometry : angle 0.54583 (35934) hydrogen bonds : bond 0.23673 ( 730) hydrogen bonds : angle 9.35516 ( 1920) *********************** 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 : 1.095 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: 0.1785 time to fit residues: 90.3128 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 : 1.203 ------------------------------------------------------------------------------- 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 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 E 391 ASN ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 500 ASN G 391 ASN ** G 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.083706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.057555 restraints weight = 83703.773| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.68 r_work: 0.2837 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1610 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= 0.174 Angle : 0.574 8.966 35934 Z= 0.321 Chirality : 0.045 0.195 4162 Planarity : 0.004 0.043 4681 Dihedral : 4.330 43.351 3378 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.86 % Allowed : 6.72 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.14), residues: 3345 helix: -0.21 (0.25), residues: 438 sheet: 0.81 (0.20), residues: 721 loop : -0.86 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 667 TYR 0.011 0.001 TYR C 486 PHE 0.012 0.001 PHE C 710 TRP 0.005 0.001 TRP G 374 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00376 (26608) covalent geometry : angle 0.57370 (35934) hydrogen bonds : bond 0.04064 ( 730) hydrogen bonds : angle 6.08290 ( 1920) *********************** 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 206 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 649 LEU cc_start: 0.7809 (tp) cc_final: 0.7471 (tt) REVERT: B 305 ASN cc_start: 0.8596 (t0) cc_final: 0.8304 (t0) REVERT: B 594 LEU cc_start: 0.8806 (tp) cc_final: 0.8601 (tp) REVERT: C 332 ASP cc_start: 0.8148 (m-30) cc_final: 0.7639 (t0) REVERT: C 519 ASP cc_start: 0.8579 (t0) cc_final: 0.8221 (t0) REVERT: C 688 LYS cc_start: 0.8801 (tppt) cc_final: 0.8217 (tppt) REVERT: E 716 ASP cc_start: 0.8640 (t0) cc_final: 0.8164 (p0) REVERT: F 519 ASP cc_start: 0.8609 (t0) cc_final: 0.8256 (t0) REVERT: G 339 SER cc_start: 0.8548 (t) cc_final: 0.8223 (p) REVERT: G 375 ASN cc_start: 0.8630 (m-40) cc_final: 0.8353 (t0) outliers start: 26 outliers final: 18 residues processed: 198 average time/residue: 0.1710 time to fit residues: 55.9756 Evaluate side-chains 169 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 GLN 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 464 ASP Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 649 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 G residue 331 THR Chi-restraints excluded: chain G residue 589 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 322 optimal weight: 0.0040 chunk 156 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 263 optimal weight: 9.9990 chunk 180 optimal weight: 30.0000 chunk 152 optimal weight: 8.9990 overall best weight: 3.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 534 GLN B 681 ASN C 435 ASN F 362 ASN ** F 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 741 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.083139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.057002 restraints weight = 83852.065| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.66 r_work: 0.2832 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2027 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= 0.147 Angle : 0.523 8.131 35934 Z= 0.295 Chirality : 0.044 0.146 4162 Planarity : 0.003 0.037 4681 Dihedral : 4.073 40.188 3373 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.23 % Allowed : 8.82 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.14), residues: 3345 helix: -0.07 (0.25), residues: 439 sheet: 0.83 (0.20), residues: 719 loop : -0.77 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 667 TYR 0.010 0.001 TYR A 668 PHE 0.011 0.001 PHE C 710 TRP 0.005 0.001 TRP G 374 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00317 (26608) covalent geometry : angle 0.52262 (35934) hydrogen bonds : bond 0.03244 ( 730) hydrogen bonds : angle 5.39744 ( 1920) *********************** 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 206 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 ASN cc_start: 0.8867 (t0) cc_final: 0.8501 (t0) REVERT: B 594 LEU cc_start: 0.8733 (tp) cc_final: 0.8383 (tp) REVERT: C 332 ASP cc_start: 0.8112 (m-30) cc_final: 0.7754 (t0) REVERT: E 476 LYS cc_start: 0.7140 (tppt) cc_final: 0.6792 (mppt) REVERT: F 490 ASN cc_start: 0.9034 (t0) cc_final: 0.8809 (t0) REVERT: G 375 ASN cc_start: 0.8677 (m-40) cc_final: 0.8405 (t0) outliers start: 37 outliers final: 26 residues processed: 195 average time/residue: 0.1694 time to fit residues: 54.8606 Evaluate side-chains 178 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 GLN 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 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 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 G residue 331 THR Chi-restraints excluded: chain G residue 589 GLU Chi-restraints excluded: chain G residue 636 THR Chi-restraints excluded: chain G residue 649 LEU Chi-restraints excluded: chain G residue 743 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 83 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 240 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 84 optimal weight: 30.0000 chunk 286 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 430 ASN D 500 ASN D 647 ASN ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN ** E 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 643 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.080300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.054549 restraints weight = 83090.493| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.59 r_work: 0.2740 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 26608 Z= 0.227 Angle : 0.563 8.087 35934 Z= 0.317 Chirality : 0.045 0.164 4162 Planarity : 0.003 0.037 4681 Dihedral : 4.400 38.150 3373 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.46 % Allowed : 10.65 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.14), residues: 3345 helix: -0.31 (0.24), residues: 452 sheet: 0.77 (0.20), residues: 720 loop : -0.80 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 324 TYR 0.013 0.001 TYR A 668 PHE 0.010 0.001 PHE C 710 TRP 0.008 0.001 TRP G 374 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00505 (26608) covalent geometry : angle 0.56327 (35934) hydrogen bonds : bond 0.03351 ( 730) hydrogen bonds : angle 5.35481 ( 1920) *********************** 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 201 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 1.075 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: 0.9017 (t0) cc_final: 0.8561 (t0) REVERT: B 594 LEU cc_start: 0.8775 (tp) cc_final: 0.8339 (tp) REVERT: C 332 ASP cc_start: 0.8231 (m-30) cc_final: 0.7833 (t0) REVERT: C 478 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: D 378 LEU cc_start: 0.7140 (tp) cc_final: 0.6659 (tt) REVERT: D 647 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8067 (m-40) REVERT: E 476 LYS cc_start: 0.7206 (tppt) cc_final: 0.6906 (mppt) REVERT: F 332 ASP cc_start: 0.8321 (t70) cc_final: 0.8031 (t70) REVERT: F 361 ASP cc_start: 0.8633 (t0) cc_final: 0.8429 (t0) REVERT: F 490 ASN cc_start: 0.9114 (t0) cc_final: 0.8822 (t0) REVERT: F 738 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8167 (p) REVERT: G 339 SER cc_start: 0.8698 (t) cc_final: 0.8387 (p) REVERT: G 375 ASN cc_start: 0.8485 (m-40) cc_final: 0.8242 (t0) REVERT: G 492 GLN cc_start: 0.9268 (mm110) cc_final: 0.9021 (mm110) REVERT: G 659 MET cc_start: 0.8496 (tpt) cc_final: 0.8204 (tpp) outliers start: 45 outliers final: 29 residues processed: 193 average time/residue: 0.1684 time to fit residues: 54.3746 Evaluate side-chains 170 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 478 GLU 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 647 ASN 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 698 VAL Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain G residue 636 THR Chi-restraints excluded: chain G residue 649 LEU Chi-restraints excluded: chain G residue 650 SER Chi-restraints excluded: chain G residue 743 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 297 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 301 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 229 optimal weight: 8.9990 chunk 203 optimal weight: 0.0980 chunk 171 optimal weight: 5.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- 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 D 647 ASN ** E 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.3583 r_free = 0.3583 target = 0.083150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.056333 restraints weight = 85674.992| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.76 r_work: 0.2865 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2530 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= 0.159 Angle : 0.521 8.020 35934 Z= 0.294 Chirality : 0.044 0.146 4162 Planarity : 0.003 0.039 4681 Dihedral : 4.195 36.407 3373 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.50 % Allowed : 11.54 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.14), residues: 3345 helix: -0.19 (0.25), residues: 447 sheet: 0.77 (0.19), residues: 743 loop : -0.71 (0.13), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 324 TYR 0.010 0.001 TYR A 668 PHE 0.010 0.001 PHE C 710 TRP 0.006 0.001 TRP G 374 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00347 (26608) covalent geometry : angle 0.52054 (35934) hydrogen bonds : bond 0.02940 ( 730) hydrogen bonds : angle 5.18324 ( 1920) *********************** 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 197 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 1.183 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: A 649 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7598 (tt) REVERT: B 305 ASN cc_start: 0.9009 (t0) cc_final: 0.8511 (t0) REVERT: C 332 ASP cc_start: 0.8222 (m-30) cc_final: 0.7780 (t0) REVERT: C 478 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: C 659 MET cc_start: 0.7217 (tpt) cc_final: 0.7002 (tpt) REVERT: D 378 LEU cc_start: 0.7003 (tp) cc_final: 0.6523 (tt) REVERT: D 647 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8167 (m-40) REVERT: E 476 LYS cc_start: 0.7253 (tppt) cc_final: 0.6985 (mppt) REVERT: F 332 ASP cc_start: 0.8335 (t70) cc_final: 0.7994 (t70) REVERT: F 361 ASP cc_start: 0.8597 (t0) cc_final: 0.8391 (t0) REVERT: F 490 ASN cc_start: 0.9099 (t0) cc_final: 0.8837 (t0) REVERT: F 519 ASP cc_start: 0.8607 (t0) cc_final: 0.8399 (t0) REVERT: F 738 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8131 (p) REVERT: G 339 SER cc_start: 0.8711 (t) cc_final: 0.8413 (p) REVERT: G 492 GLN cc_start: 0.9295 (mm110) cc_final: 0.9053 (mm110) REVERT: G 659 MET cc_start: 0.8442 (tpt) cc_final: 0.8206 (tpp) outliers start: 46 outliers final: 31 residues processed: 189 average time/residue: 0.1555 time to fit residues: 50.3738 Evaluate side-chains 174 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 649 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 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 478 GLU 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 647 ASN 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 723 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 737 ILE Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 331 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 292 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 303 optimal weight: 9.9990 chunk 214 optimal weight: 4.9990 chunk 233 optimal weight: 30.0000 chunk 248 optimal weight: 8.9990 chunk 241 optimal weight: 0.0030 chunk 44 optimal weight: 20.0000 chunk 225 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 overall best weight: 4.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 GLN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 609 ASN ** E 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.084941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.057886 restraints weight = 85879.113| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.80 r_work: 0.2861 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2646 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= 0.155 Angle : 0.516 8.429 35934 Z= 0.291 Chirality : 0.044 0.148 4162 Planarity : 0.003 0.038 4681 Dihedral : 4.128 34.993 3373 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.26 % Allowed : 12.54 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.14), residues: 3345 helix: -0.13 (0.25), residues: 447 sheet: 0.78 (0.19), residues: 744 loop : -0.68 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 667 TYR 0.010 0.001 TYR A 668 PHE 0.010 0.001 PHE C 710 TRP 0.008 0.001 TRP G 374 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00338 (26608) covalent geometry : angle 0.51597 (35934) hydrogen bonds : bond 0.02831 ( 730) hydrogen bonds : angle 5.07909 ( 1920) *********************** 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 180 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 1.192 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: 0.9043 (t0) cc_final: 0.8572 (t0) REVERT: C 332 ASP cc_start: 0.8237 (m-30) cc_final: 0.7786 (t0) REVERT: C 478 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8089 (mt-10) REVERT: D 378 LEU cc_start: 0.6993 (tp) cc_final: 0.6523 (tt) REVERT: D 659 MET cc_start: 0.7965 (tpp) cc_final: 0.7762 (tpp) REVERT: E 476 LYS cc_start: 0.7285 (tppt) cc_final: 0.7027 (mppt) REVERT: E 697 LEU cc_start: 0.9150 (tt) cc_final: 0.8924 (pp) REVERT: F 332 ASP cc_start: 0.8352 (t70) cc_final: 0.8007 (t70) REVERT: F 361 ASP cc_start: 0.8605 (t0) cc_final: 0.8396 (t0) REVERT: F 490 ASN cc_start: 0.9116 (t0) cc_final: 0.8821 (t0) REVERT: F 519 ASP cc_start: 0.8640 (t0) cc_final: 0.8395 (t0) REVERT: F 738 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8127 (p) REVERT: G 339 SER cc_start: 0.8732 (t) cc_final: 0.8442 (p) REVERT: G 659 MET cc_start: 0.8484 (tpt) cc_final: 0.8138 (tpp) outliers start: 39 outliers final: 31 residues processed: 174 average time/residue: 0.1500 time to fit residues: 44.8467 Evaluate side-chains 171 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 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 C residue 360 THR Chi-restraints excluded: chain C residue 478 GLU 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 F residue 738 THR Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 649 LEU Chi-restraints excluded: chain G residue 650 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 292 optimal weight: 6.9990 chunk 275 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 318 optimal weight: 7.9990 chunk 296 optimal weight: 6.9990 chunk 199 optimal weight: 0.0070 chunk 226 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 169 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 176 optimal weight: 30.0000 overall best weight: 4.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 647 ASN ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 741 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 = 0.3603 r_free = 0.3603 target = 0.084650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.057559 restraints weight = 85303.127| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.81 r_work: 0.2858 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2760 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= 0.163 Angle : 0.516 7.107 35934 Z= 0.292 Chirality : 0.044 0.213 4162 Planarity : 0.003 0.038 4681 Dihedral : 4.131 33.509 3373 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.43 % Allowed : 13.01 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.14), residues: 3345 helix: -0.11 (0.25), residues: 447 sheet: 0.76 (0.19), residues: 773 loop : -0.67 (0.13), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 667 TYR 0.010 0.001 TYR A 668 PHE 0.010 0.001 PHE C 710 TRP 0.009 0.001 TRP G 374 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00357 (26608) covalent geometry : angle 0.51633 (35934) hydrogen bonds : bond 0.02815 ( 730) hydrogen bonds : angle 5.00096 ( 1920) *********************** 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 192 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 1.178 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: 0.9053 (t0) cc_final: 0.8566 (t0) REVERT: B 702 ASP cc_start: 0.7847 (m-30) cc_final: 0.7309 (p0) REVERT: C 332 ASP cc_start: 0.8240 (m-30) cc_final: 0.7783 (t0) REVERT: C 478 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8114 (mt-10) REVERT: D 378 LEU cc_start: 0.7016 (tp) cc_final: 0.6548 (tt) REVERT: D 647 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8144 (t0) REVERT: D 659 MET cc_start: 0.8020 (tpp) cc_final: 0.7244 (mmm) REVERT: E 476 LYS cc_start: 0.7363 (tppt) cc_final: 0.7160 (mppt) REVERT: F 332 ASP cc_start: 0.8367 (t70) cc_final: 0.7998 (t70) REVERT: F 361 ASP cc_start: 0.8625 (t0) cc_final: 0.8415 (t0) REVERT: F 490 ASN cc_start: 0.9119 (t0) cc_final: 0.8805 (t0) REVERT: F 738 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8104 (p) REVERT: G 330 LYS cc_start: 0.8263 (mptt) cc_final: 0.7966 (mmtp) REVERT: G 339 SER cc_start: 0.8725 (t) cc_final: 0.8441 (p) REVERT: G 659 MET cc_start: 0.8517 (tpt) cc_final: 0.8205 (tpp) outliers start: 44 outliers final: 33 residues processed: 185 average time/residue: 0.1669 time to fit residues: 52.3163 Evaluate side-chains 176 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 478 GLU 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 420 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 647 ASN 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 605 GLU Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 737 ILE Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 331 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 26 optimal weight: 20.0000 chunk 242 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 chunk 324 optimal weight: 0.6980 chunk 285 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 301 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 ASN ** 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 = 0.3613 r_free = 0.3613 target = 0.085918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.058407 restraints weight = 86541.681| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.80 r_work: 0.2883 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2838 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= 0.126 Angle : 0.515 11.330 35934 Z= 0.288 Chirality : 0.044 0.312 4162 Planarity : 0.003 0.039 4681 Dihedral : 3.899 16.280 3371 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.93 % Allowed : 13.67 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.14), residues: 3345 helix: -0.04 (0.25), residues: 447 sheet: 0.89 (0.19), residues: 764 loop : -0.61 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 324 TYR 0.011 0.001 TYR F 668 PHE 0.010 0.001 PHE C 710 TRP 0.007 0.001 TRP G 374 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00269 (26608) covalent geometry : angle 0.51512 (35934) hydrogen bonds : bond 0.02599 ( 730) hydrogen bonds : angle 4.87245 ( 1920) *********************** 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 184 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.884 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: 0.9064 (t0) cc_final: 0.8573 (t0) REVERT: B 702 ASP cc_start: 0.7872 (m-30) cc_final: 0.7326 (p0) REVERT: C 332 ASP cc_start: 0.8207 (m-30) cc_final: 0.7748 (t0) REVERT: C 478 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: D 378 LEU cc_start: 0.7112 (tp) cc_final: 0.6645 (tt) REVERT: D 659 MET cc_start: 0.7950 (tpp) cc_final: 0.7237 (mmm) REVERT: F 332 ASP cc_start: 0.8371 (t70) cc_final: 0.7994 (t70) REVERT: F 490 ASN cc_start: 0.9132 (t0) cc_final: 0.8838 (t0) REVERT: F 738 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.7528 (p) REVERT: G 330 LYS cc_start: 0.8214 (mptt) cc_final: 0.7965 (mmtp) REVERT: G 339 SER cc_start: 0.8712 (t) cc_final: 0.8421 (p) REVERT: G 659 MET cc_start: 0.8520 (tpt) cc_final: 0.8192 (tpp) outliers start: 29 outliers final: 26 residues processed: 179 average time/residue: 0.1627 time to fit residues: 48.7164 Evaluate side-chains 169 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 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 478 GLU 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 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 738 THR Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 649 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 287 optimal weight: 9.9990 chunk 176 optimal weight: 0.0670 chunk 182 optimal weight: 8.9990 chunk 329 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 273 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 292 optimal weight: 0.9980 chunk 242 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 overall best weight: 3.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 ASN ** E 391 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 = 0.3585 r_free = 0.3585 target = 0.083305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.056415 restraints weight = 86036.795| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.78 r_work: 0.2877 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26608 Z= 0.141 Angle : 0.525 11.544 35934 Z= 0.292 Chirality : 0.044 0.278 4162 Planarity : 0.003 0.038 4681 Dihedral : 3.913 16.434 3371 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.13 % Allowed : 13.81 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.15), residues: 3345 helix: -0.01 (0.25), residues: 447 sheet: 0.87 (0.19), residues: 772 loop : -0.61 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 527 TYR 0.009 0.001 TYR C 486 PHE 0.010 0.001 PHE C 710 TRP 0.007 0.001 TRP G 374 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00307 (26608) covalent geometry : angle 0.52483 (35934) hydrogen bonds : bond 0.02652 ( 730) hydrogen bonds : angle 4.81435 ( 1920) *********************** 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 181 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.180 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: 0.6539 (tmm) cc_final: 0.5942 (tpp) REVERT: B 305 ASN cc_start: 0.9059 (t0) cc_final: 0.8600 (t0) REVERT: B 702 ASP cc_start: 0.7853 (m-30) cc_final: 0.7349 (p0) REVERT: C 332 ASP cc_start: 0.8210 (m-30) cc_final: 0.7765 (t0) REVERT: C 478 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: D 378 LEU cc_start: 0.7117 (tp) cc_final: 0.6646 (tt) REVERT: D 659 MET cc_start: 0.8042 (tpp) cc_final: 0.7326 (mmm) REVERT: F 332 ASP cc_start: 0.8399 (t70) cc_final: 0.8022 (t70) REVERT: F 738 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7825 (p) REVERT: G 330 LYS cc_start: 0.8253 (mptt) cc_final: 0.7993 (mmtp) REVERT: G 339 SER cc_start: 0.8693 (t) cc_final: 0.8397 (p) REVERT: G 659 MET cc_start: 0.8536 (tpt) cc_final: 0.8209 (tpp) outliers start: 35 outliers final: 29 residues processed: 177 average time/residue: 0.1596 time to fit residues: 48.0749 Evaluate side-chains 171 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 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 478 GLU 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 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 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 738 THR Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 331 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 226 optimal weight: 20.0000 chunk 188 optimal weight: 0.0570 chunk 295 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 276 optimal weight: 30.0000 chunk 151 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 overall best weight: 5.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 647 ASN E 391 ASN ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.082570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.055870 restraints weight = 85936.712| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.75 r_work: 0.2854 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2961 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= 0.182 Angle : 0.548 11.514 35934 Z= 0.305 Chirality : 0.045 0.266 4162 Planarity : 0.003 0.039 4681 Dihedral : 4.087 16.778 3371 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.10 % Allowed : 14.17 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.14), residues: 3345 helix: -0.06 (0.25), residues: 447 sheet: 0.84 (0.19), residues: 777 loop : -0.63 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 457 TYR 0.013 0.001 TYR C 486 PHE 0.009 0.001 PHE C 710 TRP 0.008 0.001 TRP G 374 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00405 (26608) covalent geometry : angle 0.54818 (35934) hydrogen bonds : bond 0.02823 ( 730) hydrogen bonds : angle 4.90653 ( 1920) ********************** 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 178 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.341 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: 0.9094 (t0) cc_final: 0.8629 (t0) REVERT: B 702 ASP cc_start: 0.7848 (m-30) cc_final: 0.7346 (p0) REVERT: C 332 ASP cc_start: 0.8226 (m-30) cc_final: 0.7783 (t0) REVERT: C 478 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: C 519 ASP cc_start: 0.8902 (t0) cc_final: 0.8669 (t0) REVERT: D 378 LEU cc_start: 0.7337 (tp) cc_final: 0.6859 (tt) REVERT: D 647 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8051 (t0) REVERT: D 659 MET cc_start: 0.8081 (tpp) cc_final: 0.7334 (mmm) REVERT: E 427 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8606 (pm20) REVERT: F 332 ASP cc_start: 0.8410 (t70) cc_final: 0.8034 (t70) REVERT: F 738 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7923 (p) REVERT: G 330 LYS cc_start: 0.8294 (mptt) cc_final: 0.8003 (mmtp) REVERT: G 339 SER cc_start: 0.8713 (t) cc_final: 0.8430 (p) REVERT: G 659 MET cc_start: 0.8543 (tpt) cc_final: 0.8217 (tpp) outliers start: 34 outliers final: 30 residues processed: 174 average time/residue: 0.1580 time to fit residues: 46.7224 Evaluate side-chains 175 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 C residue 478 GLU 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 411 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 647 ASN 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 427 GLN 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 738 THR Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 331 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 313 optimal weight: 7.9990 chunk 222 optimal weight: 5.9990 chunk 99 optimal weight: 0.0070 chunk 279 optimal weight: 0.0970 chunk 149 optimal weight: 0.6980 chunk 255 optimal weight: 6.9990 chunk 294 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 167 optimal weight: 0.2980 chunk 172 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 overall best weight: 1.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN A 692 GLN ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.084225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.057486 restraints weight = 85404.165| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.78 r_work: 0.2859 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26608 Z= 0.116 Angle : 0.530 11.165 35934 Z= 0.294 Chirality : 0.044 0.254 4162 Planarity : 0.003 0.041 4681 Dihedral : 3.883 21.184 3371 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.06 % Allowed : 14.07 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.15), residues: 3345 helix: 0.02 (0.25), residues: 447 sheet: 0.91 (0.19), residues: 783 loop : -0.55 (0.14), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 667 TYR 0.011 0.001 TYR F 668 PHE 0.011 0.001 PHE C 710 TRP 0.006 0.001 TRP E 631 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00241 (26608) covalent geometry : angle 0.52976 (35934) hydrogen bonds : bond 0.02509 ( 730) hydrogen bonds : angle 4.82551 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5732.96 seconds wall clock time: 99 minutes 26.73 seconds (5966.73 seconds total)