Starting phenix.real_space_refine on Fri Feb 23 19:23:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppi_20437/02_2024/6ppi_20437.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppi_20437/02_2024/6ppi_20437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppi_20437/02_2024/6ppi_20437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppi_20437/02_2024/6ppi_20437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppi_20437/02_2024/6ppi_20437.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppi_20437/02_2024/6ppi_20437.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 204 5.16 5 C 25212 2.51 5 N 6696 2.21 5 O 7392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39504 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3292 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 1 Chain: "B" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3292 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 1 Chain: "C" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3292 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 1 Chain: "D" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3292 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 1 Chain: "E" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3292 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 1 Chain: "F" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3292 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 1 Chain: "G" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3292 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 1 Chain: "H" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3292 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 1 Chain: "I" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3292 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 1 Chain: "J" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3292 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 1 Chain: "K" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3292 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 1 Chain: "L" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3292 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 1 Time building chain proxies: 20.22, per 1000 atoms: 0.51 Number of scatterers: 39504 At special positions: 0 Unit cell: (155.53, 155.53, 139.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 204 16.00 O 7392 8.00 N 6696 7.00 C 25212 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 - 3.50 Amino acid : False - 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: 14.72 Conformation dependent library (CDL) restraints added in 6.8 seconds 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9504 Finding SS restraints... Secondary structure from input PDB file: 276 helices and 48 sheets defined 62.0% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.34 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 removed outlier: 3.752A pdb=" N SER A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 37 through 44 removed outlier: 3.547A pdb=" N CYS A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 62 removed outlier: 3.691A pdb=" N ALA A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 85 removed outlier: 3.582A pdb=" N VAL A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 73 " --> pdb=" O HIS A 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 114 removed outlier: 3.718A pdb=" N ARG A 96 " --> pdb=" O TRP A 92 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET A 107 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET A 109 " --> pdb=" O GLN A 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 124 removed outlier: 3.814A pdb=" N ALA A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 154 through 169 removed outlier: 3.686A pdb=" N SER A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.539A pdb=" N ILE A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 200 removed outlier: 3.620A pdb=" N GLU A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 250 through 271 removed outlier: 3.706A pdb=" N HIS A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 removed outlier: 3.734A pdb=" N GLY A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 removed outlier: 3.560A pdb=" N GLN A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 434' Processing helix chain 'A' and resid 458 through 469 removed outlier: 4.286A pdb=" N MET A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 477 removed outlier: 3.875A pdb=" N PHE A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.629A pdb=" N PHE A 523 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 524 " --> pdb=" O HIS A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 527 through 537 removed outlier: 3.527A pdb=" N ALA A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 removed outlier: 3.987A pdb=" N VAL A 543 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 551 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 29 removed outlier: 3.751A pdb=" N SER B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 28 " --> pdb=" O PHE B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 37 through 44 removed outlier: 3.547A pdb=" N CYS B 41 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.691A pdb=" N ALA B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 85 removed outlier: 3.582A pdb=" N VAL B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP B 73 " --> pdb=" O HIS B 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 114 removed outlier: 3.718A pdb=" N ARG B 96 " --> pdb=" O TRP B 92 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 99 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET B 107 " --> pdb=" O TRP B 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.814A pdb=" N ALA B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 154 through 169 removed outlier: 3.685A pdb=" N SER B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN B 162 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET B 164 " --> pdb=" O GLN B 160 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 removed outlier: 4.539A pdb=" N ILE B 180 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 181 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 200 removed outlier: 3.620A pdb=" N GLU B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 250 through 271 removed outlier: 3.707A pdb=" N HIS B 258 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN B 271 " --> pdb=" O CYS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 428 removed outlier: 3.735A pdb=" N GLY B 426 " --> pdb=" O PHE B 422 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 removed outlier: 3.559A pdb=" N GLN B 434 " --> pdb=" O ASP B 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 434' Processing helix chain 'B' and resid 458 through 469 removed outlier: 4.286A pdb=" N MET B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 477 removed outlier: 3.875A pdb=" N PHE B 474 " --> pdb=" O GLU B 470 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 487 No H-bonds generated for 'chain 'B' and resid 485 through 487' Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 502 through 508 Processing helix chain 'B' and resid 520 through 524 removed outlier: 3.628A pdb=" N PHE B 523 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 524 " --> pdb=" O HIS B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 524' Processing helix chain 'B' and resid 527 through 537 removed outlier: 3.528A pdb=" N ALA B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 553 removed outlier: 3.987A pdb=" N VAL B 543 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 551 " --> pdb=" O ASP B 547 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR B 552 " --> pdb=" O VAL B 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 29 removed outlier: 3.751A pdb=" N SER C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE C 24 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN C 28 " --> pdb=" O PHE C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 37 through 44 removed outlier: 3.548A pdb=" N CYS C 41 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 42 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 62 removed outlier: 3.691A pdb=" N ALA C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 85 removed outlier: 3.582A pdb=" N VAL C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 114 removed outlier: 3.718A pdb=" N ARG C 96 " --> pdb=" O TRP C 92 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG C 97 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP C 101 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET C 107 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 108 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET C 109 " --> pdb=" O GLN C 105 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.813A pdb=" N ALA C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 121 " --> pdb=" O ASN C 117 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 139 Processing helix chain 'C' and resid 154 through 169 removed outlier: 3.685A pdb=" N SER C 158 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET C 164 " --> pdb=" O GLN C 160 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS C 167 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 182 removed outlier: 4.539A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 181 " --> pdb=" O ILE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 200 removed outlier: 3.621A pdb=" N GLU C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA C 197 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 250 through 271 removed outlier: 3.706A pdb=" N HIS C 258 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 271 " --> pdb=" O CYS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 428 removed outlier: 3.734A pdb=" N GLY C 426 " --> pdb=" O PHE C 422 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG C 427 " --> pdb=" O GLN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 434 removed outlier: 3.560A pdb=" N GLN C 434 " --> pdb=" O ASP C 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 430 through 434' Processing helix chain 'C' and resid 458 through 469 removed outlier: 4.286A pdb=" N MET C 462 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN C 467 " --> pdb=" O LYS C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 477 removed outlier: 3.875A pdb=" N PHE C 474 " --> pdb=" O GLU C 470 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN C 475 " --> pdb=" O SER C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 487 No H-bonds generated for 'chain 'C' and resid 485 through 487' Processing helix chain 'C' and resid 497 through 502 Processing helix chain 'C' and resid 502 through 508 Processing helix chain 'C' and resid 520 through 524 removed outlier: 3.629A pdb=" N PHE C 523 " --> pdb=" O SER C 520 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL C 524 " --> pdb=" O HIS C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 524' Processing helix chain 'C' and resid 527 through 537 removed outlier: 3.527A pdb=" N ALA C 532 " --> pdb=" O LEU C 528 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR C 536 " --> pdb=" O ALA C 532 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 553 removed outlier: 3.987A pdb=" N VAL C 543 " --> pdb=" O SER C 539 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS C 551 " --> pdb=" O ASP C 547 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR C 552 " --> pdb=" O VAL C 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 removed outlier: 3.751A pdb=" N SER D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE D 24 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU D 25 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN D 28 " --> pdb=" O PHE D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 37 through 44 removed outlier: 3.548A pdb=" N CYS D 41 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 62 removed outlier: 3.691A pdb=" N ALA D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 85 removed outlier: 3.583A pdb=" N VAL D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP D 73 " --> pdb=" O HIS D 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP D 74 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR D 76 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 114 removed outlier: 3.718A pdb=" N ARG D 96 " --> pdb=" O TRP D 92 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG D 97 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR D 99 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP D 101 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET D 107 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 124 removed outlier: 3.812A pdb=" N ALA D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG D 121 " --> pdb=" O ASN D 117 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 139 Processing helix chain 'D' and resid 154 through 169 removed outlier: 3.686A pdb=" N SER D 158 " --> pdb=" O LYS D 154 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN D 162 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET D 164 " --> pdb=" O GLN D 160 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 removed outlier: 4.538A pdb=" N ILE D 180 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 181 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 200 removed outlier: 3.621A pdb=" N GLU D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN D 190 " --> pdb=" O GLN D 186 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA D 197 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 250 through 271 removed outlier: 3.706A pdb=" N HIS D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN D 271 " --> pdb=" O CYS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 428 removed outlier: 3.734A pdb=" N GLY D 426 " --> pdb=" O PHE D 422 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.560A pdb=" N GLN D 434 " --> pdb=" O ASP D 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 430 through 434' Processing helix chain 'D' and resid 458 through 469 removed outlier: 4.287A pdb=" N MET D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 477 removed outlier: 3.875A pdb=" N PHE D 474 " --> pdb=" O GLU D 470 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN D 475 " --> pdb=" O SER D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 487 No H-bonds generated for 'chain 'D' and resid 485 through 487' Processing helix chain 'D' and resid 497 through 502 Processing helix chain 'D' and resid 502 through 508 Processing helix chain 'D' and resid 520 through 524 removed outlier: 3.629A pdb=" N PHE D 523 " --> pdb=" O SER D 520 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 524 " --> pdb=" O HIS D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 524' Processing helix chain 'D' and resid 527 through 537 removed outlier: 3.527A pdb=" N ALA D 532 " --> pdb=" O LEU D 528 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 553 removed outlier: 3.987A pdb=" N VAL D 543 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS D 551 " --> pdb=" O ASP D 547 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR D 552 " --> pdb=" O VAL D 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 29 removed outlier: 3.751A pdb=" N SER E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE E 24 " --> pdb=" O SER E 20 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU E 25 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU E 27 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN E 28 " --> pdb=" O PHE E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 36 No H-bonds generated for 'chain 'E' and resid 34 through 36' Processing helix chain 'E' and resid 37 through 44 removed outlier: 3.547A pdb=" N CYS E 41 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER E 42 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 62 removed outlier: 3.690A pdb=" N ALA E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 85 removed outlier: 3.582A pdb=" N VAL E 70 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP E 73 " --> pdb=" O HIS E 69 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP E 74 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR E 76 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 114 removed outlier: 3.718A pdb=" N ARG E 96 " --> pdb=" O TRP E 92 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG E 97 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER E 98 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR E 99 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET E 107 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET E 109 " --> pdb=" O GLN E 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 124 removed outlier: 3.814A pdb=" N ALA E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG E 121 " --> pdb=" O ASN E 117 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 139 Processing helix chain 'E' and resid 154 through 169 removed outlier: 3.685A pdb=" N SER E 158 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET E 164 " --> pdb=" O GLN E 160 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG E 169 " --> pdb=" O LYS E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 removed outlier: 4.539A pdb=" N ILE E 180 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 181 " --> pdb=" O ILE E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 200 removed outlier: 3.620A pdb=" N GLU E 187 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN E 190 " --> pdb=" O GLN E 186 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E 193 " --> pdb=" O SER E 189 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA E 197 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 249 No H-bonds generated for 'chain 'E' and resid 247 through 249' Processing helix chain 'E' and resid 250 through 271 removed outlier: 3.707A pdb=" N HIS E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN E 271 " --> pdb=" O CYS E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 428 removed outlier: 3.735A pdb=" N GLY E 426 " --> pdb=" O PHE E 422 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG E 427 " --> pdb=" O GLN E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 removed outlier: 3.559A pdb=" N GLN E 434 " --> pdb=" O ASP E 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 430 through 434' Processing helix chain 'E' and resid 458 through 469 removed outlier: 4.287A pdb=" N MET E 462 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN E 467 " --> pdb=" O LYS E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 477 removed outlier: 3.875A pdb=" N PHE E 474 " --> pdb=" O GLU E 470 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN E 475 " --> pdb=" O SER E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 487 No H-bonds generated for 'chain 'E' and resid 485 through 487' Processing helix chain 'E' and resid 497 through 502 Processing helix chain 'E' and resid 502 through 508 Processing helix chain 'E' and resid 520 through 524 removed outlier: 3.629A pdb=" N PHE E 523 " --> pdb=" O SER E 520 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL E 524 " --> pdb=" O HIS E 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 520 through 524' Processing helix chain 'E' and resid 527 through 537 removed outlier: 3.526A pdb=" N ALA E 532 " --> pdb=" O LEU E 528 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR E 536 " --> pdb=" O ALA E 532 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN E 537 " --> pdb=" O ALA E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 553 removed outlier: 3.987A pdb=" N VAL E 543 " --> pdb=" O SER E 539 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS E 551 " --> pdb=" O ASP E 547 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR E 552 " --> pdb=" O VAL E 548 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 29 removed outlier: 3.751A pdb=" N SER F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE F 24 " --> pdb=" O SER F 20 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU F 25 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 36 No H-bonds generated for 'chain 'F' and resid 34 through 36' Processing helix chain 'F' and resid 37 through 44 removed outlier: 3.548A pdb=" N CYS F 41 " --> pdb=" O GLN F 37 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER F 42 " --> pdb=" O THR F 38 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU F 43 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 62 removed outlier: 3.691A pdb=" N ALA F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 85 removed outlier: 3.582A pdb=" N VAL F 70 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP F 73 " --> pdb=" O HIS F 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR F 76 " --> pdb=" O SER F 72 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 114 removed outlier: 3.718A pdb=" N ARG F 96 " --> pdb=" O TRP F 92 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR F 99 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP F 101 " --> pdb=" O ARG F 97 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR F 106 " --> pdb=" O SER F 102 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET F 107 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET F 109 " --> pdb=" O GLN F 105 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR F 110 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 124 removed outlier: 3.813A pdb=" N ALA F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE F 119 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN F 120 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG F 121 " --> pdb=" O ASN F 117 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 139 Processing helix chain 'F' and resid 154 through 169 removed outlier: 3.686A pdb=" N SER F 158 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN F 162 " --> pdb=" O SER F 158 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET F 164 " --> pdb=" O GLN F 160 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS F 167 " --> pdb=" O LEU F 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG F 169 " --> pdb=" O LYS F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 182 removed outlier: 4.539A pdb=" N ILE F 180 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU F 181 " --> pdb=" O ILE F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 200 removed outlier: 3.620A pdb=" N GLU F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN F 190 " --> pdb=" O GLN F 186 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA F 197 " --> pdb=" O SER F 193 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 250 through 271 removed outlier: 3.706A pdb=" N HIS F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN F 271 " --> pdb=" O CYS F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 428 removed outlier: 3.735A pdb=" N GLY F 426 " --> pdb=" O PHE F 422 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG F 427 " --> pdb=" O GLN F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 434 removed outlier: 3.559A pdb=" N GLN F 434 " --> pdb=" O ASP F 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 430 through 434' Processing helix chain 'F' and resid 458 through 469 removed outlier: 4.286A pdb=" N MET F 462 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN F 467 " --> pdb=" O LYS F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 477 removed outlier: 3.874A pdb=" N PHE F 474 " --> pdb=" O GLU F 470 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN F 475 " --> pdb=" O SER F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 487 No H-bonds generated for 'chain 'F' and resid 485 through 487' Processing helix chain 'F' and resid 497 through 502 Processing helix chain 'F' and resid 502 through 508 Processing helix chain 'F' and resid 520 through 524 removed outlier: 3.628A pdb=" N PHE F 523 " --> pdb=" O SER F 520 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL F 524 " --> pdb=" O HIS F 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 520 through 524' Processing helix chain 'F' and resid 527 through 537 removed outlier: 3.527A pdb=" N ALA F 532 " --> pdb=" O LEU F 528 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN F 537 " --> pdb=" O ALA F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 553 removed outlier: 3.986A pdb=" N VAL F 543 " --> pdb=" O SER F 539 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS F 551 " --> pdb=" O ASP F 547 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR F 552 " --> pdb=" O VAL F 548 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 29 removed outlier: 3.751A pdb=" N SER G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE G 24 " --> pdb=" O SER G 20 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU G 25 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN G 28 " --> pdb=" O PHE G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 36 No H-bonds generated for 'chain 'G' and resid 34 through 36' Processing helix chain 'G' and resid 37 through 44 removed outlier: 3.547A pdb=" N CYS G 41 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 43 " --> pdb=" O LEU G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 62 removed outlier: 3.691A pdb=" N ALA G 61 " --> pdb=" O LEU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 85 removed outlier: 3.582A pdb=" N VAL G 70 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP G 73 " --> pdb=" O HIS G 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP G 74 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR G 76 " --> pdb=" O SER G 72 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR G 83 " --> pdb=" O SER G 79 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 114 removed outlier: 3.718A pdb=" N ARG G 96 " --> pdb=" O TRP G 92 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG G 97 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER G 98 " --> pdb=" O SER G 94 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR G 99 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR G 106 " --> pdb=" O SER G 102 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET G 107 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG G 108 " --> pdb=" O ALA G 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET G 109 " --> pdb=" O GLN G 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR G 110 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 124 removed outlier: 3.813A pdb=" N ALA G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE G 119 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG G 121 " --> pdb=" O ASN G 117 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL G 122 " --> pdb=" O ALA G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 139 Processing helix chain 'G' and resid 154 through 169 removed outlier: 3.686A pdb=" N SER G 158 " --> pdb=" O LYS G 154 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN G 162 " --> pdb=" O SER G 158 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET G 164 " --> pdb=" O GLN G 160 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS G 167 " --> pdb=" O LEU G 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG G 169 " --> pdb=" O LYS G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 182 removed outlier: 4.539A pdb=" N ILE G 180 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU G 181 " --> pdb=" O ILE G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 200 removed outlier: 3.620A pdb=" N GLU G 187 " --> pdb=" O SER G 183 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE G 188 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN G 190 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER G 193 " --> pdb=" O SER G 189 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA G 197 " --> pdb=" O SER G 193 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU G 198 " --> pdb=" O SER G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 249 No H-bonds generated for 'chain 'G' and resid 247 through 249' Processing helix chain 'G' and resid 250 through 271 removed outlier: 3.707A pdb=" N HIS G 258 " --> pdb=" O ILE G 254 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN G 271 " --> pdb=" O CYS G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 428 removed outlier: 3.735A pdb=" N GLY G 426 " --> pdb=" O PHE G 422 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG G 427 " --> pdb=" O GLN G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 434 removed outlier: 3.559A pdb=" N GLN G 434 " --> pdb=" O ASP G 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 430 through 434' Processing helix chain 'G' and resid 458 through 469 removed outlier: 4.287A pdb=" N MET G 462 " --> pdb=" O VAL G 458 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN G 467 " --> pdb=" O LYS G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 469 through 477 removed outlier: 3.875A pdb=" N PHE G 474 " --> pdb=" O GLU G 470 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN G 475 " --> pdb=" O SER G 471 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 487 No H-bonds generated for 'chain 'G' and resid 485 through 487' Processing helix chain 'G' and resid 497 through 502 Processing helix chain 'G' and resid 502 through 508 Processing helix chain 'G' and resid 520 through 524 removed outlier: 3.629A pdb=" N PHE G 523 " --> pdb=" O SER G 520 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL G 524 " --> pdb=" O HIS G 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 520 through 524' Processing helix chain 'G' and resid 527 through 537 removed outlier: 3.527A pdb=" N ALA G 532 " --> pdb=" O LEU G 528 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR G 536 " --> pdb=" O ALA G 532 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN G 537 " --> pdb=" O ALA G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 553 removed outlier: 3.988A pdb=" N VAL G 543 " --> pdb=" O SER G 539 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS G 551 " --> pdb=" O ASP G 547 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR G 552 " --> pdb=" O VAL G 548 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 29 removed outlier: 3.751A pdb=" N SER H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE H 24 " --> pdb=" O SER H 20 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU H 25 " --> pdb=" O ILE H 21 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU H 27 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN H 28 " --> pdb=" O PHE H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 36 No H-bonds generated for 'chain 'H' and resid 34 through 36' Processing helix chain 'H' and resid 37 through 44 removed outlier: 3.548A pdb=" N CYS H 41 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 62 removed outlier: 3.691A pdb=" N ALA H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 85 removed outlier: 3.582A pdb=" N VAL H 70 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP H 73 " --> pdb=" O HIS H 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP H 74 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG H 75 " --> pdb=" O LEU H 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR H 76 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR H 83 " --> pdb=" O SER H 79 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP H 85 " --> pdb=" O ALA H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 114 removed outlier: 3.718A pdb=" N ARG H 96 " --> pdb=" O TRP H 92 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG H 97 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER H 98 " --> pdb=" O SER H 94 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR H 99 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP H 101 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR H 106 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET H 107 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET H 109 " --> pdb=" O GLN H 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR H 110 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 124 removed outlier: 3.814A pdb=" N ALA H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE H 119 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN H 120 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG H 121 " --> pdb=" O ASN H 117 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL H 122 " --> pdb=" O ALA H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 139 Processing helix chain 'H' and resid 154 through 169 removed outlier: 3.686A pdb=" N SER H 158 " --> pdb=" O LYS H 154 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET H 164 " --> pdb=" O GLN H 160 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS H 167 " --> pdb=" O LEU H 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG H 169 " --> pdb=" O LYS H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 182 removed outlier: 4.539A pdb=" N ILE H 180 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU H 181 " --> pdb=" O ILE H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 200 removed outlier: 3.621A pdb=" N GLU H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE H 188 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN H 190 " --> pdb=" O GLN H 186 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER H 193 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA H 197 " --> pdb=" O SER H 193 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 249 No H-bonds generated for 'chain 'H' and resid 247 through 249' Processing helix chain 'H' and resid 250 through 271 removed outlier: 3.707A pdb=" N HIS H 258 " --> pdb=" O ILE H 254 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN H 271 " --> pdb=" O CYS H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 420 through 428 removed outlier: 3.735A pdb=" N GLY H 426 " --> pdb=" O PHE H 422 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG H 427 " --> pdb=" O GLN H 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 434 removed outlier: 3.559A pdb=" N GLN H 434 " --> pdb=" O ASP H 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 430 through 434' Processing helix chain 'H' and resid 458 through 469 removed outlier: 4.286A pdb=" N MET H 462 " --> pdb=" O VAL H 458 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN H 467 " --> pdb=" O LYS H 463 " (cutoff:3.500A) Processing helix chain 'H' and resid 469 through 477 removed outlier: 3.875A pdb=" N PHE H 474 " --> pdb=" O GLU H 470 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN H 475 " --> pdb=" O SER H 471 " (cutoff:3.500A) Processing helix chain 'H' and resid 485 through 487 No H-bonds generated for 'chain 'H' and resid 485 through 487' Processing helix chain 'H' and resid 497 through 502 Processing helix chain 'H' and resid 502 through 508 Processing helix chain 'H' and resid 520 through 524 removed outlier: 3.628A pdb=" N PHE H 523 " --> pdb=" O SER H 520 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL H 524 " --> pdb=" O HIS H 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 520 through 524' Processing helix chain 'H' and resid 527 through 537 removed outlier: 3.527A pdb=" N ALA H 532 " --> pdb=" O LEU H 528 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR H 536 " --> pdb=" O ALA H 532 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN H 537 " --> pdb=" O ALA H 533 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 553 removed outlier: 3.987A pdb=" N VAL H 543 " --> pdb=" O SER H 539 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS H 551 " --> pdb=" O ASP H 547 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR H 552 " --> pdb=" O VAL H 548 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 29 removed outlier: 3.751A pdb=" N SER I 22 " --> pdb=" O GLU I 18 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE I 24 " --> pdb=" O SER I 20 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU I 25 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU I 27 " --> pdb=" O LEU I 23 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN I 28 " --> pdb=" O PHE I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 36 No H-bonds generated for 'chain 'I' and resid 34 through 36' Processing helix chain 'I' and resid 37 through 44 removed outlier: 3.548A pdb=" N CYS I 41 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER I 42 " --> pdb=" O THR I 38 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU I 43 " --> pdb=" O LEU I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 62 removed outlier: 3.690A pdb=" N ALA I 61 " --> pdb=" O LEU I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 85 removed outlier: 3.582A pdb=" N VAL I 70 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP I 73 " --> pdb=" O HIS I 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP I 74 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR I 76 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR I 83 " --> pdb=" O SER I 79 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP I 85 " --> pdb=" O ALA I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 114 removed outlier: 3.718A pdb=" N ARG I 96 " --> pdb=" O TRP I 92 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG I 97 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER I 98 " --> pdb=" O SER I 94 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR I 99 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP I 101 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR I 106 " --> pdb=" O SER I 102 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET I 107 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET I 109 " --> pdb=" O GLN I 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR I 110 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 124 removed outlier: 3.814A pdb=" N ALA I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE I 119 " --> pdb=" O LEU I 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG I 121 " --> pdb=" O ASN I 117 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL I 122 " --> pdb=" O ALA I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 139 Processing helix chain 'I' and resid 154 through 169 removed outlier: 3.685A pdb=" N SER I 158 " --> pdb=" O LYS I 154 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN I 162 " --> pdb=" O SER I 158 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET I 164 " --> pdb=" O GLN I 160 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS I 167 " --> pdb=" O LEU I 163 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG I 169 " --> pdb=" O LYS I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 182 removed outlier: 4.538A pdb=" N ILE I 180 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU I 181 " --> pdb=" O ILE I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 200 removed outlier: 3.619A pdb=" N GLU I 187 " --> pdb=" O SER I 183 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE I 188 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN I 190 " --> pdb=" O GLN I 186 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER I 193 " --> pdb=" O SER I 189 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA I 197 " --> pdb=" O SER I 193 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU I 198 " --> pdb=" O SER I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 249 No H-bonds generated for 'chain 'I' and resid 247 through 249' Processing helix chain 'I' and resid 250 through 271 removed outlier: 3.707A pdb=" N HIS I 258 " --> pdb=" O ILE I 254 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN I 271 " --> pdb=" O CYS I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 420 through 428 removed outlier: 3.734A pdb=" N GLY I 426 " --> pdb=" O PHE I 422 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG I 427 " --> pdb=" O GLN I 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 430 through 434 removed outlier: 3.559A pdb=" N GLN I 434 " --> pdb=" O ASP I 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 430 through 434' Processing helix chain 'I' and resid 458 through 469 removed outlier: 4.287A pdb=" N MET I 462 " --> pdb=" O VAL I 458 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN I 467 " --> pdb=" O LYS I 463 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 477 removed outlier: 3.875A pdb=" N PHE I 474 " --> pdb=" O GLU I 470 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN I 475 " --> pdb=" O SER I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 485 through 487 No H-bonds generated for 'chain 'I' and resid 485 through 487' Processing helix chain 'I' and resid 497 through 502 Processing helix chain 'I' and resid 502 through 508 Processing helix chain 'I' and resid 520 through 524 removed outlier: 3.629A pdb=" N PHE I 523 " --> pdb=" O SER I 520 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL I 524 " --> pdb=" O HIS I 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 520 through 524' Processing helix chain 'I' and resid 527 through 537 removed outlier: 3.527A pdb=" N ALA I 532 " --> pdb=" O LEU I 528 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR I 536 " --> pdb=" O ALA I 532 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN I 537 " --> pdb=" O ALA I 533 " (cutoff:3.500A) Processing helix chain 'I' and resid 539 through 553 removed outlier: 3.987A pdb=" N VAL I 543 " --> pdb=" O SER I 539 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS I 551 " --> pdb=" O ASP I 547 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR I 552 " --> pdb=" O VAL I 548 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 29 removed outlier: 3.752A pdb=" N SER J 22 " --> pdb=" O GLU J 18 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE J 24 " --> pdb=" O SER J 20 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU J 25 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU J 27 " --> pdb=" O LEU J 23 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN J 28 " --> pdb=" O PHE J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 36 No H-bonds generated for 'chain 'J' and resid 34 through 36' Processing helix chain 'J' and resid 37 through 44 removed outlier: 3.548A pdb=" N CYS J 41 " --> pdb=" O GLN J 37 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER J 42 " --> pdb=" O THR J 38 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU J 43 " --> pdb=" O LEU J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 62 removed outlier: 3.692A pdb=" N ALA J 61 " --> pdb=" O LEU J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 85 removed outlier: 3.582A pdb=" N VAL J 70 " --> pdb=" O SER J 66 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP J 73 " --> pdb=" O HIS J 69 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP J 74 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR J 76 " --> pdb=" O SER J 72 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR J 83 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP J 85 " --> pdb=" O ALA J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 114 removed outlier: 3.719A pdb=" N ARG J 96 " --> pdb=" O TRP J 92 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG J 97 " --> pdb=" O GLY J 93 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER J 98 " --> pdb=" O SER J 94 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR J 99 " --> pdb=" O TYR J 95 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP J 101 " --> pdb=" O ARG J 97 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR J 106 " --> pdb=" O SER J 102 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET J 107 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET J 109 " --> pdb=" O GLN J 105 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR J 110 " --> pdb=" O THR J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 124 removed outlier: 3.813A pdb=" N ALA J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE J 119 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN J 120 " --> pdb=" O LEU J 116 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG J 121 " --> pdb=" O ASN J 117 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL J 122 " --> pdb=" O ALA J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 139 Processing helix chain 'J' and resid 154 through 169 removed outlier: 3.686A pdb=" N SER J 158 " --> pdb=" O LYS J 154 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN J 162 " --> pdb=" O SER J 158 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET J 164 " --> pdb=" O GLN J 160 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS J 167 " --> pdb=" O LEU J 163 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG J 169 " --> pdb=" O LYS J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 182 removed outlier: 4.539A pdb=" N ILE J 180 " --> pdb=" O THR J 176 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU J 181 " --> pdb=" O ILE J 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 200 removed outlier: 3.620A pdb=" N GLU J 187 " --> pdb=" O SER J 183 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE J 188 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN J 190 " --> pdb=" O GLN J 186 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER J 193 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA J 197 " --> pdb=" O SER J 193 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU J 198 " --> pdb=" O SER J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 249 No H-bonds generated for 'chain 'J' and resid 247 through 249' Processing helix chain 'J' and resid 250 through 271 removed outlier: 3.707A pdb=" N HIS J 258 " --> pdb=" O ILE J 254 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN J 271 " --> pdb=" O CYS J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 420 through 428 removed outlier: 3.735A pdb=" N GLY J 426 " --> pdb=" O PHE J 422 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG J 427 " --> pdb=" O GLN J 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 434 removed outlier: 3.560A pdb=" N GLN J 434 " --> pdb=" O ASP J 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 430 through 434' Processing helix chain 'J' and resid 458 through 469 removed outlier: 4.287A pdb=" N MET J 462 " --> pdb=" O VAL J 458 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN J 467 " --> pdb=" O LYS J 463 " (cutoff:3.500A) Processing helix chain 'J' and resid 469 through 477 removed outlier: 3.875A pdb=" N PHE J 474 " --> pdb=" O GLU J 470 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN J 475 " --> pdb=" O SER J 471 " (cutoff:3.500A) Processing helix chain 'J' and resid 485 through 487 No H-bonds generated for 'chain 'J' and resid 485 through 487' Processing helix chain 'J' and resid 497 through 502 Processing helix chain 'J' and resid 502 through 508 Processing helix chain 'J' and resid 520 through 524 removed outlier: 3.629A pdb=" N PHE J 523 " --> pdb=" O SER J 520 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL J 524 " --> pdb=" O HIS J 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 520 through 524' Processing helix chain 'J' and resid 527 through 537 removed outlier: 3.527A pdb=" N ALA J 532 " --> pdb=" O LEU J 528 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR J 536 " --> pdb=" O ALA J 532 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN J 537 " --> pdb=" O ALA J 533 " (cutoff:3.500A) Processing helix chain 'J' and resid 539 through 553 removed outlier: 3.987A pdb=" N VAL J 543 " --> pdb=" O SER J 539 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS J 551 " --> pdb=" O ASP J 547 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR J 552 " --> pdb=" O VAL J 548 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 29 removed outlier: 3.751A pdb=" N SER K 22 " --> pdb=" O GLU K 18 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE K 24 " --> pdb=" O SER K 20 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU K 25 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU K 27 " --> pdb=" O LEU K 23 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN K 28 " --> pdb=" O PHE K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 36 No H-bonds generated for 'chain 'K' and resid 34 through 36' Processing helix chain 'K' and resid 37 through 44 removed outlier: 3.548A pdb=" N CYS K 41 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER K 42 " --> pdb=" O THR K 38 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU K 43 " --> pdb=" O LEU K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 62 removed outlier: 3.691A pdb=" N ALA K 61 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 85 removed outlier: 3.582A pdb=" N VAL K 70 " --> pdb=" O SER K 66 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP K 73 " --> pdb=" O HIS K 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP K 74 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG K 75 " --> pdb=" O LEU K 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR K 76 " --> pdb=" O SER K 72 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR K 83 " --> pdb=" O SER K 79 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP K 85 " --> pdb=" O ALA K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 114 removed outlier: 3.718A pdb=" N ARG K 96 " --> pdb=" O TRP K 92 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG K 97 " --> pdb=" O GLY K 93 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR K 99 " --> pdb=" O TYR K 95 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP K 101 " --> pdb=" O ARG K 97 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR K 106 " --> pdb=" O SER K 102 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET K 107 " --> pdb=" O TRP K 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET K 109 " --> pdb=" O GLN K 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR K 110 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 124 removed outlier: 3.813A pdb=" N ALA K 118 " --> pdb=" O LEU K 114 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE K 119 " --> pdb=" O LEU K 115 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG K 121 " --> pdb=" O ASN K 117 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL K 122 " --> pdb=" O ALA K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 139 Processing helix chain 'K' and resid 154 through 169 removed outlier: 3.685A pdb=" N SER K 158 " --> pdb=" O LYS K 154 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN K 162 " --> pdb=" O SER K 158 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET K 164 " --> pdb=" O GLN K 160 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS K 167 " --> pdb=" O LEU K 163 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG K 169 " --> pdb=" O LYS K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 182 removed outlier: 4.538A pdb=" N ILE K 180 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU K 181 " --> pdb=" O ILE K 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 200 removed outlier: 3.620A pdb=" N GLU K 187 " --> pdb=" O SER K 183 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE K 188 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN K 190 " --> pdb=" O GLN K 186 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER K 193 " --> pdb=" O SER K 189 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA K 197 " --> pdb=" O SER K 193 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU K 198 " --> pdb=" O SER K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 249 No H-bonds generated for 'chain 'K' and resid 247 through 249' Processing helix chain 'K' and resid 250 through 271 removed outlier: 3.706A pdb=" N HIS K 258 " --> pdb=" O ILE K 254 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN K 271 " --> pdb=" O CYS K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 428 removed outlier: 3.735A pdb=" N GLY K 426 " --> pdb=" O PHE K 422 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG K 427 " --> pdb=" O GLN K 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 430 through 434 removed outlier: 3.560A pdb=" N GLN K 434 " --> pdb=" O ASP K 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 430 through 434' Processing helix chain 'K' and resid 458 through 469 removed outlier: 4.286A pdb=" N MET K 462 " --> pdb=" O VAL K 458 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN K 467 " --> pdb=" O LYS K 463 " (cutoff:3.500A) Processing helix chain 'K' and resid 469 through 477 removed outlier: 3.874A pdb=" N PHE K 474 " --> pdb=" O GLU K 470 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN K 475 " --> pdb=" O SER K 471 " (cutoff:3.500A) Processing helix chain 'K' and resid 485 through 487 No H-bonds generated for 'chain 'K' and resid 485 through 487' Processing helix chain 'K' and resid 497 through 502 Processing helix chain 'K' and resid 502 through 508 Processing helix chain 'K' and resid 520 through 524 removed outlier: 3.628A pdb=" N PHE K 523 " --> pdb=" O SER K 520 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL K 524 " --> pdb=" O HIS K 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 520 through 524' Processing helix chain 'K' and resid 527 through 537 removed outlier: 3.526A pdb=" N ALA K 532 " --> pdb=" O LEU K 528 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR K 536 " --> pdb=" O ALA K 532 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN K 537 " --> pdb=" O ALA K 533 " (cutoff:3.500A) Processing helix chain 'K' and resid 539 through 553 removed outlier: 3.987A pdb=" N VAL K 543 " --> pdb=" O SER K 539 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS K 551 " --> pdb=" O ASP K 547 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR K 552 " --> pdb=" O VAL K 548 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 29 removed outlier: 3.751A pdb=" N SER L 22 " --> pdb=" O GLU L 18 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE L 24 " --> pdb=" O SER L 20 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU L 25 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU L 27 " --> pdb=" O LEU L 23 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN L 28 " --> pdb=" O PHE L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 36 No H-bonds generated for 'chain 'L' and resid 34 through 36' Processing helix chain 'L' and resid 37 through 44 removed outlier: 3.547A pdb=" N CYS L 41 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER L 42 " --> pdb=" O THR L 38 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU L 43 " --> pdb=" O LEU L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 62 removed outlier: 3.691A pdb=" N ALA L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 85 removed outlier: 3.582A pdb=" N VAL L 70 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP L 73 " --> pdb=" O HIS L 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP L 74 " --> pdb=" O VAL L 70 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR L 76 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR L 83 " --> pdb=" O SER L 79 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP L 85 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 114 removed outlier: 3.718A pdb=" N ARG L 96 " --> pdb=" O TRP L 92 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG L 97 " --> pdb=" O GLY L 93 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER L 98 " --> pdb=" O SER L 94 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR L 99 " --> pdb=" O TYR L 95 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP L 101 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR L 106 " --> pdb=" O SER L 102 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET L 107 " --> pdb=" O TRP L 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG L 108 " --> pdb=" O ALA L 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET L 109 " --> pdb=" O GLN L 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR L 110 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 124 removed outlier: 3.814A pdb=" N ALA L 118 " --> pdb=" O LEU L 114 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE L 119 " --> pdb=" O LEU L 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN L 120 " --> pdb=" O LEU L 116 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG L 121 " --> pdb=" O ASN L 117 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL L 122 " --> pdb=" O ALA L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 139 Processing helix chain 'L' and resid 154 through 169 removed outlier: 3.686A pdb=" N SER L 158 " --> pdb=" O LYS L 154 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN L 162 " --> pdb=" O SER L 158 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET L 164 " --> pdb=" O GLN L 160 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS L 167 " --> pdb=" O LEU L 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG L 169 " --> pdb=" O LYS L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 182 removed outlier: 4.538A pdb=" N ILE L 180 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 200 removed outlier: 3.621A pdb=" N GLU L 187 " --> pdb=" O SER L 183 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE L 188 " --> pdb=" O VAL L 184 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN L 190 " --> pdb=" O GLN L 186 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER L 193 " --> pdb=" O SER L 189 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA L 197 " --> pdb=" O SER L 193 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU L 198 " --> pdb=" O SER L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 249 No H-bonds generated for 'chain 'L' and resid 247 through 249' Processing helix chain 'L' and resid 250 through 271 removed outlier: 3.706A pdb=" N HIS L 258 " --> pdb=" O ILE L 254 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN L 271 " --> pdb=" O CYS L 267 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 428 removed outlier: 3.734A pdb=" N GLY L 426 " --> pdb=" O PHE L 422 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG L 427 " --> pdb=" O GLN L 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 430 through 434 removed outlier: 3.559A pdb=" N GLN L 434 " --> pdb=" O ASP L 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 430 through 434' Processing helix chain 'L' and resid 458 through 469 removed outlier: 4.287A pdb=" N MET L 462 " --> pdb=" O VAL L 458 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN L 467 " --> pdb=" O LYS L 463 " (cutoff:3.500A) Processing helix chain 'L' and resid 469 through 477 removed outlier: 3.875A pdb=" N PHE L 474 " --> pdb=" O GLU L 470 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN L 475 " --> pdb=" O SER L 471 " (cutoff:3.500A) Processing helix chain 'L' and resid 485 through 487 No H-bonds generated for 'chain 'L' and resid 485 through 487' Processing helix chain 'L' and resid 497 through 502 Processing helix chain 'L' and resid 502 through 508 Processing helix chain 'L' and resid 520 through 524 removed outlier: 3.628A pdb=" N PHE L 523 " --> pdb=" O SER L 520 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL L 524 " --> pdb=" O HIS L 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 520 through 524' Processing helix chain 'L' and resid 527 through 537 removed outlier: 3.527A pdb=" N ALA L 532 " --> pdb=" O LEU L 528 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR L 536 " --> pdb=" O ALA L 532 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN L 537 " --> pdb=" O ALA L 533 " (cutoff:3.500A) Processing helix chain 'L' and resid 539 through 553 removed outlier: 3.987A pdb=" N VAL L 543 " --> pdb=" O SER L 539 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS L 551 " --> pdb=" O ASP L 547 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR L 552 " --> pdb=" O VAL L 548 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.668A pdb=" N LYS A 148 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N ARG A 225 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR A 210 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 235 through 236 Processing sheet with id=AA3, first strand: chain 'A' and resid 435 through 436 removed outlier: 3.864A pdb=" N THR A 436 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA A 277 " --> pdb=" O THR A 436 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 449 through 451 removed outlier: 3.863A pdb=" N THR L 436 " --> pdb=" O THR L 275 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA L 277 " --> pdb=" O THR L 436 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 481 through 483 removed outlier: 5.460A pdb=" N VAL A 482 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.668A pdb=" N LYS B 148 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N ARG B 225 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR B 210 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 235 through 236 Processing sheet with id=AA8, first strand: chain 'B' and resid 435 through 436 removed outlier: 3.863A pdb=" N THR B 436 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B 277 " --> pdb=" O THR B 436 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 481 through 483 removed outlier: 5.460A pdb=" N VAL B 482 " --> pdb=" O LEU B 490 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.667A pdb=" N LYS C 148 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N ARG C 225 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR C 210 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 235 through 236 Processing sheet with id=AB3, first strand: chain 'C' and resid 435 through 436 removed outlier: 3.863A pdb=" N THR C 436 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA C 277 " --> pdb=" O THR C 436 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 481 through 483 removed outlier: 5.460A pdb=" N VAL C 482 " --> pdb=" O LEU C 490 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 202 through 203 removed outlier: 6.668A pdb=" N LYS D 148 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N ARG D 225 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR D 210 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 235 through 236 Processing sheet with id=AB7, first strand: chain 'D' and resid 435 through 436 removed outlier: 3.863A pdb=" N THR D 436 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA D 277 " --> pdb=" O THR D 436 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 481 through 483 removed outlier: 5.459A pdb=" N VAL D 482 " --> pdb=" O LEU D 490 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.668A pdb=" N LYS E 148 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N ARG E 225 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR E 210 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 235 through 236 Processing sheet with id=AC2, first strand: chain 'E' and resid 435 through 436 removed outlier: 3.863A pdb=" N THR E 436 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA E 277 " --> pdb=" O THR E 436 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 481 through 483 removed outlier: 5.460A pdb=" N VAL E 482 " --> pdb=" O LEU E 490 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.667A pdb=" N LYS F 148 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N ARG F 225 " --> pdb=" O LYS F 148 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR F 210 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 235 through 236 Processing sheet with id=AC6, first strand: chain 'F' and resid 435 through 436 removed outlier: 3.863A pdb=" N THR F 436 " --> pdb=" O THR F 275 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA F 277 " --> pdb=" O THR F 436 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 481 through 483 removed outlier: 5.460A pdb=" N VAL F 482 " --> pdb=" O LEU F 490 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.668A pdb=" N LYS G 148 " --> pdb=" O ARG G 225 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N ARG G 225 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR G 210 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 235 through 236 Processing sheet with id=AD1, first strand: chain 'G' and resid 435 through 436 removed outlier: 3.864A pdb=" N THR G 436 " --> pdb=" O THR G 275 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA G 277 " --> pdb=" O THR G 436 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 481 through 483 removed outlier: 5.460A pdb=" N VAL G 482 " --> pdb=" O LEU G 490 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 202 through 203 removed outlier: 6.667A pdb=" N LYS H 148 " --> pdb=" O ARG H 225 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N ARG H 225 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR H 210 " --> pdb=" O LEU H 220 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 235 through 236 Processing sheet with id=AD5, first strand: chain 'H' and resid 435 through 436 removed outlier: 3.863A pdb=" N THR H 436 " --> pdb=" O THR H 275 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA H 277 " --> pdb=" O THR H 436 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 481 through 483 removed outlier: 5.459A pdb=" N VAL H 482 " --> pdb=" O LEU H 490 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.667A pdb=" N LYS I 148 " --> pdb=" O ARG I 225 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N ARG I 225 " --> pdb=" O LYS I 148 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR I 210 " --> pdb=" O LEU I 220 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 235 through 236 Processing sheet with id=AD9, first strand: chain 'I' and resid 435 through 436 removed outlier: 3.864A pdb=" N THR I 436 " --> pdb=" O THR I 275 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA I 277 " --> pdb=" O THR I 436 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 481 through 483 removed outlier: 5.460A pdb=" N VAL I 482 " --> pdb=" O LEU I 490 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 202 through 203 removed outlier: 6.667A pdb=" N LYS J 148 " --> pdb=" O ARG J 225 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N ARG J 225 " --> pdb=" O LYS J 148 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR J 210 " --> pdb=" O LEU J 220 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 235 through 236 Processing sheet with id=AE4, first strand: chain 'J' and resid 435 through 436 removed outlier: 3.863A pdb=" N THR J 436 " --> pdb=" O THR J 275 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA J 277 " --> pdb=" O THR J 436 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 481 through 483 removed outlier: 5.459A pdb=" N VAL J 482 " --> pdb=" O LEU J 490 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 202 through 203 removed outlier: 6.667A pdb=" N LYS K 148 " --> pdb=" O ARG K 225 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N ARG K 225 " --> pdb=" O LYS K 148 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR K 210 " --> pdb=" O LEU K 220 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 235 through 236 Processing sheet with id=AE8, first strand: chain 'K' and resid 435 through 436 removed outlier: 3.863A pdb=" N THR K 436 " --> pdb=" O THR K 275 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA K 277 " --> pdb=" O THR K 436 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 481 through 483 removed outlier: 5.459A pdb=" N VAL K 482 " --> pdb=" O LEU K 490 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 202 through 203 removed outlier: 6.667A pdb=" N LYS L 148 " --> pdb=" O ARG L 225 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N ARG L 225 " --> pdb=" O LYS L 148 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR L 210 " --> pdb=" O LEU L 220 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 235 through 236 Processing sheet with id=AF3, first strand: chain 'L' and resid 481 through 483 removed outlier: 5.460A pdb=" N VAL L 482 " --> pdb=" O LEU L 490 " (cutoff:3.500A) 1452 hydrogen bonds defined for protein. 4284 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: 14.94 Time building geometry restraints manager: 15.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 12561 1.34 - 1.46: 9732 1.46 - 1.58: 17763 1.58 - 1.70: 0 1.70 - 1.82: 324 Bond restraints: 40380 Sorted by residual: bond pdb=" C ILE F 200 " pdb=" N PRO F 201 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.46e+00 bond pdb=" C ILE H 200 " pdb=" N PRO H 201 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.40e+00 bond pdb=" C ILE K 200 " pdb=" N PRO K 201 " ideal model delta sigma weight residual 1.334 1.397 -0.064 2.34e-02 1.83e+03 7.38e+00 bond pdb=" C ILE E 200 " pdb=" N PRO E 201 " ideal model delta sigma weight residual 1.334 1.397 -0.064 2.34e-02 1.83e+03 7.38e+00 bond pdb=" C ILE G 200 " pdb=" N PRO G 201 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.30e+00 ... (remaining 40375 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.00: 790 106.00 - 113.00: 22030 113.00 - 120.00: 14138 120.00 - 127.00: 17457 127.00 - 134.00: 437 Bond angle restraints: 54852 Sorted by residual: angle pdb=" C PRO H 86 " pdb=" N GLU H 87 " pdb=" CA GLU H 87 " ideal model delta sigma weight residual 122.08 127.49 -5.41 1.47e+00 4.63e-01 1.35e+01 angle pdb=" C PRO D 86 " pdb=" N GLU D 87 " pdb=" CA GLU D 87 " ideal model delta sigma weight residual 122.08 127.49 -5.41 1.47e+00 4.63e-01 1.35e+01 angle pdb=" C PRO K 86 " pdb=" N GLU K 87 " pdb=" CA GLU K 87 " ideal model delta sigma weight residual 122.08 127.47 -5.39 1.47e+00 4.63e-01 1.35e+01 angle pdb=" N PRO B 441 " pdb=" CA PRO B 441 " pdb=" C PRO B 441 " ideal model delta sigma weight residual 111.33 116.57 -5.24 1.43e+00 4.89e-01 1.34e+01 angle pdb=" N PRO A 441 " pdb=" CA PRO A 441 " pdb=" C PRO A 441 " ideal model delta sigma weight residual 111.33 116.57 -5.24 1.43e+00 4.89e-01 1.34e+01 ... (remaining 54847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 23216 15.02 - 30.03: 748 30.03 - 45.05: 204 45.05 - 60.07: 12 60.07 - 75.08: 24 Dihedral angle restraints: 24204 sinusoidal: 9504 harmonic: 14700 Sorted by residual: dihedral pdb=" CA ILE I 455 " pdb=" C ILE I 455 " pdb=" N PRO I 456 " pdb=" CA PRO I 456 " ideal model delta harmonic sigma weight residual 180.00 150.79 29.21 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA ILE A 455 " pdb=" C ILE A 455 " pdb=" N PRO A 456 " pdb=" CA PRO A 456 " ideal model delta harmonic sigma weight residual 180.00 150.80 29.20 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA ILE E 455 " pdb=" C ILE E 455 " pdb=" N PRO E 456 " pdb=" CA PRO E 456 " ideal model delta harmonic sigma weight residual 180.00 150.81 29.19 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 24201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 5973 0.089 - 0.178: 339 0.178 - 0.267: 12 0.267 - 0.356: 0 0.356 - 0.446: 12 Chirality restraints: 6336 Sorted by residual: chirality pdb=" CB ILE L 455 " pdb=" CA ILE L 455 " pdb=" CG1 ILE L 455 " pdb=" CG2 ILE L 455 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CB ILE C 455 " pdb=" CA ILE C 455 " pdb=" CG1 ILE C 455 " pdb=" CG2 ILE C 455 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CB ILE I 455 " pdb=" CA ILE I 455 " pdb=" CG1 ILE I 455 " pdb=" CG2 ILE I 455 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.89e+00 ... (remaining 6333 not shown) Planarity restraints: 6852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 455 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.12e+00 pdb=" N PRO G 456 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO G 456 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO G 456 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 455 " -0.047 5.00e-02 4.00e+02 7.12e-02 8.10e+00 pdb=" N PRO J 456 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO J 456 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO J 456 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 455 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO C 456 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 456 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 456 " -0.039 5.00e-02 4.00e+02 ... (remaining 6849 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 11435 2.82 - 3.34: 35688 3.34 - 3.86: 61759 3.86 - 4.38: 70535 4.38 - 4.90: 121120 Nonbonded interactions: 300537 Sorted by model distance: nonbonded pdb=" O LEU B 535 " pdb=" OG SER B 539 " model vdw 2.302 2.440 nonbonded pdb=" O LEU G 535 " pdb=" OG SER G 539 " model vdw 2.302 2.440 nonbonded pdb=" O LEU J 535 " pdb=" OG SER J 539 " model vdw 2.302 2.440 nonbonded pdb=" O LEU K 535 " pdb=" OG SER K 539 " model vdw 2.302 2.440 nonbonded pdb=" O LEU H 535 " pdb=" OG SER H 539 " model vdw 2.302 2.440 ... (remaining 300532 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set refine NCS operators NCS operators will be refined. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 4.160 Check model and map are aligned: 0.560 Set scattering table: 0.500 Process input model: 99.570 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 40380 Z= 0.208 Angle : 0.714 8.474 54852 Z= 0.397 Chirality : 0.048 0.446 6336 Planarity : 0.006 0.071 6852 Dihedral : 9.197 75.082 14700 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.08), residues: 4908 helix: -4.18 (0.04), residues: 2316 sheet: -0.95 (0.31), residues: 288 loop : -2.22 (0.11), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 74 HIS 0.009 0.002 HIS L 40 PHE 0.008 0.001 PHE D 217 TYR 0.018 0.001 TYR J 199 ARG 0.005 0.001 ARG E 540 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ILE cc_start: 0.8456 (tt) cc_final: 0.8178 (mm) REVERT: A 32 SER cc_start: 0.9135 (t) cc_final: 0.8835 (p) REVERT: A 35 ARG cc_start: 0.8695 (ttp-170) cc_final: 0.7547 (mmt180) REVERT: A 45 ASN cc_start: 0.9272 (t0) cc_final: 0.8931 (t0) REVERT: A 50 PHE cc_start: 0.9589 (m-10) cc_final: 0.9277 (m-80) REVERT: A 77 TYR cc_start: 0.9127 (t80) cc_final: 0.8552 (t80) REVERT: A 97 ARG cc_start: 0.8840 (mtp85) cc_final: 0.8354 (mmp-170) REVERT: A 101 ASP cc_start: 0.9523 (t70) cc_final: 0.9279 (t70) REVERT: A 133 ARG cc_start: 0.9014 (mtt-85) cc_final: 0.8415 (mtp180) REVERT: A 146 VAL cc_start: 0.9020 (t) cc_final: 0.7880 (t) REVERT: A 153 HIS cc_start: 0.8859 (m-70) cc_final: 0.8493 (p90) REVERT: A 154 LYS cc_start: 0.9424 (tttt) cc_final: 0.9166 (tppt) REVERT: A 159 ILE cc_start: 0.9492 (mm) cc_final: 0.9263 (mm) REVERT: A 164 MET cc_start: 0.8799 (mmm) cc_final: 0.8547 (mpp) REVERT: A 203 TYR cc_start: 0.8804 (t80) cc_final: 0.8338 (t80) REVERT: A 232 THR cc_start: 0.9355 (p) cc_final: 0.8918 (t) REVERT: A 237 LEU cc_start: 0.9083 (tp) cc_final: 0.8871 (tp) REVERT: A 248 GLN cc_start: 0.9378 (tp40) cc_final: 0.9147 (tp40) REVERT: A 256 SER cc_start: 0.8938 (t) cc_final: 0.8675 (p) REVERT: A 268 GLN cc_start: 0.9268 (mt0) cc_final: 0.9039 (mm110) REVERT: A 427 ARG cc_start: 0.9032 (mmt180) cc_final: 0.8608 (tpt-90) REVERT: A 433 LEU cc_start: 0.9406 (mt) cc_final: 0.8851 (mt) REVERT: A 460 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8608 (mm-30) REVERT: A 462 MET cc_start: 0.9420 (mtt) cc_final: 0.9156 (ptp) REVERT: A 485 ASN cc_start: 0.7990 (m-40) cc_final: 0.7624 (m-40) REVERT: A 490 LEU cc_start: 0.9163 (mt) cc_final: 0.8454 (mp) REVERT: A 497 ASP cc_start: 0.8825 (t0) cc_final: 0.8429 (t0) REVERT: A 515 GLN cc_start: 0.9138 (mp10) cc_final: 0.8817 (pm20) REVERT: A 516 MET cc_start: 0.9215 (mmm) cc_final: 0.8986 (tpp) REVERT: A 520 SER cc_start: 0.8794 (t) cc_final: 0.8572 (p) REVERT: A 523 PHE cc_start: 0.9552 (m-10) cc_final: 0.9155 (m-10) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.1826 time to fit residues: 55.5619 Evaluate side-chains 220 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 415 optimal weight: 20.0000 chunk 372 optimal weight: 20.0000 chunk 206 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 251 optimal weight: 20.0000 chunk 199 optimal weight: 20.0000 chunk 385 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 234 optimal weight: 20.0000 chunk 287 optimal weight: 20.0000 chunk 446 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN F 113 HIS ** F 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 40380 Z= 0.204 Angle : 0.613 5.960 54852 Z= 0.332 Chirality : 0.042 0.231 6336 Planarity : 0.006 0.067 6852 Dihedral : 4.991 26.196 5436 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.27 % Allowed : 1.60 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.10), residues: 4908 helix: -2.15 (0.08), residues: 2568 sheet: -0.68 (0.31), residues: 288 loop : -1.51 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 103 HIS 0.004 0.001 HIS E 69 PHE 0.010 0.001 PHE L 49 TYR 0.015 0.002 TYR B 477 ARG 0.010 0.001 ARG H 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8998 Ramachandran restraints generated. 4499 Oldfield, 0 Emsley, 4499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8998 Ramachandran restraints generated. 4499 Oldfield, 0 Emsley, 4499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 ILE cc_start: 0.8417 (tt) cc_final: 0.8149 (mm) REVERT: F 28 GLN cc_start: 0.9202 (mt0) cc_final: 0.8986 (mt0) REVERT: F 32 SER cc_start: 0.9216 (t) cc_final: 0.8858 (m) REVERT: F 35 ARG cc_start: 0.8230 (ttp-170) cc_final: 0.7737 (tpt170) REVERT: F 37 GLN cc_start: 0.8795 (mm110) cc_final: 0.8078 (mm110) REVERT: F 49 PHE cc_start: 0.9497 (t80) cc_final: 0.8808 (t80) REVERT: F 53 LEU cc_start: 0.9331 (mt) cc_final: 0.8796 (mt) REVERT: F 60 ASN cc_start: 0.9568 (m110) cc_final: 0.9332 (m-40) REVERT: F 68 ASP cc_start: 0.9547 (m-30) cc_final: 0.9067 (p0) REVERT: F 69 HIS cc_start: 0.9055 (m90) cc_final: 0.8643 (m90) REVERT: F 73 ASP cc_start: 0.9337 (p0) cc_final: 0.8820 (p0) REVERT: F 77 TYR cc_start: 0.9197 (t80) cc_final: 0.8651 (t80) REVERT: F 84 ARG cc_start: 0.5004 (ttt180) cc_final: 0.4623 (ttm170) REVERT: F 88 LYS cc_start: 0.9490 (mmtp) cc_final: 0.9020 (mttt) REVERT: F 96 ARG cc_start: 0.8811 (mmt180) cc_final: 0.8155 (mmt-90) REVERT: F 97 ARG cc_start: 0.9005 (mtp85) cc_final: 0.8266 (mmp-170) REVERT: F 101 ASP cc_start: 0.9517 (t70) cc_final: 0.9258 (t70) REVERT: F 154 LYS cc_start: 0.9376 (tttt) cc_final: 0.9060 (tppt) REVERT: F 164 MET cc_start: 0.8862 (mmm) cc_final: 0.8566 (mpp) REVERT: F 180 ILE cc_start: 0.8697 (mp) cc_final: 0.7969 (mp) REVERT: F 203 TYR cc_start: 0.8802 (t80) cc_final: 0.8151 (t80) REVERT: F 237 LEU cc_start: 0.9056 (tp) cc_final: 0.8792 (tp) REVERT: F 248 GLN cc_start: 0.9421 (tp40) cc_final: 0.9095 (tp40) REVERT: F 251 TYR cc_start: 0.8886 (t80) cc_final: 0.8583 (t80) REVERT: F 254 ILE cc_start: 0.9109 (mt) cc_final: 0.8855 (mt) REVERT: F 256 SER cc_start: 0.9145 (t) cc_final: 0.8832 (p) REVERT: F 268 GLN cc_start: 0.9248 (mt0) cc_final: 0.8998 (mm-40) REVERT: F 423 GLN cc_start: 0.9162 (mt0) cc_final: 0.8901 (mt0) REVERT: F 427 ARG cc_start: 0.8947 (mmt180) cc_final: 0.8643 (tpt-90) REVERT: F 433 LEU cc_start: 0.9273 (mt) cc_final: 0.9042 (mt) REVERT: F 460 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8577 (mm-30) REVERT: F 469 TRP cc_start: 0.8919 (m100) cc_final: 0.8533 (m100) REVERT: F 472 GLU cc_start: 0.9232 (tp30) cc_final: 0.8534 (tp30) REVERT: F 473 MET cc_start: 0.9484 (mmp) cc_final: 0.8678 (mmp) REVERT: F 477 TYR cc_start: 0.9307 (m-10) cc_final: 0.8948 (m-10) REVERT: F 496 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7849 (tm-30) REVERT: F 515 GLN cc_start: 0.9208 (mp10) cc_final: 0.8851 (pm20) REVERT: F 519 ILE cc_start: 0.8706 (mm) cc_final: 0.8484 (mm) outliers start: 1 outliers final: 0 residues processed: 242 average time/residue: 0.1642 time to fit residues: 47.2671 Evaluate side-chains 194 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 248 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 chunk 371 optimal weight: 0.9990 chunk 304 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 447 optimal weight: 7.9990 chunk 483 optimal weight: 9.9990 chunk 398 optimal weight: 20.0000 chunk 443 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 359 optimal weight: 7.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN C 423 GLN ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 40380 Z= 0.229 Angle : 0.633 7.294 54852 Z= 0.341 Chirality : 0.041 0.215 6336 Planarity : 0.006 0.069 6852 Dihedral : 4.913 25.441 5436 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.27 % Allowed : 1.60 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.11), residues: 4908 helix: -1.01 (0.09), residues: 2604 sheet: -0.22 (0.40), residues: 168 loop : -1.27 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 85 HIS 0.008 0.002 HIS G 56 PHE 0.013 0.002 PHE J 422 TYR 0.044 0.002 TYR B 67 ARG 0.008 0.001 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 244 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 ILE cc_start: 0.8318 (tt) cc_final: 0.8022 (mm) REVERT: C 28 GLN cc_start: 0.9095 (mt0) cc_final: 0.8892 (mt0) REVERT: C 32 SER cc_start: 0.9159 (t) cc_final: 0.8827 (m) REVERT: C 35 ARG cc_start: 0.8399 (ttp-170) cc_final: 0.7544 (mmt180) REVERT: C 49 PHE cc_start: 0.9496 (t80) cc_final: 0.8917 (t80) REVERT: C 50 PHE cc_start: 0.9628 (m-80) cc_final: 0.9373 (m-80) REVERT: C 53 LEU cc_start: 0.9363 (mt) cc_final: 0.8984 (mt) REVERT: C 60 ASN cc_start: 0.9495 (m110) cc_final: 0.9215 (m110) REVERT: C 68 ASP cc_start: 0.9565 (m-30) cc_final: 0.9161 (p0) REVERT: C 77 TYR cc_start: 0.9256 (t80) cc_final: 0.8859 (t80) REVERT: C 84 ARG cc_start: 0.4948 (ttt180) cc_final: 0.4716 (ttt180) REVERT: C 86 PRO cc_start: 0.9320 (Cg_exo) cc_final: 0.8854 (Cg_endo) REVERT: C 87 GLU cc_start: 0.9097 (pt0) cc_final: 0.8654 (pm20) REVERT: C 88 LYS cc_start: 0.9519 (mmtp) cc_final: 0.9175 (mttt) REVERT: C 97 ARG cc_start: 0.9078 (mtp85) cc_final: 0.8410 (mmp-170) REVERT: C 101 ASP cc_start: 0.9529 (t70) cc_final: 0.9263 (t70) REVERT: C 133 ARG cc_start: 0.9173 (mtt-85) cc_final: 0.8716 (mtt-85) REVERT: C 154 LYS cc_start: 0.9413 (tttt) cc_final: 0.9068 (tppt) REVERT: C 164 MET cc_start: 0.8904 (mmm) cc_final: 0.8606 (mpp) REVERT: C 170 LEU cc_start: 0.8564 (mt) cc_final: 0.7890 (tt) REVERT: C 203 TYR cc_start: 0.8656 (t80) cc_final: 0.8047 (t80) REVERT: C 224 LYS cc_start: 0.9433 (mmtm) cc_final: 0.9209 (mmtm) REVERT: C 232 THR cc_start: 0.9309 (p) cc_final: 0.8972 (t) REVERT: C 248 GLN cc_start: 0.9454 (tp40) cc_final: 0.9238 (tp40) REVERT: C 423 GLN cc_start: 0.9333 (mt0) cc_final: 0.9100 (mt0) REVERT: C 427 ARG cc_start: 0.9040 (mmt180) cc_final: 0.8677 (tpt-90) REVERT: C 433 LEU cc_start: 0.9264 (mt) cc_final: 0.9047 (mt) REVERT: C 460 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8616 (mm-30) REVERT: C 472 GLU cc_start: 0.9173 (tp30) cc_final: 0.8649 (tp30) REVERT: C 477 TYR cc_start: 0.9289 (m-10) cc_final: 0.8645 (m-10) REVERT: C 515 GLN cc_start: 0.9155 (mp10) cc_final: 0.8799 (pm20) outliers start: 1 outliers final: 0 residues processed: 244 average time/residue: 0.1535 time to fit residues: 44.9577 Evaluate side-chains 192 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 442 optimal weight: 9.9990 chunk 336 optimal weight: 6.9990 chunk 232 optimal weight: 0.0470 chunk 49 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 300 optimal weight: 9.9990 chunk 449 optimal weight: 9.9990 chunk 475 optimal weight: 4.9990 chunk 234 optimal weight: 20.0000 chunk 425 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 GLN ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS E 162 GLN ** E 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40380 Z= 0.201 Angle : 0.608 6.098 54852 Z= 0.324 Chirality : 0.041 0.189 6336 Planarity : 0.005 0.065 6852 Dihedral : 4.841 24.325 5436 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.12), residues: 4908 helix: -0.53 (0.10), residues: 2604 sheet: -0.35 (0.39), residues: 168 loop : -1.11 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 85 HIS 0.007 0.001 HIS B 56 PHE 0.014 0.001 PHE E 54 TYR 0.015 0.002 TYR L 58 ARG 0.004 0.000 ARG H 179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 12 ILE cc_start: 0.8370 (tt) cc_final: 0.8095 (mm) REVERT: E 24 PHE cc_start: 0.8264 (m-80) cc_final: 0.7818 (m-10) REVERT: E 31 TYR cc_start: 0.7949 (t80) cc_final: 0.7699 (t80) REVERT: E 35 ARG cc_start: 0.8492 (ttp-170) cc_final: 0.7598 (mmt180) REVERT: E 49 PHE cc_start: 0.9534 (t80) cc_final: 0.9121 (t80) REVERT: E 53 LEU cc_start: 0.9412 (mt) cc_final: 0.8994 (mt) REVERT: E 60 ASN cc_start: 0.9438 (m110) cc_final: 0.9216 (m110) REVERT: E 68 ASP cc_start: 0.9336 (m-30) cc_final: 0.8920 (p0) REVERT: E 77 TYR cc_start: 0.9182 (t80) cc_final: 0.8929 (t80) REVERT: E 83 THR cc_start: 0.9370 (p) cc_final: 0.9138 (p) REVERT: E 84 ARG cc_start: 0.6455 (ttt180) cc_final: 0.6143 (tpt90) REVERT: E 86 PRO cc_start: 0.9276 (Cg_exo) cc_final: 0.8850 (Cg_endo) REVERT: E 87 GLU cc_start: 0.8980 (pt0) cc_final: 0.8548 (pm20) REVERT: E 88 LYS cc_start: 0.9485 (mmtp) cc_final: 0.9189 (mptt) REVERT: E 89 GLU cc_start: 0.8456 (mp0) cc_final: 0.8069 (mp0) REVERT: E 96 ARG cc_start: 0.8740 (mmt180) cc_final: 0.8306 (mmt-90) REVERT: E 97 ARG cc_start: 0.9079 (mtp85) cc_final: 0.8603 (mmp-170) REVERT: E 113 HIS cc_start: 0.9357 (t70) cc_final: 0.9136 (t70) REVERT: E 153 HIS cc_start: 0.9363 (m90) cc_final: 0.8216 (p90) REVERT: E 154 LYS cc_start: 0.9376 (tttt) cc_final: 0.8998 (tppt) REVERT: E 232 THR cc_start: 0.9293 (p) cc_final: 0.8919 (t) REVERT: E 248 GLN cc_start: 0.9441 (tp40) cc_final: 0.9152 (tp40) REVERT: E 427 ARG cc_start: 0.9084 (mmt180) cc_final: 0.8675 (tpt-90) REVERT: E 460 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8729 (tp30) REVERT: E 463 LYS cc_start: 0.9183 (ptmt) cc_final: 0.8713 (ptmt) REVERT: E 469 TRP cc_start: 0.8988 (m100) cc_final: 0.8696 (m100) REVERT: E 473 MET cc_start: 0.9413 (mmp) cc_final: 0.9202 (mmp) REVERT: E 513 LEU cc_start: 0.8892 (mt) cc_final: 0.8655 (mt) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1586 time to fit residues: 44.1640 Evaluate side-chains 190 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 396 optimal weight: 0.0870 chunk 269 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 354 optimal weight: 6.9990 chunk 196 optimal weight: 8.9990 chunk 405 optimal weight: 0.0970 chunk 328 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 242 optimal weight: 0.0770 chunk 426 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 HIS B 69 HIS B 268 GLN ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40380 Z= 0.175 Angle : 0.594 7.474 54852 Z= 0.308 Chirality : 0.041 0.200 6336 Planarity : 0.005 0.061 6852 Dihedral : 4.633 23.141 5436 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.12), residues: 4908 helix: -0.51 (0.10), residues: 2700 sheet: -0.69 (0.36), residues: 168 loop : -1.21 (0.15), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 137 HIS 0.003 0.001 HIS L 69 PHE 0.020 0.002 PHE I 50 TYR 0.013 0.001 TYR H 477 ARG 0.006 0.001 ARG F 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6544 Ramachandran restraints generated. 3272 Oldfield, 0 Emsley, 3272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6544 Ramachandran restraints generated. 3272 Oldfield, 0 Emsley, 3272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 12 ILE cc_start: 0.8410 (tt) cc_final: 0.8133 (mm) REVERT: B 19 LEU cc_start: 0.9445 (tp) cc_final: 0.9193 (tp) REVERT: B 25 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8846 (tm-30) REVERT: B 26 ILE cc_start: 0.9666 (mt) cc_final: 0.9430 (mt) REVERT: B 35 ARG cc_start: 0.8551 (ttp-170) cc_final: 0.7838 (ttm-80) REVERT: B 49 PHE cc_start: 0.9466 (t80) cc_final: 0.8858 (t80) REVERT: B 53 LEU cc_start: 0.9403 (mt) cc_final: 0.8900 (mt) REVERT: B 58 TYR cc_start: 0.9375 (t80) cc_final: 0.9172 (t80) REVERT: B 60 ASN cc_start: 0.9505 (m110) cc_final: 0.9229 (m110) REVERT: B 67 TYR cc_start: 0.8575 (t80) cc_final: 0.8230 (t80) REVERT: B 68 ASP cc_start: 0.9326 (m-30) cc_final: 0.8964 (p0) REVERT: B 84 ARG cc_start: 0.6574 (ttt180) cc_final: 0.5967 (tpt90) REVERT: B 87 GLU cc_start: 0.8942 (pt0) cc_final: 0.8531 (pm20) REVERT: B 88 LYS cc_start: 0.9484 (mmtp) cc_final: 0.9206 (mttt) REVERT: B 97 ARG cc_start: 0.9084 (mtp85) cc_final: 0.8577 (mmp-170) REVERT: B 131 TYR cc_start: 0.7829 (t80) cc_final: 0.7538 (t80) REVERT: B 133 ARG cc_start: 0.9012 (mtt-85) cc_final: 0.8252 (mtp180) REVERT: B 136 ASP cc_start: 0.9594 (t0) cc_final: 0.9330 (t0) REVERT: B 153 HIS cc_start: 0.9338 (m90) cc_final: 0.8084 (p90) REVERT: B 154 LYS cc_start: 0.9365 (tttt) cc_final: 0.8976 (tppt) REVERT: B 203 TYR cc_start: 0.8848 (t80) cc_final: 0.8500 (t80) REVERT: B 243 PHE cc_start: 0.8149 (m-10) cc_final: 0.7833 (m-10) REVERT: B 247 ILE cc_start: 0.9693 (mt) cc_final: 0.9486 (mt) REVERT: B 248 GLN cc_start: 0.9369 (tp40) cc_final: 0.9083 (tp40) REVERT: B 427 ARG cc_start: 0.9081 (mmt180) cc_final: 0.8623 (tpt-90) REVERT: B 460 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8633 (tp30) REVERT: B 463 LYS cc_start: 0.9254 (ptmt) cc_final: 0.8796 (ptmt) REVERT: B 465 LEU cc_start: 0.9542 (mp) cc_final: 0.9294 (mp) REVERT: B 469 TRP cc_start: 0.9119 (m100) cc_final: 0.8644 (m100) REVERT: B 473 MET cc_start: 0.9422 (mmp) cc_final: 0.9142 (mmp) REVERT: B 513 LEU cc_start: 0.8979 (mt) cc_final: 0.8679 (mt) REVERT: B 517 GLU cc_start: 0.9105 (tp30) cc_final: 0.8878 (tp30) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1522 time to fit residues: 40.6243 Evaluate side-chains 199 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 160 optimal weight: 0.4980 chunk 428 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 279 optimal weight: 0.0050 chunk 117 optimal weight: 4.9990 chunk 476 optimal weight: 8.9990 chunk 395 optimal weight: 6.9990 chunk 220 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 249 optimal weight: 20.0000 overall best weight: 2.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 40380 Z= 0.170 Angle : 0.589 5.862 54852 Z= 0.305 Chirality : 0.041 0.205 6336 Planarity : 0.004 0.056 6852 Dihedral : 4.628 22.809 5436 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.12), residues: 4908 helix: -0.52 (0.09), residues: 2712 sheet: -0.94 (0.36), residues: 168 loop : -1.39 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 137 HIS 0.002 0.001 HIS D 15 PHE 0.017 0.002 PHE I 450 TYR 0.018 0.001 TYR G 251 ARG 0.003 0.000 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6544 Ramachandran restraints generated. 3272 Oldfield, 0 Emsley, 3272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6544 Ramachandran restraints generated. 3272 Oldfield, 0 Emsley, 3272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 12 ILE cc_start: 0.8428 (tt) cc_final: 0.8137 (mm) REVERT: B 19 LEU cc_start: 0.9408 (tp) cc_final: 0.9183 (tp) REVERT: B 35 ARG cc_start: 0.8534 (ttp-170) cc_final: 0.7638 (mmt180) REVERT: B 49 PHE cc_start: 0.9499 (t80) cc_final: 0.8990 (t80) REVERT: B 53 LEU cc_start: 0.9413 (mt) cc_final: 0.8929 (mt) REVERT: B 59 LYS cc_start: 0.9500 (ttmt) cc_final: 0.9070 (tmtt) REVERT: B 60 ASN cc_start: 0.9468 (m110) cc_final: 0.9167 (m110) REVERT: B 68 ASP cc_start: 0.9323 (m-30) cc_final: 0.8941 (p0) REVERT: B 74 TRP cc_start: 0.9129 (t60) cc_final: 0.8505 (t60) REVERT: B 84 ARG cc_start: 0.6616 (ttt180) cc_final: 0.6014 (tpt90) REVERT: B 87 GLU cc_start: 0.8895 (pt0) cc_final: 0.8558 (pm20) REVERT: B 88 LYS cc_start: 0.9416 (mmtp) cc_final: 0.9143 (mttt) REVERT: B 96 ARG cc_start: 0.8766 (mmt180) cc_final: 0.8566 (mmt-90) REVERT: B 97 ARG cc_start: 0.9177 (mtp85) cc_final: 0.8754 (mmp-170) REVERT: B 131 TYR cc_start: 0.7843 (t80) cc_final: 0.7560 (t80) REVERT: B 133 ARG cc_start: 0.9016 (mtt-85) cc_final: 0.8338 (ttm170) REVERT: B 153 HIS cc_start: 0.9344 (m90) cc_final: 0.7913 (p90) REVERT: B 154 LYS cc_start: 0.9371 (tttt) cc_final: 0.8930 (tppt) REVERT: B 164 MET cc_start: 0.8595 (mmm) cc_final: 0.8365 (ppp) REVERT: B 224 LYS cc_start: 0.9316 (mmtm) cc_final: 0.9081 (mmtm) REVERT: B 237 LEU cc_start: 0.9190 (tp) cc_final: 0.8891 (tp) REVERT: B 248 GLN cc_start: 0.9343 (tp40) cc_final: 0.9018 (tp40) REVERT: B 250 MET cc_start: 0.8692 (ptp) cc_final: 0.8436 (ptp) REVERT: B 251 TYR cc_start: 0.9001 (t80) cc_final: 0.8749 (t80) REVERT: B 255 MET cc_start: 0.9232 (mmm) cc_final: 0.8857 (mmm) REVERT: B 256 SER cc_start: 0.9362 (t) cc_final: 0.9073 (p) REVERT: B 268 GLN cc_start: 0.7875 (mm110) cc_final: 0.7438 (mm-40) REVERT: B 427 ARG cc_start: 0.9086 (mmt180) cc_final: 0.8645 (tpt-90) REVERT: B 460 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8764 (tp30) REVERT: B 463 LYS cc_start: 0.9277 (ptmt) cc_final: 0.8828 (ptmt) REVERT: B 469 TRP cc_start: 0.8903 (m100) cc_final: 0.8696 (m100) REVERT: B 473 MET cc_start: 0.9438 (mmp) cc_final: 0.9162 (mmp) REVERT: B 513 LEU cc_start: 0.8928 (mt) cc_final: 0.8708 (mt) REVERT: B 516 MET cc_start: 0.9188 (mmm) cc_final: 0.8967 (mmm) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1605 time to fit residues: 42.3282 Evaluate side-chains 202 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 458 optimal weight: 0.0370 chunk 53 optimal weight: 20.0000 chunk 271 optimal weight: 5.9990 chunk 347 optimal weight: 0.7980 chunk 269 optimal weight: 8.9990 chunk 400 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 474 optimal weight: 20.0000 chunk 296 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.6636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 40380 Z= 0.167 Angle : 0.593 5.796 54852 Z= 0.312 Chirality : 0.042 0.205 6336 Planarity : 0.004 0.049 6852 Dihedral : 4.740 22.992 5436 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.12), residues: 4908 helix: -0.55 (0.09), residues: 2712 sheet: -1.26 (0.35), residues: 168 loop : -1.38 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 74 HIS 0.001 0.000 HIS K 56 PHE 0.015 0.001 PHE J 50 TYR 0.018 0.001 TYR B 251 ARG 0.008 0.001 ARG H 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6544 Ramachandran restraints generated. 3272 Oldfield, 0 Emsley, 3272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6544 Ramachandran restraints generated. 3272 Oldfield, 0 Emsley, 3272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 ILE cc_start: 0.8365 (tt) cc_final: 0.8070 (mm) REVERT: B 35 ARG cc_start: 0.8553 (ttp-170) cc_final: 0.7705 (tpp-160) REVERT: B 49 PHE cc_start: 0.9458 (t80) cc_final: 0.9004 (t80) REVERT: B 53 LEU cc_start: 0.9418 (mt) cc_final: 0.9010 (mt) REVERT: B 58 TYR cc_start: 0.9083 (t80) cc_final: 0.8833 (t80) REVERT: B 59 LYS cc_start: 0.9510 (ttmt) cc_final: 0.9096 (tmtt) REVERT: B 60 ASN cc_start: 0.9468 (m110) cc_final: 0.9175 (m110) REVERT: B 68 ASP cc_start: 0.9325 (m-30) cc_final: 0.8972 (p0) REVERT: B 78 GLU cc_start: 0.9199 (mp0) cc_final: 0.8713 (mp0) REVERT: B 87 GLU cc_start: 0.8883 (pt0) cc_final: 0.8560 (pm20) REVERT: B 97 ARG cc_start: 0.9115 (mtp85) cc_final: 0.8608 (mmp-170) REVERT: B 113 HIS cc_start: 0.9311 (t70) cc_final: 0.9089 (t70) REVERT: B 131 TYR cc_start: 0.7857 (t80) cc_final: 0.7579 (t80) REVERT: B 133 ARG cc_start: 0.9055 (mtt-85) cc_final: 0.8314 (mtp180) REVERT: B 153 HIS cc_start: 0.9351 (m90) cc_final: 0.7882 (p90) REVERT: B 154 LYS cc_start: 0.9381 (tttt) cc_final: 0.8926 (tppt) REVERT: B 180 ILE cc_start: 0.8761 (pt) cc_final: 0.8485 (mp) REVERT: B 203 TYR cc_start: 0.8997 (t80) cc_final: 0.8670 (t80) REVERT: B 224 LYS cc_start: 0.9352 (mmtm) cc_final: 0.9070 (mmtm) REVERT: B 237 LEU cc_start: 0.9085 (tp) cc_final: 0.8831 (tp) REVERT: B 248 GLN cc_start: 0.9247 (tp40) cc_final: 0.8989 (tp40) REVERT: B 251 TYR cc_start: 0.9050 (t80) cc_final: 0.8688 (t80) REVERT: B 254 ILE cc_start: 0.9391 (mp) cc_final: 0.9140 (mp) REVERT: B 255 MET cc_start: 0.9153 (mmm) cc_final: 0.8736 (mmm) REVERT: B 256 SER cc_start: 0.9350 (t) cc_final: 0.9047 (p) REVERT: B 265 LYS cc_start: 0.6390 (tttt) cc_final: 0.5958 (tmmt) REVERT: B 427 ARG cc_start: 0.9061 (mmt180) cc_final: 0.8632 (tpt-90) REVERT: B 460 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8692 (tp30) REVERT: B 463 LYS cc_start: 0.9345 (ptmt) cc_final: 0.8767 (ptmt) REVERT: B 473 MET cc_start: 0.9429 (mmp) cc_final: 0.9173 (mmp) REVERT: B 513 LEU cc_start: 0.8914 (mt) cc_final: 0.8689 (mt) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1510 time to fit residues: 39.9700 Evaluate side-chains 189 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 293 optimal weight: 9.9990 chunk 189 optimal weight: 4.9990 chunk 283 optimal weight: 9.9990 chunk 142 optimal weight: 0.0170 chunk 93 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 301 optimal weight: 0.1980 chunk 323 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 44 optimal weight: 0.0770 chunk 372 optimal weight: 20.0000 overall best weight: 2.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 GLN ** E 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.6806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 40380 Z= 0.168 Angle : 0.600 7.092 54852 Z= 0.308 Chirality : 0.042 0.215 6336 Planarity : 0.004 0.052 6852 Dihedral : 4.621 21.481 5436 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.11), residues: 4908 helix: -0.36 (0.10), residues: 2664 sheet: -1.33 (0.35), residues: 168 loop : -1.48 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP K 74 HIS 0.002 0.000 HIS J 40 PHE 0.011 0.001 PHE F 100 TYR 0.017 0.001 TYR B 251 ARG 0.008 0.001 ARG L 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6544 Ramachandran restraints generated. 3272 Oldfield, 0 Emsley, 3272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6544 Ramachandran restraints generated. 3272 Oldfield, 0 Emsley, 3272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 12 ILE cc_start: 0.8396 (tt) cc_final: 0.8086 (mm) REVERT: E 35 ARG cc_start: 0.8546 (ttp-170) cc_final: 0.7716 (mmt180) REVERT: E 49 PHE cc_start: 0.9532 (t80) cc_final: 0.9098 (t80) REVERT: E 53 LEU cc_start: 0.9453 (mt) cc_final: 0.9013 (mt) REVERT: E 58 TYR cc_start: 0.9097 (t80) cc_final: 0.8873 (t80) REVERT: E 60 ASN cc_start: 0.9434 (m110) cc_final: 0.9206 (m110) REVERT: E 68 ASP cc_start: 0.9493 (m-30) cc_final: 0.8823 (p0) REVERT: E 87 GLU cc_start: 0.8915 (pt0) cc_final: 0.8557 (pm20) REVERT: E 97 ARG cc_start: 0.9165 (mtp85) cc_final: 0.8714 (mmp-170) REVERT: E 113 HIS cc_start: 0.9295 (t70) cc_final: 0.9075 (t70) REVERT: E 131 TYR cc_start: 0.7863 (t80) cc_final: 0.7492 (t80) REVERT: E 133 ARG cc_start: 0.9126 (mtt-85) cc_final: 0.8460 (ttm170) REVERT: E 153 HIS cc_start: 0.9368 (m90) cc_final: 0.7863 (p90) REVERT: E 154 LYS cc_start: 0.9397 (tttt) cc_final: 0.8937 (tppt) REVERT: E 180 ILE cc_start: 0.8869 (pt) cc_final: 0.8616 (mp) REVERT: E 224 LYS cc_start: 0.9317 (mmtm) cc_final: 0.9013 (mmtm) REVERT: E 237 LEU cc_start: 0.9028 (tp) cc_final: 0.8784 (tp) REVERT: E 248 GLN cc_start: 0.9191 (tp40) cc_final: 0.8919 (tp40) REVERT: E 251 TYR cc_start: 0.9083 (t80) cc_final: 0.8695 (t80) REVERT: E 255 MET cc_start: 0.9062 (mmm) cc_final: 0.8631 (mmm) REVERT: E 256 SER cc_start: 0.9329 (t) cc_final: 0.9004 (p) REVERT: E 427 ARG cc_start: 0.9038 (mmt180) cc_final: 0.8729 (tmt170) REVERT: E 460 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8864 (mm-30) REVERT: E 463 LYS cc_start: 0.9300 (ptmt) cc_final: 0.9056 (pttt) REVERT: E 469 TRP cc_start: 0.8823 (m100) cc_final: 0.8591 (m-10) REVERT: E 473 MET cc_start: 0.9432 (mmp) cc_final: 0.9178 (mmp) REVERT: E 490 LEU cc_start: 0.8872 (mp) cc_final: 0.8646 (mt) REVERT: E 516 MET cc_start: 0.9102 (mmm) cc_final: 0.8268 (tpp) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1471 time to fit residues: 38.4805 Evaluate side-chains 210 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 431 optimal weight: 5.9990 chunk 454 optimal weight: 6.9990 chunk 414 optimal weight: 9.9990 chunk 441 optimal weight: 8.9990 chunk 265 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 346 optimal weight: 3.9990 chunk 135 optimal weight: 0.0070 chunk 399 optimal weight: 2.9990 chunk 417 optimal weight: 0.0570 chunk 440 optimal weight: 0.3980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 HIS ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.7044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 40380 Z= 0.155 Angle : 0.598 6.855 54852 Z= 0.307 Chirality : 0.043 0.212 6336 Planarity : 0.006 0.086 6852 Dihedral : 4.619 20.958 5436 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.12), residues: 4908 helix: -0.43 (0.10), residues: 2652 sheet: -2.03 (0.25), residues: 288 loop : -1.39 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 469 HIS 0.003 0.000 HIS E 263 PHE 0.019 0.002 PHE I 50 TYR 0.043 0.002 TYR H 67 ARG 0.006 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6544 Ramachandran restraints generated. 3272 Oldfield, 0 Emsley, 3272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6544 Ramachandran restraints generated. 3272 Oldfield, 0 Emsley, 3272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 ILE cc_start: 0.8380 (tt) cc_final: 0.8101 (mm) REVERT: B 35 ARG cc_start: 0.8512 (ttp-170) cc_final: 0.7683 (mmp-170) REVERT: B 49 PHE cc_start: 0.9463 (t80) cc_final: 0.9042 (t80) REVERT: B 53 LEU cc_start: 0.9417 (mt) cc_final: 0.8989 (mt) REVERT: B 58 TYR cc_start: 0.9183 (t80) cc_final: 0.8784 (t80) REVERT: B 59 LYS cc_start: 0.9489 (tttt) cc_final: 0.9143 (tmtt) REVERT: B 60 ASN cc_start: 0.9395 (m110) cc_final: 0.9139 (m110) REVERT: B 62 LEU cc_start: 0.9535 (mp) cc_final: 0.9163 (mp) REVERT: B 68 ASP cc_start: 0.9388 (m-30) cc_final: 0.8886 (p0) REVERT: B 73 ASP cc_start: 0.8750 (p0) cc_final: 0.8248 (p0) REVERT: B 78 GLU cc_start: 0.9179 (mp0) cc_final: 0.8874 (mp0) REVERT: B 87 GLU cc_start: 0.8916 (pt0) cc_final: 0.8398 (pm20) REVERT: B 96 ARG cc_start: 0.8891 (mmt180) cc_final: 0.8414 (mmt-90) REVERT: B 97 ARG cc_start: 0.9152 (mtp85) cc_final: 0.8733 (mmp-170) REVERT: B 113 HIS cc_start: 0.9289 (t70) cc_final: 0.9070 (t70) REVERT: B 131 TYR cc_start: 0.7928 (t80) cc_final: 0.7706 (t80) REVERT: B 133 ARG cc_start: 0.9105 (mtt-85) cc_final: 0.8273 (ttm170) REVERT: B 137 TRP cc_start: 0.9351 (m100) cc_final: 0.8598 (m100) REVERT: B 153 HIS cc_start: 0.9374 (m90) cc_final: 0.8884 (m90) REVERT: B 154 LYS cc_start: 0.9366 (tttt) cc_final: 0.8906 (tppt) REVERT: B 164 MET cc_start: 0.8615 (mmm) cc_final: 0.8196 (mpp) REVERT: B 180 ILE cc_start: 0.8763 (pt) cc_final: 0.8441 (mp) REVERT: B 200 ILE cc_start: 0.9002 (mt) cc_final: 0.8531 (tt) REVERT: B 224 LYS cc_start: 0.9329 (mmtm) cc_final: 0.9008 (mmtm) REVERT: B 232 THR cc_start: 0.9452 (p) cc_final: 0.9162 (t) REVERT: B 237 LEU cc_start: 0.9020 (tp) cc_final: 0.8789 (tp) REVERT: B 251 TYR cc_start: 0.9081 (t80) cc_final: 0.8722 (t80) REVERT: B 255 MET cc_start: 0.9063 (mmm) cc_final: 0.8660 (mmm) REVERT: B 256 SER cc_start: 0.9308 (t) cc_final: 0.8996 (p) REVERT: B 427 ARG cc_start: 0.8998 (mmt180) cc_final: 0.8663 (tmt170) REVERT: B 463 LYS cc_start: 0.9237 (ptmt) cc_final: 0.8870 (pttp) REVERT: B 469 TRP cc_start: 0.8843 (m100) cc_final: 0.8624 (m-10) REVERT: B 473 MET cc_start: 0.9468 (mmp) cc_final: 0.9115 (mmp) REVERT: B 516 MET cc_start: 0.9068 (mmm) cc_final: 0.8336 (mmm) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1528 time to fit residues: 40.1541 Evaluate side-chains 205 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 290 optimal weight: 3.9990 chunk 467 optimal weight: 0.6980 chunk 285 optimal weight: 0.0370 chunk 221 optimal weight: 0.0070 chunk 324 optimal weight: 3.9990 chunk 490 optimal weight: 0.0270 chunk 451 optimal weight: 20.0000 chunk 390 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 301 optimal weight: 0.3980 chunk 239 optimal weight: 0.2980 overall best weight: 0.1534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.7267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 40380 Z= 0.164 Angle : 0.651 7.949 54852 Z= 0.327 Chirality : 0.043 0.203 6336 Planarity : 0.005 0.053 6852 Dihedral : 4.743 20.114 5436 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.12), residues: 4908 helix: -0.53 (0.10), residues: 2592 sheet: -1.48 (0.28), residues: 288 loop : -1.32 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 137 HIS 0.002 0.001 HIS B 113 PHE 0.010 0.001 PHE H 54 TYR 0.013 0.001 TYR B 251 ARG 0.005 0.001 ARG G 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6544 Ramachandran restraints generated. 3272 Oldfield, 0 Emsley, 3272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6544 Ramachandran restraints generated. 3272 Oldfield, 0 Emsley, 3272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 12 ILE cc_start: 0.8429 (tt) cc_final: 0.8151 (mm) REVERT: E 35 ARG cc_start: 0.8426 (ttp-170) cc_final: 0.7835 (mmt180) REVERT: E 49 PHE cc_start: 0.9490 (t80) cc_final: 0.9014 (t80) REVERT: E 53 LEU cc_start: 0.9397 (mt) cc_final: 0.8825 (mt) REVERT: E 58 TYR cc_start: 0.9208 (t80) cc_final: 0.8740 (t80) REVERT: E 59 LYS cc_start: 0.9482 (tttt) cc_final: 0.9118 (tmtt) REVERT: E 62 LEU cc_start: 0.9458 (mp) cc_final: 0.8996 (mp) REVERT: E 73 ASP cc_start: 0.8688 (p0) cc_final: 0.8226 (p0) REVERT: E 74 TRP cc_start: 0.8526 (t60) cc_final: 0.8313 (t60) REVERT: E 87 GLU cc_start: 0.8812 (pt0) cc_final: 0.8548 (pm20) REVERT: E 96 ARG cc_start: 0.8907 (mmt180) cc_final: 0.8177 (mmt-90) REVERT: E 97 ARG cc_start: 0.9145 (mtp85) cc_final: 0.8677 (mmp-170) REVERT: E 106 THR cc_start: 0.9324 (p) cc_final: 0.9044 (p) REVERT: E 107 MET cc_start: 0.9434 (mtt) cc_final: 0.9158 (mmm) REVERT: E 113 HIS cc_start: 0.9259 (t70) cc_final: 0.9015 (t70) REVERT: E 131 TYR cc_start: 0.7926 (t80) cc_final: 0.7642 (t80) REVERT: E 133 ARG cc_start: 0.9159 (mtt-85) cc_final: 0.8369 (ttm170) REVERT: E 137 TRP cc_start: 0.9349 (m100) cc_final: 0.8478 (m100) REVERT: E 154 LYS cc_start: 0.9374 (tttt) cc_final: 0.8866 (tppt) REVERT: E 164 MET cc_start: 0.8615 (mmm) cc_final: 0.8229 (mpp) REVERT: E 180 ILE cc_start: 0.8613 (pt) cc_final: 0.8316 (mp) REVERT: E 200 ILE cc_start: 0.8988 (mt) cc_final: 0.8541 (tt) REVERT: E 224 LYS cc_start: 0.9281 (mmtm) cc_final: 0.8970 (mmtm) REVERT: E 237 LEU cc_start: 0.8922 (tp) cc_final: 0.8678 (tp) REVERT: E 251 TYR cc_start: 0.9028 (t80) cc_final: 0.8644 (t80) REVERT: E 255 MET cc_start: 0.9000 (mmm) cc_final: 0.8739 (mmm) REVERT: E 256 SER cc_start: 0.9248 (t) cc_final: 0.8940 (p) REVERT: E 427 ARG cc_start: 0.8977 (mmt180) cc_final: 0.8663 (tmt170) REVERT: E 433 LEU cc_start: 0.9555 (mt) cc_final: 0.9332 (mt) REVERT: E 450 PHE cc_start: 0.5482 (m-10) cc_final: 0.5067 (m-10) REVERT: E 463 LYS cc_start: 0.9313 (ptmt) cc_final: 0.8943 (pttp) REVERT: E 473 MET cc_start: 0.9470 (mmp) cc_final: 0.9172 (mmp) REVERT: E 484 ASP cc_start: 0.8519 (m-30) cc_final: 0.7816 (p0) REVERT: E 498 THR cc_start: 0.8862 (t) cc_final: 0.8655 (t) REVERT: E 516 MET cc_start: 0.8908 (mmm) cc_final: 0.8339 (mmm) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1587 time to fit residues: 41.1563 Evaluate side-chains 200 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 310 optimal weight: 6.9990 chunk 415 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 359 optimal weight: 0.9980 chunk 57 optimal weight: 0.1980 chunk 108 optimal weight: 8.9990 chunk 390 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 401 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.114603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.095693 restraints weight = 8451.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.099039 restraints weight = 5297.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.101538 restraints weight = 3690.818| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.7306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 40380 Z= 0.196 Angle : 0.647 9.213 54852 Z= 0.326 Chirality : 0.044 0.225 6336 Planarity : 0.006 0.055 6852 Dihedral : 4.911 20.618 5436 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.11), residues: 4908 helix: -0.57 (0.09), residues: 2772 sheet: -1.37 (0.28), residues: 288 loop : -1.60 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 469 HIS 0.003 0.001 HIS B 263 PHE 0.009 0.002 PHE A 54 TYR 0.015 0.002 TYR H 251 ARG 0.005 0.001 ARG L 459 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4489.07 seconds wall clock time: 87 minutes 40.89 seconds (5260.89 seconds total)