Starting phenix.real_space_refine on Sat Mar 7 11:44:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uzd_20957/03_2026/6uzd_20957.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uzd_20957/03_2026/6uzd_20957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uzd_20957/03_2026/6uzd_20957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uzd_20957/03_2026/6uzd_20957.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uzd_20957/03_2026/6uzd_20957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uzd_20957/03_2026/6uzd_20957.map" } resolution = 3.4 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= 0.000 sd= 0.007 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 14 9.91 5 S 54 5.16 5 C 26902 2.51 5 N 7305 2.21 5 O 8547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42822 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "B" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "C" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "D" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "E" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "F" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "G" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "H" Number of atoms: 5871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5871 Classifications: {'peptide': 720} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 699} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 5871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5871 Classifications: {'peptide': 720} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 699} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.35, per 1000 atoms: 0.22 Number of scatterers: 42822 At special positions: 0 Unit cell: (174.41, 175.48, 298.53, 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 14 19.99 S 54 16.00 O 8547 8.00 N 7305 7.00 C 26902 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: 3.22 Conformation dependent library (CDL) restraints added in 1.5 seconds 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10200 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 80 sheets defined 25.2% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 removed outlier: 3.791A pdb=" N GLU A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 241 removed outlier: 3.566A pdb=" N VAL A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.724A pdb=" N ARG A 252 " --> pdb=" O PRO A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.870A pdb=" N LEU A 401 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.720A pdb=" N LYS A 518 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 removed outlier: 3.626A pdb=" N ALA A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 555 through 569 removed outlier: 3.522A pdb=" N ASN A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 568 " --> pdb=" O ASN A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 577 removed outlier: 3.518A pdb=" N THR A 576 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 615 Processing helix chain 'A' and resid 635 through 637 No H-bonds generated for 'chain 'A' and resid 635 through 637' Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.867A pdb=" N GLU B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 213 removed outlier: 4.506A pdb=" N LYS B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.715A pdb=" N ARG B 252 " --> pdb=" O PRO B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 401 removed outlier: 3.647A pdb=" N LEU B 401 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.528A pdb=" N LYS B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 486 removed outlier: 3.592A pdb=" N GLU B 486 " --> pdb=" O PRO B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.865A pdb=" N LYS B 518 " --> pdb=" O GLU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 532 removed outlier: 3.711A pdb=" N GLY B 532 " --> pdb=" O LYS B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 568 removed outlier: 3.722A pdb=" N ASN B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 563 " --> pdb=" O SER B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 613 through 617 removed outlier: 3.709A pdb=" N ARG B 617 " --> pdb=" O GLU B 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 191 removed outlier: 3.579A pdb=" N GLU C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.757A pdb=" N GLU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.793A pdb=" N ARG C 252 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 removed outlier: 3.582A pdb=" N LEU C 401 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 446 removed outlier: 3.646A pdb=" N LYS C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 487 removed outlier: 3.531A pdb=" N GLU C 486 " --> pdb=" O PRO C 482 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.530A pdb=" N THR C 517 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS C 518 " --> pdb=" O GLU C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 514 through 518' Processing helix chain 'C' and resid 522 through 531 removed outlier: 3.565A pdb=" N ALA C 526 " --> pdb=" O THR C 522 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 570 removed outlier: 3.707A pdb=" N ASN C 561 " --> pdb=" O GLN C 557 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 567 " --> pdb=" O LYS C 563 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C 568 " --> pdb=" O ASN C 564 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 569 " --> pdb=" O GLN C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 577 Processing helix chain 'C' and resid 634 through 638 removed outlier: 3.925A pdb=" N ILE C 638 " --> pdb=" O ASP C 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 634 through 638' Processing helix chain 'C' and resid 679 through 683 removed outlier: 3.761A pdb=" N ASN C 682 " --> pdb=" O LYS C 679 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP C 683 " --> pdb=" O LYS C 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 679 through 683' Processing helix chain 'C' and resid 731 through 735 Processing helix chain 'D' and resid 184 through 191 removed outlier: 3.856A pdb=" N GLU D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 212 removed outlier: 3.867A pdb=" N GLU D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 241 removed outlier: 3.707A pdb=" N VAL D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 252 removed outlier: 3.557A pdb=" N ARG D 252 " --> pdb=" O PRO D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 446 removed outlier: 3.501A pdb=" N THR D 445 " --> pdb=" O GLU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 486 Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.525A pdb=" N THR D 517 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS D 518 " --> pdb=" O GLU D 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 514 through 518' Processing helix chain 'D' and resid 522 through 531 removed outlier: 3.643A pdb=" N ALA D 526 " --> pdb=" O THR D 522 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 548 No H-bonds generated for 'chain 'D' and resid 546 through 548' Processing helix chain 'D' and resid 555 through 568 Processing helix chain 'D' and resid 609 through 615 removed outlier: 4.048A pdb=" N LYS D 613 " --> pdb=" O GLU D 609 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 614 " --> pdb=" O SER D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 637 removed outlier: 3.739A pdb=" N LYS D 637 " --> pdb=" O LYS D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 734 removed outlier: 3.916A pdb=" N ILE D 734 " --> pdb=" O GLY D 731 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 191 removed outlier: 3.649A pdb=" N VAL E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU E 190 " --> pdb=" O SER E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 214 removed outlier: 3.826A pdb=" N LYS E 213 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS E 214 " --> pdb=" O ILE E 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 209 through 214' Processing helix chain 'E' and resid 234 through 241 removed outlier: 3.952A pdb=" N VAL E 239 " --> pdb=" O ASP E 235 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR E 240 " --> pdb=" O PHE E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 252 Processing helix chain 'E' and resid 397 through 401 removed outlier: 3.517A pdb=" N LEU E 401 " --> pdb=" O GLU E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 446 removed outlier: 3.693A pdb=" N GLU E 441 " --> pdb=" O ASN E 437 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS E 444 " --> pdb=" O LEU E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 486 Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.792A pdb=" N LYS E 518 " --> pdb=" O GLU E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 531 removed outlier: 3.537A pdb=" N ALA E 530 " --> pdb=" O ALA E 526 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 548 No H-bonds generated for 'chain 'E' and resid 546 through 548' Processing helix chain 'E' and resid 557 through 569 removed outlier: 3.518A pdb=" N ASN E 561 " --> pdb=" O GLN E 557 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN E 564 " --> pdb=" O GLN E 560 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 567 " --> pdb=" O LYS E 563 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU E 568 " --> pdb=" O ASN E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 577 removed outlier: 3.606A pdb=" N THR E 576 " --> pdb=" O ASN E 573 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL E 577 " --> pdb=" O ILE E 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 573 through 577' Processing helix chain 'E' and resid 613 through 617 removed outlier: 3.738A pdb=" N HIS E 616 " --> pdb=" O LYS E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 637 removed outlier: 4.088A pdb=" N LYS E 637 " --> pdb=" O LYS E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 664 removed outlier: 3.694A pdb=" N LEU E 663 " --> pdb=" O TYR E 660 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN E 664 " --> pdb=" O ASP E 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 660 through 664' Processing helix chain 'E' and resid 732 through 734 No H-bonds generated for 'chain 'E' and resid 732 through 734' Processing helix chain 'F' and resid 184 through 191 removed outlier: 3.733A pdb=" N VAL F 189 " --> pdb=" O ASP F 185 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU F 190 " --> pdb=" O SER F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 241 removed outlier: 3.620A pdb=" N VAL F 239 " --> pdb=" O ASP F 235 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR F 240 " --> pdb=" O PHE F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 252 Processing helix chain 'F' and resid 435 through 445 Processing helix chain 'F' and resid 480 through 485 removed outlier: 3.503A pdb=" N GLN F 485 " --> pdb=" O LEU F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 518 Processing helix chain 'F' and resid 522 through 531 removed outlier: 3.574A pdb=" N LEU F 527 " --> pdb=" O LEU F 523 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA F 530 " --> pdb=" O ALA F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 548 No H-bonds generated for 'chain 'F' and resid 546 through 548' Processing helix chain 'F' and resid 555 through 568 removed outlier: 3.604A pdb=" N GLN F 560 " --> pdb=" O GLN F 556 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN F 561 " --> pdb=" O GLN F 557 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA F 567 " --> pdb=" O LYS F 563 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU F 568 " --> pdb=" O ASN F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 581 removed outlier: 3.821A pdb=" N THR F 576 " --> pdb=" O ASN F 573 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU F 578 " --> pdb=" O TYR F 575 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ASP F 579 " --> pdb=" O THR F 576 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE F 581 " --> pdb=" O LEU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 616 removed outlier: 3.658A pdb=" N GLU F 614 " --> pdb=" O VAL F 611 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA F 615 " --> pdb=" O VAL F 612 " (cutoff:3.500A) Processing helix chain 'F' and resid 635 through 639 removed outlier: 3.598A pdb=" N ILE F 638 " --> pdb=" O ILE F 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 702 through 706 Processing helix chain 'G' and resid 184 through 189 removed outlier: 3.520A pdb=" N VAL G 189 " --> pdb=" O ASP G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 212 removed outlier: 4.006A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 241 removed outlier: 3.999A pdb=" N VAL G 239 " --> pdb=" O ASP G 235 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR G 240 " --> pdb=" O PHE G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 252 removed outlier: 3.733A pdb=" N ARG G 252 " --> pdb=" O PRO G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 401 removed outlier: 3.721A pdb=" N LEU G 401 " --> pdb=" O GLU G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 446 removed outlier: 3.677A pdb=" N LEU G 442 " --> pdb=" O GLN G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 480 through 487 removed outlier: 4.345A pdb=" N GLU G 486 " --> pdb=" O PRO G 482 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR G 487 " --> pdb=" O GLN G 483 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.563A pdb=" N THR G 517 " --> pdb=" O LEU G 514 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS G 518 " --> pdb=" O GLU G 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 514 through 518' Processing helix chain 'G' and resid 522 through 531 removed outlier: 3.531A pdb=" N LEU G 527 " --> pdb=" O LEU G 523 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA G 530 " --> pdb=" O ALA G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 548 No H-bonds generated for 'chain 'G' and resid 546 through 548' Processing helix chain 'G' and resid 555 through 569 removed outlier: 3.504A pdb=" N ASN G 561 " --> pdb=" O GLN G 557 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN G 564 " --> pdb=" O GLN G 560 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU G 568 " --> pdb=" O ASN G 564 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 577 removed outlier: 3.752A pdb=" N THR G 576 " --> pdb=" O ASN G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 610 through 614 Processing helix chain 'G' and resid 634 through 638 removed outlier: 3.837A pdb=" N LYS G 637 " --> pdb=" O ASP G 634 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 27 removed outlier: 3.604A pdb=" N LYS H 27 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 54 removed outlier: 3.882A pdb=" N LYS H 45 " --> pdb=" O GLU H 41 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP H 51 " --> pdb=" O GLN H 47 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU H 52 " --> pdb=" O GLN H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 67 removed outlier: 3.808A pdb=" N LEU H 61 " --> pdb=" O PRO H 57 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU H 62 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE H 63 " --> pdb=" O ASP H 59 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER H 65 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU H 67 " --> pdb=" O ILE H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 removed outlier: 3.857A pdb=" N GLN H 85 " --> pdb=" O LYS H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 107 removed outlier: 3.513A pdb=" N ARG H 107 " --> pdb=" O PHE H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 144 removed outlier: 3.864A pdb=" N TYR H 137 " --> pdb=" O SER H 133 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 149 removed outlier: 3.631A pdb=" N ILE H 148 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 167 removed outlier: 4.166A pdb=" N LEU H 162 " --> pdb=" O GLU H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 183 Processing helix chain 'H' and resid 193 through 198 removed outlier: 3.684A pdb=" N ILE H 197 " --> pdb=" O ASP H 193 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS H 198 " --> pdb=" O ILE H 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 193 through 198' Processing helix chain 'H' and resid 200 through 217 removed outlier: 3.515A pdb=" N PHE H 204 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE H 208 " --> pdb=" O PHE H 204 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA H 211 " --> pdb=" O ALA H 207 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR H 215 " --> pdb=" O ALA H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 228 removed outlier: 3.519A pdb=" N LEU H 226 " --> pdb=" O THR H 222 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 240 Processing helix chain 'H' and resid 241 through 252 removed outlier: 3.597A pdb=" N LYS H 251 " --> pdb=" O SER H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 272 removed outlier: 3.744A pdb=" N LEU H 269 " --> pdb=" O GLY H 265 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS H 270 " --> pdb=" O GLU H 266 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA H 271 " --> pdb=" O LYS H 267 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER H 272 " --> pdb=" O ALA H 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 265 through 272' Processing helix chain 'H' and resid 275 through 290 removed outlier: 3.772A pdb=" N ALA H 279 " --> pdb=" O VAL H 275 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP H 280 " --> pdb=" O PRO H 276 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS H 284 " --> pdb=" O ASP H 280 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE H 285 " --> pdb=" O ALA H 281 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA H 286 " --> pdb=" O PHE H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 307 removed outlier: 4.335A pdb=" N LEU H 305 " --> pdb=" O LEU H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 338 removed outlier: 3.710A pdb=" N LEU H 337 " --> pdb=" O ASP H 334 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER H 338 " --> pdb=" O GLN H 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 334 through 338' Processing helix chain 'H' and resid 345 through 350 Processing helix chain 'H' and resid 350 through 355 removed outlier: 3.628A pdb=" N LYS H 355 " --> pdb=" O ASN H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 373 through 377 removed outlier: 3.774A pdb=" N ARG H 376 " --> pdb=" O ASP H 373 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE H 377 " --> pdb=" O HIS H 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 373 through 377' Processing helix chain 'H' and resid 469 through 475 removed outlier: 3.892A pdb=" N LYS H 473 " --> pdb=" O THR H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 479 through 484 removed outlier: 3.552A pdb=" N VAL H 484 " --> pdb=" O TRP H 480 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 493 Processing helix chain 'H' and resid 497 through 502 removed outlier: 3.544A pdb=" N LYS H 502 " --> pdb=" O ASN H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 520 through 528 removed outlier: 4.085A pdb=" N ASP H 525 " --> pdb=" O LYS H 521 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG H 526 " --> pdb=" O GLN H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 574 through 583 Processing helix chain 'H' and resid 626 through 639 removed outlier: 4.169A pdb=" N ILE H 637 " --> pdb=" O ASN H 633 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG H 638 " --> pdb=" O LEU H 634 " (cutoff:3.500A) Processing helix chain 'H' and resid 651 through 669 removed outlier: 3.683A pdb=" N PHE H 655 " --> pdb=" O ASP H 651 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS H 663 " --> pdb=" O GLU H 659 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE H 664 " --> pdb=" O SER H 660 " (cutoff:3.500A) Processing helix chain 'H' and resid 680 through 704 removed outlier: 3.767A pdb=" N ILE H 687 " --> pdb=" O LYS H 683 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE H 689 " --> pdb=" O ARG H 685 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLY H 692 " --> pdb=" O SER H 688 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU H 698 " --> pdb=" O GLN H 694 " (cutoff:3.500A) Processing helix chain 'H' and resid 712 through 734 removed outlier: 3.833A pdb=" N ARG H 722 " --> pdb=" O TYR H 718 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL H 727 " --> pdb=" O ILE H 723 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN H 728 " --> pdb=" O THR H 724 " (cutoff:3.500A) Processing helix chain 'H' and resid 739 through 747 Processing helix chain 'H' and resid 757 through 765 Processing helix chain 'I' and resid 21 through 28 removed outlier: 3.538A pdb=" N LYS I 27 " --> pdb=" O LYS I 23 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP I 28 " --> pdb=" O GLU I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 41 through 54 removed outlier: 3.863A pdb=" N LYS I 45 " --> pdb=" O GLU I 41 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE I 46 " --> pdb=" O THR I 42 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP I 51 " --> pdb=" O GLN I 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU I 52 " --> pdb=" O GLN I 48 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU I 53 " --> pdb=" O THR I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 67 removed outlier: 3.520A pdb=" N LEU I 61 " --> pdb=" O PRO I 57 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU I 67 " --> pdb=" O ILE I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 93 Processing helix chain 'I' and resid 129 through 144 removed outlier: 3.792A pdb=" N GLU I 135 " --> pdb=" O GLU I 131 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL I 136 " --> pdb=" O GLN I 132 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR I 137 " --> pdb=" O SER I 133 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY I 143 " --> pdb=" O GLU I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 149 removed outlier: 3.560A pdb=" N ILE I 148 " --> pdb=" O ILE I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 168 removed outlier: 3.508A pdb=" N LEU I 162 " --> pdb=" O GLU I 158 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP I 168 " --> pdb=" O LYS I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 177 removed outlier: 4.068A pdb=" N LEU I 175 " --> pdb=" O ASP I 171 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 184 Processing helix chain 'I' and resid 193 through 200 Processing helix chain 'I' and resid 202 through 217 removed outlier: 3.972A pdb=" N PHE I 208 " --> pdb=" O PHE I 204 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA I 211 " --> pdb=" O ALA I 207 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE I 216 " --> pdb=" O PHE I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 226 Processing helix chain 'I' and resid 228 through 240 removed outlier: 3.695A pdb=" N GLU I 233 " --> pdb=" O PRO I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 252 removed outlier: 3.686A pdb=" N LYS I 245 " --> pdb=" O GLY I 241 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE I 246 " --> pdb=" O GLY I 242 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER I 249 " --> pdb=" O LYS I 245 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU I 250 " --> pdb=" O ILE I 246 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS I 251 " --> pdb=" O SER I 247 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS I 252 " --> pdb=" O GLU I 248 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 266 No H-bonds generated for 'chain 'I' and resid 264 through 266' Processing helix chain 'I' and resid 267 through 272 removed outlier: 3.985A pdb=" N ALA I 271 " --> pdb=" O LYS I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 275 through 290 removed outlier: 3.854A pdb=" N ALA I 281 " --> pdb=" O GLU I 277 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE I 282 " --> pdb=" O HIS I 278 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS I 283 " --> pdb=" O ALA I 279 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS I 284 " --> pdb=" O ASP I 280 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE I 285 " --> pdb=" O ALA I 281 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG I 287 " --> pdb=" O LYS I 283 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU I 288 " --> pdb=" O LYS I 284 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 305 Processing helix chain 'I' and resid 334 through 338 Processing helix chain 'I' and resid 348 through 357 removed outlier: 4.023A pdb=" N SER I 357 " --> pdb=" O GLU I 353 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 474 removed outlier: 3.665A pdb=" N LYS I 472 " --> pdb=" O THR I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 498 removed outlier: 3.517A pdb=" N GLN I 493 " --> pdb=" O SER I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 500 through 504 Processing helix chain 'I' and resid 517 through 530 removed outlier: 3.738A pdb=" N LEU I 527 " --> pdb=" O MET I 523 " (cutoff:3.500A) Processing helix chain 'I' and resid 574 through 585 Processing helix chain 'I' and resid 626 through 636 removed outlier: 3.893A pdb=" N ILE I 631 " --> pdb=" O SER I 627 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS I 632 " --> pdb=" O ALA I 628 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU I 634 " --> pdb=" O PHE I 630 " (cutoff:3.500A) Processing helix chain 'I' and resid 651 through 665 removed outlier: 3.708A pdb=" N LYS I 658 " --> pdb=" O GLU I 654 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER I 660 " --> pdb=" O ALA I 656 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL I 661 " --> pdb=" O LYS I 657 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS I 662 " --> pdb=" O LYS I 658 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS I 663 " --> pdb=" O GLU I 659 " (cutoff:3.500A) Processing helix chain 'I' and resid 673 through 679 removed outlier: 3.908A pdb=" N ASN I 676 " --> pdb=" O ASN I 673 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS I 677 " --> pdb=" O SER I 674 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE I 678 " --> pdb=" O ALA I 675 " (cutoff:3.500A) Processing helix chain 'I' and resid 680 through 703 removed outlier: 3.636A pdb=" N SER I 688 " --> pdb=" O LYS I 684 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE I 689 " --> pdb=" O ARG I 685 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG I 691 " --> pdb=" O ILE I 687 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU I 698 " --> pdb=" O GLN I 694 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE I 699 " --> pdb=" O ALA I 695 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU I 703 " --> pdb=" O ILE I 699 " (cutoff:3.500A) Processing helix chain 'I' and resid 709 through 732 removed outlier: 4.048A pdb=" N TYR I 715 " --> pdb=" O GLU I 711 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG I 722 " --> pdb=" O TYR I 718 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN I 725 " --> pdb=" O GLU I 721 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN I 728 " --> pdb=" O THR I 724 " (cutoff:3.500A) Processing helix chain 'I' and resid 739 through 746 Processing helix chain 'I' and resid 754 through 765 removed outlier: 3.794A pdb=" N PHE I 760 " --> pdb=" O ASN I 756 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE I 763 " --> pdb=" O VAL I 759 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE I 764 " --> pdb=" O PHE I 760 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 196 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 273 removed outlier: 6.718A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE A 269 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN A 361 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU A 271 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG A 359 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 409 through 411 removed outlier: 3.703A pdb=" N ASN A 409 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 321 through 325 removed outlier: 3.677A pdb=" N ALA C 307 " --> pdb=" O ALA B 322 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP C 276 " --> pdb=" O GLY C 351 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 278 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN C 280 " --> pdb=" O ALA C 347 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR C 282 " --> pdb=" O THR C 345 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 333 " --> pdb=" O SER C 294 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 320 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D 309 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 322 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA D 307 " --> pdb=" O ALA C 322 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN C 326 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR D 300 " --> pdb=" O SER D 327 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER D 296 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER D 294 " --> pdb=" O ALA D 333 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN D 292 " --> pdb=" O ASP D 335 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 337 " --> pdb=" O SER D 290 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER D 290 " --> pdb=" O SER D 337 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS C 336 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE C 334 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET C 350 " --> pdb=" O THR D 279 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 317 through 324 removed outlier: 4.770A pdb=" N GLY E 317 " --> pdb=" O HIS E 310 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N HIS E 310 " --> pdb=" O GLY E 317 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER E 319 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE E 289 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN E 285 " --> pdb=" O ARG D 344 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU D 348 " --> pdb=" O ASN E 281 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET D 350 " --> pdb=" O THR E 279 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR E 279 " --> pdb=" O MET D 350 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN E 280 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA E 341 " --> pdb=" O THR E 286 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER E 290 " --> pdb=" O SER E 337 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN E 292 " --> pdb=" O ASP E 335 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER E 294 " --> pdb=" O ALA E 333 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR E 298 " --> pdb=" O SER E 329 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN E 328 " --> pdb=" O SER F 301 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER F 301 " --> pdb=" O ASN E 328 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL E 332 " --> pdb=" O ARG F 297 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE F 289 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY E 318 " --> pdb=" O ALA F 311 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 276 through 311 removed outlier: 4.093A pdb=" N ASP F 276 " --> pdb=" O GLY F 351 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER F 284 " --> pdb=" O GLU F 343 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA F 341 " --> pdb=" O THR F 286 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR F 288 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER F 337 " --> pdb=" O SER F 290 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR F 331 " --> pdb=" O SER F 296 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLY F 318 " --> pdb=" O ALA G 311 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA G 311 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL F 320 " --> pdb=" O VAL G 309 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL G 309 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP F 346 " --> pdb=" O ASP G 283 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP G 276 " --> pdb=" O GLY G 351 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN G 280 " --> pdb=" O ALA G 347 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER G 327 " --> pdb=" O THR G 300 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER G 321 " --> pdb=" O ASN G 306 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU G 308 " --> pdb=" O SER G 319 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER G 319 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY G 318 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL G 320 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL A 309 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA G 322 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 307 " --> pdb=" O ALA G 322 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS A 299 " --> pdb=" O SER G 330 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU G 340 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY G 342 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP A 276 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 290 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY A 317 " --> pdb=" O HIS A 310 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN A 326 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR B 295 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 340 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 278 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 282 " --> pdb=" O THR B 345 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER B 329 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 332 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 342 " --> pdb=" O ARG C 287 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 350 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 395 removed outlier: 6.922A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LYS A 395 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR A 375 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE A 404 " --> pdb=" O TYR A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 395 removed outlier: 6.922A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LYS A 395 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL A 377 " --> pdb=" O TYR A 456 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TYR A 456 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLN A 454 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A 381 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR A 452 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 383 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU A 450 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU A 385 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A 448 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 10.871A pdb=" N VAL A 455 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N ASN A 476 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N GLY A 457 " --> pdb=" O GLY A 474 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N GLY A 474 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE A 459 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 461 " --> pdb=" O ARG A 470 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.857A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASP A 593 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 551 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 596 through 598 removed outlier: 6.632A pdb=" N HIS A 597 " --> pdb=" O VAL A 605 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 626 through 629 removed outlier: 3.885A pdb=" N LEU A 629 " --> pdb=" O THR A 674 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 4.075A pdb=" N GLU A 654 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 646 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 701 " --> pdb=" O SER A 640 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR A 642 " --> pdb=" O TYR A 699 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR A 699 " --> pdb=" O TYR A 642 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL A 644 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASN A 697 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE A 646 " --> pdb=" O LYS A 695 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LYS A 695 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 698 " --> pdb=" O PHE A 727 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 192 through 196 Processing sheet with id=AB5, first strand: chain 'B' and resid 262 through 269 removed outlier: 3.511A pdb=" N ASP B 265 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN B 409 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 262 through 269 removed outlier: 3.511A pdb=" N ASP B 265 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 358 through 360 removed outlier: 3.614A pdb=" N MET B 434 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 432 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.894A pdb=" N LEU B 383 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N THR B 393 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR B 381 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LYS B 395 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR B 375 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 404 " --> pdb=" O TYR B 375 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 402 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.894A pdb=" N LEU B 383 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N THR B 393 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR B 381 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LYS B 395 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 377 " --> pdb=" O TYR B 456 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR B 456 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN B 454 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR B 381 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR B 452 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU B 383 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU B 450 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU B 385 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 448 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N VAL B 455 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N ASN B 476 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N GLY B 457 " --> pdb=" O GLY B 474 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N GLY B 474 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE B 459 " --> pdb=" O ASP B 472 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 501 through 506 removed outlier: 8.811A pdb=" N ILE B 589 " --> pdb=" O THR B 488 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG B 490 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE B 591 " --> pdb=" O ARG B 490 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE B 492 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ASP B 593 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 596 through 598 removed outlier: 3.985A pdb=" N GLY B 606 " --> pdb=" O HIS B 597 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 619 through 622 removed outlier: 3.654A pdb=" N THR B 674 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 667 " --> pdb=" O PHE B 675 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 653 through 655 removed outlier: 3.523A pdb=" N LYS B 695 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 696 " --> pdb=" O LYS B 729 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS B 729 " --> pdb=" O VAL B 696 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 192 through 196 Processing sheet with id=AC6, first strand: chain 'C' and resid 262 through 269 removed outlier: 6.770A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN C 409 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 262 through 269 removed outlier: 6.770A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 358 through 359 removed outlier: 3.690A pdb=" N MET C 434 " --> pdb=" O ALA C 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 389 through 395 removed outlier: 5.197A pdb=" N THR C 390 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C 385 " --> pdb=" O THR C 390 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA C 392 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 375 " --> pdb=" O ASN C 458 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL C 377 " --> pdb=" O TYR C 456 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR C 456 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLN C 454 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR C 381 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR C 452 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU C 383 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU C 450 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU C 385 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU C 448 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 10.898A pdb=" N VAL C 455 " --> pdb=" O ASN C 476 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N ASN C 476 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N GLY C 457 " --> pdb=" O GLY C 474 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N GLY C 474 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE C 459 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 501 through 506 removed outlier: 7.650A pdb=" N THR C 488 " --> pdb=" O MET C 587 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AD3, first strand: chain 'C' and resid 597 through 598 removed outlier: 7.100A pdb=" N HIS C 597 " --> pdb=" O VAL C 605 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 619 through 622 removed outlier: 5.966A pdb=" N LEU C 628 " --> pdb=" O ILE C 620 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.540A pdb=" N GLU C 654 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL C 701 " --> pdb=" O SER C 640 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR C 642 " --> pdb=" O TYR C 699 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR C 699 " --> pdb=" O TYR C 642 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL C 644 " --> pdb=" O ASN C 697 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASN C 697 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE C 646 " --> pdb=" O LYS C 695 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS C 695 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 698 " --> pdb=" O PHE C 727 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE C 727 " --> pdb=" O VAL C 698 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 192 through 196 Processing sheet with id=AD7, first strand: chain 'D' and resid 262 through 269 removed outlier: 6.660A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 262 through 269 removed outlier: 6.660A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 272 through 273 Processing sheet with id=AE1, first strand: chain 'D' and resid 389 through 395 removed outlier: 6.938A pdb=" N LEU D 383 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR D 393 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR D 381 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LYS D 395 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TYR D 375 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 404 " --> pdb=" O TYR D 375 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 389 through 395 removed outlier: 6.938A pdb=" N LEU D 383 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR D 393 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR D 381 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LYS D 395 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR D 375 " --> pdb=" O ASN D 458 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL D 377 " --> pdb=" O TYR D 456 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR D 456 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN D 454 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR D 381 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR D 452 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU D 383 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU D 450 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU D 385 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU D 448 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N VAL D 455 " --> pdb=" O ASN D 476 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N ASN D 476 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 10.248A pdb=" N GLY D 457 " --> pdb=" O GLY D 474 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N GLY D 474 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE D 459 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG D 468 " --> pdb=" O ASN D 463 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 501 through 506 removed outlier: 9.027A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP D 551 " --> pdb=" O ARG D 592 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 596 through 598 removed outlier: 4.480A pdb=" N GLY D 606 " --> pdb=" O HIS D 597 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 626 through 627 Processing sheet with id=AE6, first strand: chain 'D' and resid 654 through 655 removed outlier: 3.585A pdb=" N GLU D 645 " --> pdb=" O ASN D 697 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 192 through 196 Processing sheet with id=AE8, first strand: chain 'E' and resid 262 through 269 removed outlier: 6.613A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN E 409 " --> pdb=" O ASN E 368 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 262 through 269 removed outlier: 6.613A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 272 through 273 removed outlier: 4.719A pdb=" N ILE E 432 " --> pdb=" O LEU E 360 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 389 through 395 removed outlier: 6.893A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LYS E 395 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR E 375 " --> pdb=" O ILE E 404 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE E 404 " --> pdb=" O TYR E 375 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 389 through 395 removed outlier: 6.893A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LYS E 395 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR E 375 " --> pdb=" O ASN E 458 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL E 377 " --> pdb=" O TYR E 456 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR E 456 " --> pdb=" O VAL E 377 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN E 454 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR E 381 " --> pdb=" O THR E 452 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR E 452 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU E 383 " --> pdb=" O LEU E 450 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU E 450 " --> pdb=" O LEU E 383 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU E 385 " --> pdb=" O LEU E 448 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU E 448 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL E 455 " --> pdb=" O ASN E 476 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ASN E 476 " --> pdb=" O VAL E 455 " (cutoff:3.500A) removed outlier: 10.501A pdb=" N GLY E 457 " --> pdb=" O GLY E 474 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N GLY E 474 " --> pdb=" O GLY E 457 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE E 459 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 501 through 506 removed outlier: 8.706A pdb=" N ILE E 589 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG E 490 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE E 591 " --> pdb=" O ARG E 490 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE E 492 " --> pdb=" O ILE E 591 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ASP E 593 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 596 through 598 Processing sheet with id=AF6, first strand: chain 'E' and resid 619 through 622 removed outlier: 3.671A pdb=" N LEU E 627 " --> pdb=" O ILE E 676 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE E 675 " --> pdb=" O SER E 667 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 639 through 647 removed outlier: 4.389A pdb=" N GLY E 641 " --> pdb=" O VAL E 701 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 701 " --> pdb=" O GLY E 641 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS E 729 " --> pdb=" O VAL E 696 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 192 through 196 Processing sheet with id=AF9, first strand: chain 'F' and resid 262 through 269 removed outlier: 3.580A pdb=" N ARG F 365 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 262 through 269 removed outlier: 3.580A pdb=" N ARG F 365 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 362 " --> pdb=" O LEU F 421 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 272 through 273 Processing sheet with id=AG3, first strand: chain 'F' and resid 389 through 394 removed outlier: 4.978A pdb=" N THR F 390 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU F 385 " --> pdb=" O THR F 390 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA F 392 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TYR F 375 " --> pdb=" O ILE F 404 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE F 404 " --> pdb=" O TYR F 375 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 389 through 394 removed outlier: 4.978A pdb=" N THR F 390 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU F 385 " --> pdb=" O THR F 390 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA F 392 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL F 377 " --> pdb=" O TYR F 456 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR F 456 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN F 454 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR F 381 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR F 452 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU F 383 " --> pdb=" O LEU F 450 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU F 450 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU F 385 " --> pdb=" O LEU F 448 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU F 448 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 10.883A pdb=" N VAL F 455 " --> pdb=" O ASN F 476 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ASN F 476 " --> pdb=" O VAL F 455 " (cutoff:3.500A) removed outlier: 10.112A pdb=" N GLY F 457 " --> pdb=" O GLY F 474 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLY F 474 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE F 459 " --> pdb=" O ASP F 472 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 501 through 506 removed outlier: 3.936A pdb=" N MET F 587 " --> pdb=" O THR F 488 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 597 through 598 removed outlier: 6.498A pdb=" N HIS F 597 " --> pdb=" O VAL F 605 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 619 through 622 removed outlier: 4.250A pdb=" N ASN F 621 " --> pdb=" O LEU F 628 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS F 673 " --> pdb=" O ARG F 669 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 654 through 655 removed outlier: 3.768A pdb=" N GLU F 654 " --> pdb=" O ILE F 646 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN F 697 " --> pdb=" O GLU F 645 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 192 through 196 Processing sheet with id=AH1, first strand: chain 'G' and resid 262 through 269 removed outlier: 6.747A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 262 through 269 removed outlier: 6.747A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 272 through 273 removed outlier: 3.510A pdb=" N SER G 272 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA G 358 " --> pdb=" O MET G 434 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 389 through 395 removed outlier: 6.835A pdb=" N LEU G 383 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR G 393 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR G 381 " --> pdb=" O THR G 393 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS G 395 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR G 375 " --> pdb=" O ILE G 404 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE G 404 " --> pdb=" O TYR G 375 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 389 through 395 removed outlier: 6.835A pdb=" N LEU G 383 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR G 393 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR G 381 " --> pdb=" O THR G 393 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS G 395 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL G 377 " --> pdb=" O TYR G 456 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR G 456 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN G 454 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR G 381 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR G 452 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU G 383 " --> pdb=" O LEU G 450 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU G 450 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU G 385 " --> pdb=" O LEU G 448 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU G 448 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N VAL G 455 " --> pdb=" O ASN G 476 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ASN G 476 " --> pdb=" O VAL G 455 " (cutoff:3.500A) removed outlier: 9.679A pdb=" N GLY G 457 " --> pdb=" O GLY G 474 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N GLY G 474 " --> pdb=" O GLY G 457 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE G 459 " --> pdb=" O ASP G 472 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.915A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 597 through 598 removed outlier: 3.685A pdb=" N GLY G 606 " --> pdb=" O HIS G 597 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 628 through 629 removed outlier: 4.217A pdb=" N LEU G 629 " --> pdb=" O THR G 674 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR G 674 " --> pdb=" O LEU G 629 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 643 through 647 removed outlier: 3.756A pdb=" N GLU G 647 " --> pdb=" O LYS G 695 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS G 695 " --> pdb=" O GLU G 647 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 70 through 74 Processing sheet with id=AI2, first strand: chain 'H' and resid 464 through 466 removed outlier: 3.616A pdb=" N ILE H 562 " --> pdb=" O ILE H 570 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'I' and resid 71 through 74 Processing sheet with id=AI4, first strand: chain 'I' and resid 291 through 292 Processing sheet with id=AI5, first strand: chain 'I' and resid 367 through 368 Processing sheet with id=AI6, first strand: chain 'I' and resid 400 through 402 removed outlier: 3.556A pdb=" N TYR I 400 " --> pdb=" O ILE I 413 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE I 411 " --> pdb=" O LEU I 402 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'I' and resid 421 through 422 Processing sheet with id=AI8, first strand: chain 'I' and resid 459 through 461 removed outlier: 8.222A pdb=" N TYR I 459 " --> pdb=" O ASN I 543 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLY I 545 " --> pdb=" O TYR I 459 " (cutoff:3.500A) 1327 hydrogen bonds defined for protein. 3636 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: 9.93 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12389 1.33 - 1.45: 6449 1.45 - 1.57: 24611 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 43557 Sorted by residual: bond pdb=" N ILE I 194 " pdb=" CA ILE I 194 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.32e+00 bond pdb=" N ASP G 497 " pdb=" CA ASP G 497 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.71e+00 bond pdb=" N GLN C 543 " pdb=" CA GLN C 543 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.09e+00 bond pdb=" N ASN H 188 " pdb=" CA ASN H 188 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.33e-02 5.65e+03 6.87e+00 bond pdb=" N ASP I 169 " pdb=" CA ASP I 169 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.81e+00 ... (remaining 43552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 57982 2.61 - 5.22: 856 5.22 - 7.82: 79 7.82 - 10.43: 16 10.43 - 13.04: 4 Bond angle restraints: 58937 Sorted by residual: angle pdb=" C ILE A 708 " pdb=" N ASN A 709 " pdb=" CA ASN A 709 " ideal model delta sigma weight residual 120.68 133.72 -13.04 1.52e+00 4.33e-01 7.36e+01 angle pdb=" N ILE A 708 " pdb=" CA ILE A 708 " pdb=" C ILE A 708 " ideal model delta sigma weight residual 111.90 106.94 4.96 8.10e-01 1.52e+00 3.74e+01 angle pdb=" C ASN H 188 " pdb=" N ASN H 189 " pdb=" CA ASN H 189 " ideal model delta sigma weight residual 121.54 132.06 -10.52 1.91e+00 2.74e-01 3.03e+01 angle pdb=" N VAL H 327 " pdb=" CA VAL H 327 " pdb=" C VAL H 327 " ideal model delta sigma weight residual 112.90 107.65 5.25 9.60e-01 1.09e+00 2.99e+01 angle pdb=" N ASN I 188 " pdb=" CA ASN I 188 " pdb=" C ASN I 188 " ideal model delta sigma weight residual 112.23 105.84 6.39 1.26e+00 6.30e-01 2.58e+01 ... (remaining 58932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 23520 18.01 - 36.03: 2572 36.03 - 54.04: 442 54.04 - 72.06: 97 72.06 - 90.07: 33 Dihedral angle restraints: 26664 sinusoidal: 10894 harmonic: 15770 Sorted by residual: dihedral pdb=" CA ASN H 756 " pdb=" C ASN H 756 " pdb=" N PHE H 757 " pdb=" CA PHE H 757 " ideal model delta harmonic sigma weight residual 180.00 152.51 27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA THR H 623 " pdb=" C THR H 623 " pdb=" N ILE H 624 " pdb=" CA ILE H 624 " ideal model delta harmonic sigma weight residual 180.00 153.50 26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA TYR I 712 " pdb=" C TYR I 712 " pdb=" N LYS I 713 " pdb=" CA LYS I 713 " ideal model delta harmonic sigma weight residual 180.00 154.52 25.48 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 26661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 5202 0.065 - 0.131: 1267 0.131 - 0.196: 146 0.196 - 0.262: 19 0.262 - 0.327: 11 Chirality restraints: 6645 Sorted by residual: chirality pdb=" CA ASP A 497 " pdb=" N ASP A 497 " pdb=" C ASP A 497 " pdb=" CB ASP A 497 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CB ILE G 316 " pdb=" CA ILE G 316 " pdb=" CG1 ILE G 316 " pdb=" CG2 ILE G 316 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB ILE D 269 " pdb=" CA ILE D 269 " pdb=" CG1 ILE D 269 " pdb=" CG2 ILE D 269 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 6642 not shown) Planarity restraints: 7701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN H 189 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C ASN H 189 " 0.060 2.00e-02 2.50e+03 pdb=" O ASN H 189 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS H 190 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE I 624 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO I 625 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO I 625 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO I 625 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 481 " 0.048 5.00e-02 4.00e+02 7.15e-02 8.18e+00 pdb=" N PRO B 482 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 482 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 482 " 0.040 5.00e-02 4.00e+02 ... (remaining 7698 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 10186 2.79 - 3.32: 36004 3.32 - 3.84: 68888 3.84 - 4.37: 80958 4.37 - 4.90: 141516 Nonbonded interactions: 337552 Sorted by model distance: nonbonded pdb=" OD1 ASP C 425 " pdb=" OG1 THR C 430 " model vdw 2.258 3.040 nonbonded pdb=" O ILE G 484 " pdb=" OG1 THR G 488 " model vdw 2.266 3.040 nonbonded pdb=" O VAL E 332 " pdb=" OG SER F 296 " model vdw 2.267 3.040 nonbonded pdb=" OD1 ASN E 328 " pdb=" OG SER F 301 " model vdw 2.268 3.040 nonbonded pdb=" O LEU H 634 " pdb=" OH TYR H 712 " model vdw 2.276 3.040 ... (remaining 337547 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.030 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 38.100 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.007 0.097 43557 Z= 0.291 Angle : 0.841 13.039 58937 Z= 0.474 Chirality : 0.057 0.327 6645 Planarity : 0.006 0.073 7701 Dihedral : 15.383 90.072 16464 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.70 % Favored : 94.26 % Rotamer: Outliers : 0.31 % Allowed : 7.78 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.30 (0.09), residues: 5348 helix: -4.44 (0.07), residues: 1042 sheet: -1.95 (0.13), residues: 1278 loop : -2.71 (0.09), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 242 TYR 0.040 0.002 TYR B 366 PHE 0.029 0.002 PHE A 313 TRP 0.014 0.002 TRP F 226 HIS 0.009 0.001 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00669 (43557) covalent geometry : angle 0.84130 (58937) hydrogen bonds : bond 0.31462 ( 1279) hydrogen bonds : angle 11.22443 ( 3636) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 HIS cc_start: 0.7221 (m90) cc_final: 0.6726 (m-70) REVERT: B 556 GLN cc_start: 0.7810 (tm-30) cc_final: 0.7483 (tm-30) REVERT: C 356 ASP cc_start: 0.7943 (t0) cc_final: 0.7527 (t0) REVERT: C 434 MET cc_start: 0.8260 (ttm) cc_final: 0.7972 (ttp) REVERT: C 597 HIS cc_start: 0.6609 (m90) cc_final: 0.6334 (m90) REVERT: F 276 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7902 (p0) REVERT: F 287 ARG cc_start: 0.7802 (mmt90) cc_final: 0.7066 (mpp-170) REVERT: G 180 ASN cc_start: 0.8125 (t0) cc_final: 0.7805 (t0) REVERT: H 295 PHE cc_start: 0.6881 (m-80) cc_final: 0.6498 (m-80) REVERT: H 553 PHE cc_start: 0.4969 (p90) cc_final: 0.3255 (m-80) REVERT: H 561 PHE cc_start: 0.5946 (t80) cc_final: 0.5323 (t80) REVERT: I 283 LYS cc_start: 0.6324 (tttp) cc_final: 0.5993 (mtmt) REVERT: I 595 PHE cc_start: 0.4349 (p90) cc_final: 0.3877 (p90) outliers start: 15 outliers final: 5 residues processed: 216 average time/residue: 0.2631 time to fit residues: 91.9553 Evaluate side-chains 143 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain H residue 164 LYS Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain I residue 198 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 0.0670 chunk 414 optimal weight: 3.9990 chunk 310 optimal weight: 1.9990 chunk 488 optimal weight: 20.0000 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 20.0000 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN A 304 HIS A 363 ASN A 437 ASN A 537 ASN A 691 ASN B 292 ASN B 299 HIS B 326 ASN B 363 ASN B 376 ASN B 389 GLN B 437 ASN B 458 ASN B 556 GLN B 601 ASN B 682 ASN B 697 ASN C 363 ASN C 389 GLN C 494 ASN C 570 ASN C 601 ASN C 693 ASN D 281 ASN D 326 ASN D 336 HIS D 363 ASN D 389 GLN ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 ASN D 697 ASN D 705 ASN E 299 HIS E 306 ASN E 409 ASN E 499 ASN E 664 ASN E 682 ASN E 719 ASN F 285 GLN F 363 ASN F 389 GLN F 539 ASN F 561 ASN F 630 ASN F 697 ASN G 310 HIS G 389 GLN G 693 ASN G 705 ASN H 31 ASN H 85 GLN H 188 ASN H 200 ASN H 341 HIS H 437 ASN H 520 GLN H 543 ASN H 633 ASN I 32 ASN I 81 HIS I 361 HIS I 395 ASN I 447 ASN I 493 GLN I 528 ASN I 550 ASN I 633 ASN I 697 ASN I 707 GLN I 737 ASN I 756 ASN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.158496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102361 restraints weight = 91399.895| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.33 r_work: 0.2993 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 43557 Z= 0.136 Angle : 0.548 11.362 58937 Z= 0.296 Chirality : 0.046 0.165 6645 Planarity : 0.004 0.068 7701 Dihedral : 5.614 58.380 5781 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.83 % Allowed : 10.65 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.10), residues: 5348 helix: -2.77 (0.12), residues: 1085 sheet: -1.31 (0.15), residues: 1082 loop : -2.36 (0.10), residues: 3181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 344 TYR 0.018 0.001 TYR I 292 PHE 0.022 0.001 PHE H 38 TRP 0.014 0.001 TRP I 480 HIS 0.006 0.001 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00307 (43557) covalent geometry : angle 0.54833 (58937) hydrogen bonds : bond 0.04302 ( 1279) hydrogen bonds : angle 6.63211 ( 3636) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8699 (mp) REVERT: C 356 ASP cc_start: 0.8923 (t0) cc_final: 0.8506 (t0) REVERT: C 556 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8529 (tm-30) REVERT: D 287 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7423 (mpt-90) REVERT: E 409 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8654 (t0) REVERT: F 285 GLN cc_start: 0.7943 (mt0) cc_final: 0.7632 (mm-40) REVERT: F 287 ARG cc_start: 0.7702 (mmt90) cc_final: 0.6813 (mpp-170) REVERT: G 180 ASN cc_start: 0.9018 (t0) cc_final: 0.8614 (t0) REVERT: G 185 ASP cc_start: 0.7864 (m-30) cc_final: 0.7436 (m-30) REVERT: H 164 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8244 (tptm) REVERT: H 295 PHE cc_start: 0.7163 (m-80) cc_final: 0.6890 (m-80) REVERT: H 561 PHE cc_start: 0.5877 (t80) cc_final: 0.5418 (t80) REVERT: H 577 MET cc_start: 0.6339 (mmt) cc_final: 0.5974 (mtt) REVERT: I 198 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8301 (mmtm) REVERT: I 283 LYS cc_start: 0.5960 (tttp) cc_final: 0.5523 (mtmt) outliers start: 40 outliers final: 12 residues processed: 203 average time/residue: 0.2355 time to fit residues: 81.2840 Evaluate side-chains 148 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 556 GLN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 409 ASN Chi-restraints excluded: chain E residue 682 ASN Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 164 LYS Chi-restraints excluded: chain H residue 420 VAL Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 358 ILE Chi-restraints excluded: chain I residue 395 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 191 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 245 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 431 optimal weight: 40.0000 chunk 387 optimal weight: 0.0770 chunk 164 optimal weight: 8.9990 chunk 252 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 286 optimal weight: 4.9990 chunk 530 optimal weight: 7.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN B 399 ASN D 409 ASN E 306 ASN E 664 ASN E 693 ASN G 253 HIS G 705 ASN H 188 ASN H 335 GLN H 550 ASN H 677 HIS H 726 GLN H 734 GLN I 343 GLN I 395 ASN ** I 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 697 ASN I 733 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.156184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.099763 restraints weight = 89126.576| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.28 r_work: 0.2978 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 43557 Z= 0.173 Angle : 0.542 10.195 58937 Z= 0.290 Chirality : 0.046 0.164 6645 Planarity : 0.004 0.065 7701 Dihedral : 5.328 56.083 5776 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.98 % Allowed : 13.29 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.10), residues: 5348 helix: -1.83 (0.14), residues: 1100 sheet: -1.09 (0.15), residues: 1106 loop : -2.14 (0.10), residues: 3142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 344 TYR 0.020 0.001 TYR B 366 PHE 0.019 0.001 PHE H 38 TRP 0.013 0.001 TRP H 575 HIS 0.008 0.001 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00408 (43557) covalent geometry : angle 0.54150 (58937) hydrogen bonds : bond 0.03744 ( 1279) hydrogen bonds : angle 5.91243 ( 3636) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8740 (mp) REVERT: A 652 LEU cc_start: 0.3470 (OUTLIER) cc_final: 0.3178 (tp) REVERT: C 356 ASP cc_start: 0.8969 (t0) cc_final: 0.8635 (t0) REVERT: D 287 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7239 (mpt-90) REVERT: D 350 MET cc_start: 0.8362 (tmm) cc_final: 0.8091 (tmm) REVERT: F 276 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8536 (p0) REVERT: F 285 GLN cc_start: 0.7985 (mt0) cc_final: 0.7701 (mm-40) REVERT: F 287 ARG cc_start: 0.7725 (mmt90) cc_final: 0.6991 (mpp-170) REVERT: G 180 ASN cc_start: 0.9106 (t0) cc_final: 0.8664 (t0) REVERT: H 33 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9159 (mp) REVERT: H 577 MET cc_start: 0.6265 (mmt) cc_final: 0.5908 (mtt) REVERT: I 283 LYS cc_start: 0.6092 (tttp) cc_final: 0.5597 (mtmt) REVERT: I 370 LEU cc_start: -0.0098 (tp) cc_final: -0.0670 (tp) outliers start: 47 outliers final: 24 residues processed: 187 average time/residue: 0.2281 time to fit residues: 74.6622 Evaluate side-chains 156 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 726 ILE Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 417 ASN Chi-restraints excluded: chain H residue 420 VAL Chi-restraints excluded: chain I residue 293 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 395 ASN Chi-restraints excluded: chain I residue 758 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 254 optimal weight: 4.9990 chunk 259 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 476 optimal weight: 1.9990 chunk 236 optimal weight: 30.0000 chunk 361 optimal weight: 5.9990 chunk 36 optimal weight: 0.0370 chunk 255 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 413 optimal weight: 5.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN B 597 HIS E 306 ASN E 409 ASN E 664 ASN E 682 ASN G 705 ASN H 188 ASN I 395 ASN I 474 GLN I 677 HIS I 697 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.154937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.098125 restraints weight = 90448.180| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.29 r_work: 0.3051 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 43557 Z= 0.092 Angle : 0.473 11.316 58937 Z= 0.252 Chirality : 0.044 0.167 6645 Planarity : 0.003 0.063 7701 Dihedral : 4.694 31.777 5768 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.33 % Allowed : 13.83 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.11), residues: 5348 helix: -1.15 (0.16), residues: 1061 sheet: -0.76 (0.15), residues: 1102 loop : -1.84 (0.10), residues: 3185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 344 TYR 0.013 0.001 TYR H 292 PHE 0.018 0.001 PHE H 38 TRP 0.011 0.001 TRP H 575 HIS 0.005 0.001 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00208 (43557) covalent geometry : angle 0.47301 (58937) hydrogen bonds : bond 0.02784 ( 1279) hydrogen bonds : angle 5.30261 ( 3636) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 160 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 356 ASP cc_start: 0.8922 (t0) cc_final: 0.8695 (t70) REVERT: D 287 ARG cc_start: 0.7722 (mtt180) cc_final: 0.7294 (mpt-90) REVERT: D 291 LYS cc_start: 0.7177 (tppt) cc_final: 0.6785 (mttm) REVERT: D 350 MET cc_start: 0.8428 (tmm) cc_final: 0.8151 (tmm) REVERT: E 340 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8448 (tt) REVERT: F 285 GLN cc_start: 0.8034 (mt0) cc_final: 0.7787 (mm-40) REVERT: F 287 ARG cc_start: 0.7677 (mmt90) cc_final: 0.7004 (mpp-170) REVERT: G 180 ASN cc_start: 0.8992 (t0) cc_final: 0.8603 (t0) REVERT: G 705 ASN cc_start: 0.3545 (OUTLIER) cc_final: 0.3183 (t0) REVERT: I 283 LYS cc_start: 0.6190 (tttp) cc_final: 0.5679 (mtmt) REVERT: I 370 LEU cc_start: -0.0531 (tp) cc_final: -0.1030 (tp) outliers start: 64 outliers final: 28 residues processed: 218 average time/residue: 0.2268 time to fit residues: 86.1595 Evaluate side-chains 158 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 409 ASN Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 682 ASN Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain G residue 705 ASN Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 417 ASN Chi-restraints excluded: chain H residue 534 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 293 ILE Chi-restraints excluded: chain I residue 402 LEU Chi-restraints excluded: chain I residue 697 ASN Chi-restraints excluded: chain I residue 758 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 187 optimal weight: 6.9990 chunk 535 optimal weight: 0.0020 chunk 328 optimal weight: 0.8980 chunk 329 optimal weight: 30.0000 chunk 377 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 452 optimal weight: 10.0000 chunk 319 optimal weight: 9.9990 chunk 361 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 375 optimal weight: 0.9980 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 597 HIS ** D 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN E 664 ASN E 682 ASN G 409 ASN G 705 ASN I 395 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.155276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.097921 restraints weight = 90768.320| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.33 r_work: 0.3072 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 43557 Z= 0.091 Angle : 0.468 11.102 58937 Z= 0.248 Chirality : 0.044 0.162 6645 Planarity : 0.003 0.063 7701 Dihedral : 4.514 26.406 5768 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.31 % Allowed : 14.54 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.11), residues: 5348 helix: -0.77 (0.16), residues: 1062 sheet: -0.49 (0.16), residues: 1092 loop : -1.66 (0.10), residues: 3194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 344 TYR 0.013 0.001 TYR D 375 PHE 0.019 0.001 PHE H 38 TRP 0.011 0.001 TRP H 575 HIS 0.005 0.001 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00208 (43557) covalent geometry : angle 0.46785 (58937) hydrogen bonds : bond 0.02685 ( 1279) hydrogen bonds : angle 5.07732 ( 3636) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 141 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 287 ARG cc_start: 0.7892 (mtt180) cc_final: 0.7507 (mpt-90) REVERT: D 291 LYS cc_start: 0.7252 (tppt) cc_final: 0.6860 (mttm) REVERT: D 350 MET cc_start: 0.8273 (tmm) cc_final: 0.8021 (tmm) REVERT: E 291 LYS cc_start: 0.7031 (tttt) cc_final: 0.6794 (tptm) REVERT: E 292 ASN cc_start: 0.4965 (t0) cc_final: 0.4580 (t0) REVERT: F 276 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8501 (p0) REVERT: F 285 GLN cc_start: 0.7983 (mt0) cc_final: 0.7709 (mm-40) REVERT: F 287 ARG cc_start: 0.7780 (mmt90) cc_final: 0.6861 (mpp-170) REVERT: G 180 ASN cc_start: 0.8953 (t0) cc_final: 0.8588 (t0) REVERT: I 198 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8264 (mmtm) REVERT: I 283 LYS cc_start: 0.6161 (tttp) cc_final: 0.5764 (mtmt) REVERT: I 370 LEU cc_start: -0.0551 (tp) cc_final: -0.1140 (tp) outliers start: 63 outliers final: 35 residues processed: 199 average time/residue: 0.2306 time to fit residues: 79.5653 Evaluate side-chains 167 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 693 ASN Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 682 ASN Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 417 ASN Chi-restraints excluded: chain H residue 420 VAL Chi-restraints excluded: chain H residue 534 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 293 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 306 ILE Chi-restraints excluded: chain I residue 402 LEU Chi-restraints excluded: chain I residue 758 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 300 optimal weight: 1.9990 chunk 405 optimal weight: 5.9990 chunk 265 optimal weight: 8.9990 chunk 290 optimal weight: 0.9990 chunk 336 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 528 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 403 optimal weight: 8.9990 chunk 236 optimal weight: 40.0000 chunk 224 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 ASN B 537 ASN ** D 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 ASN E 409 ASN E 664 ASN E 682 ASN F 541 GLN G 409 ASN H 488 ASN I 518 ASN I 697 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.157400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101733 restraints weight = 91459.276| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.28 r_work: 0.2968 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 43557 Z= 0.198 Angle : 0.542 10.981 58937 Z= 0.287 Chirality : 0.047 0.163 6645 Planarity : 0.004 0.063 7701 Dihedral : 4.938 26.469 5768 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.41 % Allowed : 15.18 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.11), residues: 5348 helix: -0.80 (0.16), residues: 1099 sheet: -0.49 (0.15), residues: 1100 loop : -1.72 (0.11), residues: 3149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 504 TYR 0.019 0.001 TYR D 366 PHE 0.021 0.001 PHE H 38 TRP 0.014 0.001 TRP H 575 HIS 0.008 0.001 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00475 (43557) covalent geometry : angle 0.54200 (58937) hydrogen bonds : bond 0.03377 ( 1279) hydrogen bonds : angle 5.27841 ( 3636) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 127 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 287 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7286 (mpt-90) REVERT: D 291 LYS cc_start: 0.7138 (tppt) cc_final: 0.6775 (mttm) REVERT: D 350 MET cc_start: 0.8513 (tmm) cc_final: 0.8214 (tmm) REVERT: F 276 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8525 (p0) REVERT: F 285 GLN cc_start: 0.7964 (mt0) cc_final: 0.7650 (mm-40) REVERT: F 287 ARG cc_start: 0.7792 (mmt90) cc_final: 0.6974 (mpp-170) REVERT: H 274 LEU cc_start: 0.3534 (OUTLIER) cc_final: 0.3131 (mt) REVERT: I 198 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8325 (mmtm) REVERT: I 283 LYS cc_start: 0.5330 (tttp) cc_final: 0.4906 (mtmt) outliers start: 68 outliers final: 48 residues processed: 190 average time/residue: 0.2234 time to fit residues: 74.1984 Evaluate side-chains 172 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 693 ASN Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 724 ILE Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 409 ASN Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 643 ILE Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 417 ASN Chi-restraints excluded: chain H residue 420 VAL Chi-restraints excluded: chain H residue 534 THR Chi-restraints excluded: chain H residue 678 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 293 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 306 ILE Chi-restraints excluded: chain I residue 402 LEU Chi-restraints excluded: chain I residue 697 ASN Chi-restraints excluded: chain I residue 758 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 317 optimal weight: 0.2980 chunk 73 optimal weight: 10.0000 chunk 213 optimal weight: 30.0000 chunk 404 optimal weight: 0.8980 chunk 357 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 420 optimal weight: 20.0000 chunk 463 optimal weight: 7.9990 chunk 435 optimal weight: 7.9990 chunk 452 optimal weight: 40.0000 chunk 146 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 ASN B 597 HIS D 389 GLN ** D 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 HIS E 409 ASN E 664 ASN G 705 ASN I 200 ASN ** I 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.158201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102294 restraints weight = 88660.121| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.35 r_work: 0.3046 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 43557 Z= 0.085 Angle : 0.463 11.996 58937 Z= 0.245 Chirality : 0.044 0.163 6645 Planarity : 0.003 0.064 7701 Dihedral : 4.464 28.273 5768 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.10 % Allowed : 15.78 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.11), residues: 5348 helix: -0.49 (0.16), residues: 1106 sheet: -0.30 (0.15), residues: 1124 loop : -1.56 (0.11), residues: 3118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 344 TYR 0.010 0.001 TYR I 292 PHE 0.018 0.001 PHE H 38 TRP 0.011 0.001 TRP H 575 HIS 0.005 0.001 HIS I 220 Details of bonding type rmsd covalent geometry : bond 0.00189 (43557) covalent geometry : angle 0.46291 (58937) hydrogen bonds : bond 0.02542 ( 1279) hydrogen bonds : angle 4.91582 ( 3636) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 287 ARG cc_start: 0.7661 (mtt180) cc_final: 0.7267 (mpt-90) REVERT: D 291 LYS cc_start: 0.7136 (tppt) cc_final: 0.6845 (mttm) REVERT: D 350 MET cc_start: 0.8413 (tmm) cc_final: 0.8077 (tmm) REVERT: D 587 MET cc_start: 0.9390 (mtt) cc_final: 0.8821 (mtt) REVERT: E 291 LYS cc_start: 0.6946 (tttt) cc_final: 0.6700 (tptm) REVERT: E 292 ASN cc_start: 0.4951 (t0) cc_final: 0.4407 (t0) REVERT: F 276 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8491 (p0) REVERT: F 285 GLN cc_start: 0.7968 (mt0) cc_final: 0.7691 (mm-40) REVERT: F 287 ARG cc_start: 0.7824 (mmt90) cc_final: 0.6945 (mpp-170) REVERT: G 180 ASN cc_start: 0.8939 (t0) cc_final: 0.8542 (t0) REVERT: I 198 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8313 (mmtm) REVERT: I 283 LYS cc_start: 0.5915 (tttp) cc_final: 0.5521 (mtmt) outliers start: 53 outliers final: 35 residues processed: 186 average time/residue: 0.2254 time to fit residues: 73.0962 Evaluate side-chains 165 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 693 ASN Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 409 ASN Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 643 ILE Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 534 THR Chi-restraints excluded: chain H residue 678 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 293 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 402 LEU Chi-restraints excluded: chain I residue 758 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 522 optimal weight: 5.9990 chunk 374 optimal weight: 9.9990 chunk 271 optimal weight: 9.9990 chunk 525 optimal weight: 4.9990 chunk 417 optimal weight: 20.0000 chunk 98 optimal weight: 7.9990 chunk 205 optimal weight: 9.9990 chunk 468 optimal weight: 2.9990 chunk 369 optimal weight: 3.9990 chunk 460 optimal weight: 5.9990 chunk 404 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 389 GLN D 438 GLN ** D 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 ASN E 664 ASN F 664 ASN H 474 GLN ** I 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 493 GLN I 697 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.155375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098768 restraints weight = 89536.174| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.15 r_work: 0.2990 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 43557 Z= 0.205 Angle : 0.546 11.232 58937 Z= 0.288 Chirality : 0.047 0.160 6645 Planarity : 0.004 0.064 7701 Dihedral : 4.882 28.169 5768 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.35 % Allowed : 15.97 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.11), residues: 5348 helix: -0.53 (0.16), residues: 1097 sheet: -0.35 (0.16), residues: 1110 loop : -1.58 (0.11), residues: 3141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 504 TYR 0.019 0.001 TYR D 366 PHE 0.021 0.001 PHE H 38 TRP 0.015 0.001 TRP H 575 HIS 0.009 0.001 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00491 (43557) covalent geometry : angle 0.54592 (58937) hydrogen bonds : bond 0.03339 ( 1279) hydrogen bonds : angle 5.16277 ( 3636) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 125 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 287 ARG cc_start: 0.7719 (mtt180) cc_final: 0.7260 (mpt-90) REVERT: D 291 LYS cc_start: 0.7158 (tppt) cc_final: 0.6845 (mttm) REVERT: D 587 MET cc_start: 0.9435 (mtt) cc_final: 0.8864 (mtt) REVERT: E 292 ASN cc_start: 0.4767 (t0) cc_final: 0.4360 (t0) REVERT: F 276 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8481 (p0) REVERT: F 285 GLN cc_start: 0.8003 (mt0) cc_final: 0.7727 (mm-40) REVERT: F 287 ARG cc_start: 0.7706 (mmt90) cc_final: 0.6935 (mpp-170) REVERT: H 33 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9217 (mp) REVERT: H 274 LEU cc_start: 0.3507 (OUTLIER) cc_final: 0.3185 (mt) REVERT: H 766 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6245 (tm-30) REVERT: I 198 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8333 (mmtm) REVERT: I 283 LYS cc_start: 0.5824 (tttp) cc_final: 0.5434 (mtmt) outliers start: 65 outliers final: 50 residues processed: 187 average time/residue: 0.2290 time to fit residues: 74.8835 Evaluate side-chains 175 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 120 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 693 ASN Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 643 ILE Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 605 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 417 ASN Chi-restraints excluded: chain H residue 534 THR Chi-restraints excluded: chain H residue 678 ILE Chi-restraints excluded: chain H residue 766 GLU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 293 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 306 ILE Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 402 LEU Chi-restraints excluded: chain I residue 626 THR Chi-restraints excluded: chain I residue 697 ASN Chi-restraints excluded: chain I residue 758 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 512 optimal weight: 30.0000 chunk 271 optimal weight: 5.9990 chunk 297 optimal weight: 5.9990 chunk 326 optimal weight: 0.9990 chunk 402 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 419 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 217 optimal weight: 50.0000 chunk 72 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 389 GLN D 438 GLN D 494 ASN E 306 ASN E 409 ASN E 664 ASN F 697 ASN I 697 ASN I 717 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.156089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.100999 restraints weight = 91086.654| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.56 r_work: 0.2920 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 43557 Z= 0.275 Angle : 0.606 11.620 58937 Z= 0.320 Chirality : 0.049 0.187 6645 Planarity : 0.004 0.066 7701 Dihedral : 5.281 27.749 5768 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.52 % Allowed : 16.24 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.11), residues: 5348 helix: -0.66 (0.16), residues: 1090 sheet: -0.47 (0.15), residues: 1110 loop : -1.68 (0.11), residues: 3148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 669 TYR 0.021 0.002 TYR D 366 PHE 0.020 0.002 PHE H 38 TRP 0.015 0.002 TRP H 575 HIS 0.009 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00661 (43557) covalent geometry : angle 0.60571 (58937) hydrogen bonds : bond 0.03704 ( 1279) hydrogen bonds : angle 5.43917 ( 3636) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 118 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 ASP cc_start: 0.9111 (t70) cc_final: 0.8750 (t70) REVERT: B 287 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.8063 (ttm170) REVERT: D 287 ARG cc_start: 0.7722 (mtt180) cc_final: 0.7255 (mpt-90) REVERT: D 291 LYS cc_start: 0.7141 (tppt) cc_final: 0.6497 (tppt) REVERT: D 587 MET cc_start: 0.9468 (mtt) cc_final: 0.8928 (mtt) REVERT: D 662 MET cc_start: 0.1144 (tmm) cc_final: 0.0599 (tmm) REVERT: E 291 LYS cc_start: 0.6800 (tttt) cc_final: 0.6542 (tptm) REVERT: E 409 ASN cc_start: 0.9028 (OUTLIER) cc_final: 0.8718 (t0) REVERT: F 276 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8588 (p0) REVERT: F 285 GLN cc_start: 0.8047 (mt0) cc_final: 0.7783 (mm-40) REVERT: F 287 ARG cc_start: 0.7699 (mmt90) cc_final: 0.7091 (mpp-170) REVERT: H 274 LEU cc_start: 0.3651 (OUTLIER) cc_final: 0.3383 (mt) REVERT: I 198 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8344 (mmtm) REVERT: I 283 LYS cc_start: 0.5633 (tttp) cc_final: 0.5203 (mtmt) REVERT: I 697 ASN cc_start: 0.7588 (OUTLIER) cc_final: 0.7307 (t0) outliers start: 73 outliers final: 53 residues processed: 186 average time/residue: 0.2254 time to fit residues: 73.4240 Evaluate side-chains 171 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 113 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 693 ASN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 724 ILE Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 409 ASN Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 643 ILE Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 605 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 534 THR Chi-restraints excluded: chain H residue 678 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 293 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 402 LEU Chi-restraints excluded: chain I residue 626 THR Chi-restraints excluded: chain I residue 676 ASN Chi-restraints excluded: chain I residue 697 ASN Chi-restraints excluded: chain I residue 758 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 129 optimal weight: 8.9990 chunk 276 optimal weight: 8.9990 chunk 481 optimal weight: 0.0470 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 20.0000 chunk 488 optimal weight: 0.0980 chunk 377 optimal weight: 9.9990 chunk 286 optimal weight: 0.8980 chunk 391 optimal weight: 30.0000 chunk 520 optimal weight: 8.9990 chunk 363 optimal weight: 4.9990 overall best weight: 1.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 597 HIS E 306 ASN E 409 ASN E 664 ASN H 318 HIS ** I 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.158707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105860 restraints weight = 91554.019| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.08 r_work: 0.2977 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 43557 Z= 0.099 Angle : 0.483 12.130 58937 Z= 0.255 Chirality : 0.044 0.161 6645 Planarity : 0.003 0.068 7701 Dihedral : 4.645 27.081 5768 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.98 % Allowed : 16.86 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.11), residues: 5348 helix: -0.36 (0.16), residues: 1091 sheet: -0.31 (0.16), residues: 1124 loop : -1.51 (0.11), residues: 3133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 669 TYR 0.011 0.001 TYR C 375 PHE 0.018 0.001 PHE H 38 TRP 0.014 0.001 TRP H 575 HIS 0.006 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00228 (43557) covalent geometry : angle 0.48307 (58937) hydrogen bonds : bond 0.02666 ( 1279) hydrogen bonds : angle 4.99694 ( 3636) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 287 ARG cc_start: 0.7707 (mtt180) cc_final: 0.7267 (mpt-90) REVERT: D 291 LYS cc_start: 0.7111 (tppt) cc_final: 0.6886 (mttm) REVERT: E 291 LYS cc_start: 0.6673 (tttt) cc_final: 0.6451 (tptm) REVERT: F 276 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8463 (p0) REVERT: F 285 GLN cc_start: 0.7919 (mt0) cc_final: 0.7631 (mm-40) REVERT: F 287 ARG cc_start: 0.7892 (mmt90) cc_final: 0.6987 (mpp-170) REVERT: G 180 ASN cc_start: 0.9025 (t0) cc_final: 0.8627 (t0) REVERT: H 274 LEU cc_start: 0.3240 (OUTLIER) cc_final: 0.2973 (mt) REVERT: I 283 LYS cc_start: 0.5566 (tttp) cc_final: 0.5140 (mtmt) REVERT: I 370 LEU cc_start: 0.1946 (mt) cc_final: 0.0828 (tp) outliers start: 47 outliers final: 37 residues processed: 176 average time/residue: 0.2353 time to fit residues: 72.9515 Evaluate side-chains 163 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 693 ASN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 724 ILE Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 643 ILE Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 534 THR Chi-restraints excluded: chain H residue 678 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 293 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 402 LEU Chi-restraints excluded: chain I residue 626 THR Chi-restraints excluded: chain I residue 758 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 489 optimal weight: 9.9990 chunk 391 optimal weight: 30.0000 chunk 172 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 360 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 237 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 514 optimal weight: 7.9990 chunk 155 optimal weight: 0.0370 chunk 292 optimal weight: 40.0000 overall best weight: 1.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 389 GLN D 438 GLN E 306 ASN E 664 ASN H 405 ASN ** I 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 697 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.158035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104416 restraints weight = 91339.497| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.03 r_work: 0.2952 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 43557 Z= 0.122 Angle : 0.491 11.361 58937 Z= 0.259 Chirality : 0.045 0.158 6645 Planarity : 0.003 0.066 7701 Dihedral : 4.589 26.765 5768 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.10 % Allowed : 16.74 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.11), residues: 5348 helix: -0.27 (0.16), residues: 1094 sheet: -0.17 (0.16), residues: 1096 loop : -1.44 (0.11), residues: 3158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 669 TYR 0.014 0.001 TYR C 375 PHE 0.021 0.001 PHE H 38 TRP 0.019 0.001 TRP I 480 HIS 0.014 0.001 HIS E 304 Details of bonding type rmsd covalent geometry : bond 0.00288 (43557) covalent geometry : angle 0.49149 (58937) hydrogen bonds : bond 0.02816 ( 1279) hydrogen bonds : angle 4.92744 ( 3636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15725.06 seconds wall clock time: 268 minutes 1.60 seconds (16081.60 seconds total)