Starting phenix.real_space_refine on Sat Mar 7 06:02:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ppi_20437/03_2026/6ppi_20437.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ppi_20437/03_2026/6ppi_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ppi_20437/03_2026/6ppi_20437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ppi_20437/03_2026/6ppi_20437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ppi_20437/03_2026/6ppi_20437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ppi_20437/03_2026/6ppi_20437.map" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39504 Number of models: 1 Model: "" Number of chains: 1 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 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 4.85, per 1000 atoms: 0.12 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.9 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: 1.30 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: 8.64 Time building geometry restraints manager: 4.30 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: 0.00 - 1.69: 53159 1.69 - 3.39: 1341 3.39 - 5.08: 208 5.08 - 6.78: 132 6.78 - 8.47: 12 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 3.040 nonbonded pdb=" O LEU G 535 " pdb=" OG SER G 539 " model vdw 2.302 3.040 nonbonded pdb=" O LEU J 535 " pdb=" OG SER J 539 " model vdw 2.302 3.040 nonbonded pdb=" O LEU K 535 " pdb=" OG SER K 539 " model vdw 2.302 3.040 nonbonded pdb=" O LEU H 535 " pdb=" OG SER H 539 " model vdw 2.302 3.040 ... (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 Time spend for trying shortcut: 0.09 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: 0.370 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 31.630 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.570 ------------------------------------------------------------------------------- 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= 0.171 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 : 4.23 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.79 (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 ARG 0.005 0.001 ARG E 540 TYR 0.018 0.001 TYR J 199 PHE 0.008 0.001 PHE D 217 TRP 0.011 0.002 TRP K 74 HIS 0.009 0.002 HIS L 40 Details of bonding type rmsd covalent geometry : bond 0.00321 (40380) covalent geometry : angle 0.71375 (54852) hydrogen bonds : bond 0.31430 ( 1452) hydrogen bonds : angle 9.89434 ( 4284) *********************** 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 to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.114 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: 0.8177 (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: 0.7546 (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: 0.9276 (m-80) REVERT: A 51 ARG cc_start: 0.9431 (mtt90) cc_final: 0.9185 (mtt180) REVERT: A 77 TYR cc_start: 0.9127 (t80) cc_final: 0.8545 (t80) REVERT: A 97 ARG cc_start: 0.8840 (mtp85) cc_final: 0.8201 (mmt180) 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: 0.8416 (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: 0.8494 (p90) REVERT: A 154 LYS cc_start: 0.9424 (tttt) cc_final: 0.9166 (tppt) REVERT: A 164 MET cc_start: 0.8799 (mmm) cc_final: 0.8552 (mpp) REVERT: A 203 TYR cc_start: 0.8804 (t80) cc_final: 0.8339 (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: 0.9146 (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: 0.8852 (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: 0.8427 (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: 0.8577 (p) REVERT: A 523 PHE cc_start: 0.9552 (m-10) cc_final: 0.9131 (m-10) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.0661 time to fit residues: 20.2512 Evaluate side-chains 220 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 0.0770 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 470 optimal weight: 9.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.113858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.094580 restraints weight = 8376.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.097922 restraints weight = 5110.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100408 restraints weight = 3520.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102389 restraints weight = 2614.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103932 restraints weight = 2017.266| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 40380 Z= 0.187 Angle : 0.661 6.684 54852 Z= 0.357 Chirality : 0.043 0.236 6336 Planarity : 0.007 0.076 6852 Dihedral : 5.236 26.842 5436 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.27 % Allowed : 2.13 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.11), residues: 4908 helix: -1.91 (0.08), residues: 2496 sheet: -0.81 (0.31), residues: 288 loop : -1.45 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 84 TYR 0.018 0.002 TYR B 477 PHE 0.010 0.002 PHE L 217 TRP 0.013 0.002 TRP G 103 HIS 0.005 0.001 HIS E 69 Details of bonding type rmsd covalent geometry : bond 0.00393 (40380) covalent geometry : angle 0.66086 (54852) hydrogen bonds : bond 0.04514 ( 1452) hydrogen bonds : angle 5.58713 ( 4284) *********************** 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 255 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 ILE cc_start: 0.8471 (tt) cc_final: 0.8160 (mm) REVERT: F 25 GLU cc_start: 0.9366 (tm-30) cc_final: 0.9116 (tm-30) REVERT: F 28 GLN cc_start: 0.9166 (mt0) cc_final: 0.8943 (mt0) REVERT: F 32 SER cc_start: 0.9196 (t) cc_final: 0.8881 (m) REVERT: F 35 ARG cc_start: 0.8414 (ttp-170) cc_final: 0.7668 (mmt180) REVERT: F 37 GLN cc_start: 0.8913 (mm110) cc_final: 0.8242 (mm110) REVERT: F 44 ARG cc_start: 0.8895 (mtp85) cc_final: 0.8280 (mtp85) REVERT: F 49 PHE cc_start: 0.9518 (t80) cc_final: 0.8863 (t80) REVERT: F 51 ARG cc_start: 0.9407 (mtt90) cc_final: 0.9144 (mtt-85) REVERT: F 53 LEU cc_start: 0.9407 (mt) cc_final: 0.8867 (mt) REVERT: F 60 ASN cc_start: 0.9520 (m110) cc_final: 0.9279 (m-40) REVERT: F 68 ASP cc_start: 0.9495 (m-30) cc_final: 0.9033 (p0) REVERT: F 69 HIS cc_start: 0.9180 (m90) cc_final: 0.8743 (m90) REVERT: F 73 ASP cc_start: 0.9199 (p0) cc_final: 0.8761 (p0) REVERT: F 77 TYR cc_start: 0.9202 (t80) cc_final: 0.8631 (t80) REVERT: F 79 SER cc_start: 0.9604 (t) cc_final: 0.9364 (p) REVERT: F 88 LYS cc_start: 0.9536 (mmtp) cc_final: 0.9035 (mttt) REVERT: F 97 ARG cc_start: 0.8716 (mtp85) cc_final: 0.8394 (mmp-170) REVERT: F 101 ASP cc_start: 0.9539 (t70) cc_final: 0.9171 (t70) REVERT: F 132 GLU cc_start: 0.9459 (mt-10) cc_final: 0.8834 (mt-10) REVERT: F 146 VAL cc_start: 0.8989 (t) cc_final: 0.7967 (t) REVERT: F 154 LYS cc_start: 0.9471 (tttt) cc_final: 0.9059 (tppt) REVERT: F 164 MET cc_start: 0.8924 (mmm) cc_final: 0.8620 (mpp) REVERT: F 180 ILE cc_start: 0.8835 (mp) cc_final: 0.8231 (mp) REVERT: F 237 LEU cc_start: 0.9091 (tp) cc_final: 0.8846 (tp) REVERT: F 248 GLN cc_start: 0.9519 (tp40) cc_final: 0.9272 (tp40) REVERT: F 251 TYR cc_start: 0.8926 (t80) cc_final: 0.8666 (t80) REVERT: F 254 ILE cc_start: 0.9201 (mt) cc_final: 0.8999 (mt) REVERT: F 256 SER cc_start: 0.9190 (t) cc_final: 0.8883 (p) REVERT: F 271 ASN cc_start: 0.9549 (t0) cc_final: 0.9330 (t0) REVERT: F 423 GLN cc_start: 0.9390 (mt0) cc_final: 0.8852 (mt0) REVERT: F 427 ARG cc_start: 0.9061 (mmt180) cc_final: 0.8634 (tpt-90) REVERT: F 433 LEU cc_start: 0.9299 (mt) cc_final: 0.9085 (mt) REVERT: F 460 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8843 (mm-30) REVERT: F 469 TRP cc_start: 0.8914 (m100) cc_final: 0.8522 (m100) REVERT: F 472 GLU cc_start: 0.9293 (tp30) cc_final: 0.8734 (tp30) REVERT: F 477 TYR cc_start: 0.9323 (m-10) cc_final: 0.8661 (m-10) REVERT: F 496 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: F 515 GLN cc_start: 0.9240 (mp10) cc_final: 0.8836 (pm20) REVERT: F 523 PHE cc_start: 0.9669 (m-10) cc_final: 0.9307 (m-80) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.0693 time to fit residues: 20.6082 Evaluate side-chains 191 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 482 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 306 optimal weight: 9.9990 chunk 172 optimal weight: 0.9980 chunk 319 optimal weight: 7.9990 chunk 324 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 164 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- 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 C 186 GLN C 215 ASN C 488 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.107164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.089379 restraints weight = 8722.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092652 restraints weight = 5103.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.095096 restraints weight = 3451.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.096778 restraints weight = 2514.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098215 restraints weight = 1955.991| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 40380 Z= 0.191 Angle : 0.651 6.510 54852 Z= 0.348 Chirality : 0.042 0.250 6336 Planarity : 0.007 0.074 6852 Dihedral : 5.118 25.453 5436 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.53 % Allowed : 2.13 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.11), residues: 4908 helix: -1.08 (0.09), residues: 2640 sheet: -0.51 (0.39), residues: 168 loop : -1.30 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 459 TYR 0.045 0.003 TYR K 67 PHE 0.014 0.002 PHE C 217 TRP 0.038 0.003 TRP G 85 HIS 0.005 0.001 HIS I 15 Details of bonding type rmsd covalent geometry : bond 0.00388 (40380) covalent geometry : angle 0.65085 (54852) hydrogen bonds : bond 0.03739 ( 1452) hydrogen bonds : angle 5.56984 ( 4284) *********************** 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 251 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 249 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 ILE cc_start: 0.8433 (tt) cc_final: 0.8095 (mm) REVERT: C 32 SER cc_start: 0.9110 (t) cc_final: 0.8750 (m) REVERT: C 35 ARG cc_start: 0.8608 (ttp-170) cc_final: 0.7576 (mmt180) REVERT: C 49 PHE cc_start: 0.9510 (t80) cc_final: 0.9017 (t80) REVERT: C 50 PHE cc_start: 0.9606 (m-80) cc_final: 0.9392 (m-80) REVERT: C 51 ARG cc_start: 0.9384 (mtt90) cc_final: 0.9114 (mtt-85) REVERT: C 53 LEU cc_start: 0.9424 (mt) cc_final: 0.8986 (mt) REVERT: C 60 ASN cc_start: 0.9391 (m110) cc_final: 0.9134 (m-40) REVERT: C 68 ASP cc_start: 0.9449 (m-30) cc_final: 0.9162 (p0) REVERT: C 86 PRO cc_start: 0.9233 (Cg_exo) cc_final: 0.8706 (Cg_endo) REVERT: C 87 GLU cc_start: 0.8971 (pt0) cc_final: 0.8621 (pm20) REVERT: C 88 LYS cc_start: 0.9571 (mmtp) cc_final: 0.9252 (mttt) REVERT: C 89 GLU cc_start: 0.8313 (mp0) cc_final: 0.8087 (mp0) REVERT: C 91 GLN cc_start: 0.9253 (pp30) cc_final: 0.9050 (tm-30) REVERT: C 97 ARG cc_start: 0.9138 (mtp85) cc_final: 0.8475 (mmp-170) REVERT: C 101 ASP cc_start: 0.9550 (t70) cc_final: 0.9244 (t70) REVERT: C 133 ARG cc_start: 0.8975 (mtt-85) cc_final: 0.8315 (mtp180) REVERT: C 146 VAL cc_start: 0.9122 (t) cc_final: 0.8227 (t) REVERT: C 164 MET cc_start: 0.8905 (mmm) cc_final: 0.8648 (mpp) REVERT: C 203 TYR cc_start: 0.8968 (t80) cc_final: 0.8634 (t80) REVERT: C 224 LYS cc_start: 0.9441 (mmtm) cc_final: 0.9186 (mmtm) REVERT: C 237 LEU cc_start: 0.9106 (tp) cc_final: 0.8840 (tp) REVERT: C 423 GLN cc_start: 0.9430 (mt0) cc_final: 0.9202 (mt0) REVERT: C 427 ARG cc_start: 0.9049 (mmt180) cc_final: 0.8661 (tpt-90) REVERT: C 465 LEU cc_start: 0.9453 (mt) cc_final: 0.9212 (mp) REVERT: C 473 MET cc_start: 0.9505 (mmp) cc_final: 0.8868 (mmp) REVERT: C 477 TYR cc_start: 0.9247 (m-10) cc_final: 0.7990 (m-10) REVERT: C 515 GLN cc_start: 0.9083 (mp10) cc_final: 0.8836 (pm20) outliers start: 2 outliers final: 0 residues processed: 250 average time/residue: 0.0604 time to fit residues: 18.1080 Evaluate side-chains 197 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 5 optimal weight: 20.0000 chunk 266 optimal weight: 0.9990 chunk 411 optimal weight: 10.0000 chunk 456 optimal weight: 20.0000 chunk 476 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 482 optimal weight: 0.2980 chunk 336 optimal weight: 0.0270 chunk 215 optimal weight: 9.9990 chunk 338 optimal weight: 4.9990 chunk 477 optimal weight: 0.3980 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN L 215 ASN L 420 ASN L 488 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.094133 restraints weight = 8489.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097569 restraints weight = 5207.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.100116 restraints weight = 3623.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.102027 restraints weight = 2708.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.103433 restraints weight = 2124.259| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40380 Z= 0.127 Angle : 0.614 7.738 54852 Z= 0.323 Chirality : 0.042 0.233 6336 Planarity : 0.007 0.124 6852 Dihedral : 4.929 23.833 5436 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.27 % Allowed : 1.87 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.11), residues: 4908 helix: -0.62 (0.09), residues: 2640 sheet: -0.51 (0.39), residues: 168 loop : -1.22 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 459 TYR 0.014 0.002 TYR F 203 PHE 0.013 0.001 PHE D 54 TRP 0.013 0.002 TRP E 85 HIS 0.007 0.001 HIS H 521 Details of bonding type rmsd covalent geometry : bond 0.00284 (40380) covalent geometry : angle 0.61423 (54852) hydrogen bonds : bond 0.03452 ( 1452) hydrogen bonds : angle 5.16861 ( 4284) *********************** 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 239 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 0.093 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: L 12 ILE cc_start: 0.8432 (tt) cc_final: 0.8058 (mm) REVERT: L 25 GLU cc_start: 0.9398 (tm-30) cc_final: 0.8937 (tm-30) REVERT: L 28 GLN cc_start: 0.9380 (mp10) cc_final: 0.9164 (mp10) REVERT: L 32 SER cc_start: 0.9093 (t) cc_final: 0.8866 (m) REVERT: L 35 ARG cc_start: 0.8490 (ttp-170) cc_final: 0.7664 (mmt180) REVERT: L 43 LEU cc_start: 0.9598 (tp) cc_final: 0.9289 (tp) REVERT: L 49 PHE cc_start: 0.9493 (t80) cc_final: 0.8795 (t80) REVERT: L 50 PHE cc_start: 0.9622 (m-80) cc_final: 0.9368 (m-80) REVERT: L 51 ARG cc_start: 0.9366 (mtt90) cc_final: 0.9038 (mtt-85) REVERT: L 53 LEU cc_start: 0.9358 (mt) cc_final: 0.8898 (mt) REVERT: L 60 ASN cc_start: 0.9470 (m110) cc_final: 0.9194 (m110) REVERT: L 68 ASP cc_start: 0.9423 (m-30) cc_final: 0.9161 (p0) REVERT: L 89 GLU cc_start: 0.8445 (mp0) cc_final: 0.8179 (mp0) REVERT: L 97 ARG cc_start: 0.9109 (mtp85) cc_final: 0.8512 (mmp-170) REVERT: L 113 HIS cc_start: 0.9376 (t70) cc_final: 0.9136 (t70) REVERT: L 146 VAL cc_start: 0.9007 (t) cc_final: 0.8016 (t) REVERT: L 164 MET cc_start: 0.8905 (mmm) cc_final: 0.8634 (mpp) REVERT: L 203 TYR cc_start: 0.9035 (t80) cc_final: 0.8492 (t80) REVERT: L 224 LYS cc_start: 0.9409 (mmtm) cc_final: 0.9124 (mmtm) REVERT: L 237 LEU cc_start: 0.9113 (tp) cc_final: 0.8850 (tp) REVERT: L 248 GLN cc_start: 0.9529 (tp40) cc_final: 0.9318 (tp40) REVERT: L 423 GLN cc_start: 0.9386 (mt0) cc_final: 0.9146 (mt0) REVERT: L 427 ARG cc_start: 0.9035 (mmt180) cc_final: 0.8659 (tpt-90) REVERT: L 460 GLU cc_start: 0.9332 (mm-30) cc_final: 0.8925 (tp30) REVERT: L 465 LEU cc_start: 0.9484 (mt) cc_final: 0.9259 (mp) REVERT: L 473 MET cc_start: 0.9493 (mmp) cc_final: 0.9290 (mmp) REVERT: L 476 THR cc_start: 0.9488 (t) cc_final: 0.8890 (t) REVERT: L 515 GLN cc_start: 0.9096 (mp10) cc_final: 0.8764 (pm20) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.0611 time to fit residues: 17.3064 Evaluate side-chains 196 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 275 optimal weight: 0.4980 chunk 327 optimal weight: 9.9990 chunk 312 optimal weight: 7.9990 chunk 206 optimal weight: 20.0000 chunk 164 optimal weight: 20.0000 chunk 70 optimal weight: 0.2980 chunk 297 optimal weight: 0.0670 chunk 266 optimal weight: 0.4980 chunk 404 optimal weight: 0.0000 chunk 310 optimal weight: 40.0000 chunk 227 optimal weight: 0.6980 overall best weight: 0.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 186 GLN L 190 ASN L 488 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.118632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097482 restraints weight = 8398.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100999 restraints weight = 5264.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103622 restraints weight = 3734.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.105632 restraints weight = 2836.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.107145 restraints weight = 2254.590| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40380 Z= 0.121 Angle : 0.585 5.397 54852 Z= 0.313 Chirality : 0.043 0.226 6336 Planarity : 0.008 0.142 6852 Dihedral : 4.898 23.526 5436 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.12), residues: 4908 helix: -0.71 (0.09), residues: 2640 sheet: -0.78 (0.37), residues: 168 loop : -1.26 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 84 TYR 0.051 0.002 TYR G 67 PHE 0.017 0.001 PHE I 523 TRP 0.012 0.001 TRP F 137 HIS 0.005 0.001 HIS G 56 Details of bonding type rmsd covalent geometry : bond 0.00264 (40380) covalent geometry : angle 0.58476 (54852) hydrogen bonds : bond 0.03305 ( 1452) hydrogen bonds : angle 4.91468 ( 4284) *********************** REFINEMENT MACRO_CYCLE 5 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 226 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 12 ILE cc_start: 0.8448 (tt) cc_final: 0.8081 (mm) REVERT: L 25 GLU cc_start: 0.9358 (tm-30) cc_final: 0.8887 (tm-30) REVERT: L 26 ILE cc_start: 0.9639 (mt) cc_final: 0.9395 (mt) REVERT: L 35 ARG cc_start: 0.8475 (ttp-170) cc_final: 0.7667 (mmt180) REVERT: L 49 PHE cc_start: 0.9440 (t80) cc_final: 0.8779 (t80) REVERT: L 50 PHE cc_start: 0.9606 (m-80) cc_final: 0.9364 (m-80) REVERT: L 51 ARG cc_start: 0.9295 (mtt90) cc_final: 0.8997 (mtt180) REVERT: L 53 LEU cc_start: 0.9330 (mt) cc_final: 0.8884 (mt) REVERT: L 67 TYR cc_start: 0.8712 (t80) cc_final: 0.8406 (t80) REVERT: L 68 ASP cc_start: 0.9294 (m-30) cc_final: 0.9087 (p0) REVERT: L 74 TRP cc_start: 0.8907 (t60) cc_final: 0.8395 (t60) REVERT: L 89 GLU cc_start: 0.8450 (mp0) cc_final: 0.8214 (mp0) REVERT: L 97 ARG cc_start: 0.9082 (mtp85) cc_final: 0.8471 (mmp-170) REVERT: L 113 HIS cc_start: 0.9379 (t70) cc_final: 0.9129 (t70) REVERT: L 133 ARG cc_start: 0.9075 (mtt-85) cc_final: 0.8509 (ttm-80) REVERT: L 146 VAL cc_start: 0.8998 (t) cc_final: 0.8025 (t) REVERT: L 164 MET cc_start: 0.8858 (mmm) cc_final: 0.8592 (mmm) REVERT: L 169 ARG cc_start: 0.8744 (tpm170) cc_final: 0.8497 (tpm170) REVERT: L 203 TYR cc_start: 0.9010 (t80) cc_final: 0.8375 (t80) REVERT: L 224 LYS cc_start: 0.9409 (mmtm) cc_final: 0.9067 (mmtm) REVERT: L 228 VAL cc_start: 0.8700 (t) cc_final: 0.8442 (p) REVERT: L 232 THR cc_start: 0.9142 (p) cc_final: 0.8778 (t) REVERT: L 237 LEU cc_start: 0.9120 (tp) cc_final: 0.8803 (tp) REVERT: L 241 VAL cc_start: 0.9628 (m) cc_final: 0.9407 (p) REVERT: L 248 GLN cc_start: 0.9461 (tp40) cc_final: 0.9240 (tp40) REVERT: L 251 TYR cc_start: 0.8924 (t80) cc_final: 0.8475 (t80) REVERT: L 254 ILE cc_start: 0.9342 (mt) cc_final: 0.9117 (mt) REVERT: L 257 CYS cc_start: 0.8712 (t) cc_final: 0.8471 (t) REVERT: L 427 ARG cc_start: 0.9001 (mmt180) cc_final: 0.8569 (tpt-90) REVERT: L 463 LYS cc_start: 0.9338 (ptmt) cc_final: 0.9017 (pttt) REVERT: L 465 LEU cc_start: 0.9500 (mt) cc_final: 0.9246 (mp) REVERT: L 469 TRP cc_start: 0.9059 (m100) cc_final: 0.8561 (m100) REVERT: L 473 MET cc_start: 0.9515 (mmp) cc_final: 0.9302 (mmp) REVERT: L 476 THR cc_start: 0.9229 (t) cc_final: 0.8961 (t) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.0622 time to fit residues: 16.8106 Evaluate side-chains 206 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 411 optimal weight: 10.0000 chunk 443 optimal weight: 0.0670 chunk 292 optimal weight: 20.0000 chunk 346 optimal weight: 0.0670 chunk 454 optimal weight: 6.9990 chunk 428 optimal weight: 0.6980 chunk 149 optimal weight: 0.0010 chunk 72 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 491 optimal weight: 8.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 HIS ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.120740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099980 restraints weight = 8192.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103442 restraints weight = 5160.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.106093 restraints weight = 3653.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107986 restraints weight = 2752.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.109599 restraints weight = 2192.628| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40380 Z= 0.124 Angle : 0.579 6.544 54852 Z= 0.306 Chirality : 0.042 0.214 6336 Planarity : 0.010 0.215 6852 Dihedral : 4.942 27.365 5436 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.11), residues: 4908 helix: -0.63 (0.09), residues: 2652 sheet: -1.80 (0.28), residues: 288 loop : -1.54 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 459 TYR 0.047 0.002 TYR E 67 PHE 0.010 0.001 PHE D 54 TRP 0.014 0.002 TRP G 137 HIS 0.005 0.001 HIS K 56 Details of bonding type rmsd covalent geometry : bond 0.00282 (40380) covalent geometry : angle 0.57939 (54852) hydrogen bonds : bond 0.03245 ( 1452) hydrogen bonds : angle 4.79893 ( 4284) *********************** REFINEMENT MACRO_CYCLE 6 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 221 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 ILE cc_start: 0.8522 (tt) cc_final: 0.8128 (mm) REVERT: C 25 GLU cc_start: 0.9352 (tm-30) cc_final: 0.8865 (tm-30) REVERT: C 26 ILE cc_start: 0.9583 (mt) cc_final: 0.9371 (mt) REVERT: C 35 ARG cc_start: 0.8508 (ttp-170) cc_final: 0.7660 (mmt180) REVERT: C 49 PHE cc_start: 0.9418 (t80) cc_final: 0.8653 (t80) REVERT: C 50 PHE cc_start: 0.9615 (m-80) cc_final: 0.9346 (m-80) REVERT: C 51 ARG cc_start: 0.9320 (mtt90) cc_final: 0.8762 (mtp85) REVERT: C 53 LEU cc_start: 0.9341 (mt) cc_final: 0.8882 (mt) REVERT: C 74 TRP cc_start: 0.8688 (t60) cc_final: 0.8480 (t60) REVERT: C 83 THR cc_start: 0.9256 (p) cc_final: 0.8950 (p) REVERT: C 84 ARG cc_start: 0.6744 (ttt180) cc_final: 0.6305 (tpt90) REVERT: C 97 ARG cc_start: 0.9110 (mtp85) cc_final: 0.8470 (mmp-170) REVERT: C 113 HIS cc_start: 0.9316 (t70) cc_final: 0.9066 (t70) REVERT: C 133 ARG cc_start: 0.8990 (mtt-85) cc_final: 0.8354 (mtp180) REVERT: C 144 VAL cc_start: 0.9467 (t) cc_final: 0.8915 (t) REVERT: C 169 ARG cc_start: 0.8736 (tpm170) cc_final: 0.8483 (tpm170) REVERT: C 203 TYR cc_start: 0.9045 (t80) cc_final: 0.8378 (t80) REVERT: C 224 LYS cc_start: 0.9389 (mmtm) cc_final: 0.9046 (mmtm) REVERT: C 228 VAL cc_start: 0.9016 (t) cc_final: 0.8791 (p) REVERT: C 232 THR cc_start: 0.9243 (p) cc_final: 0.8900 (t) REVERT: C 237 LEU cc_start: 0.9104 (tp) cc_final: 0.8774 (tp) REVERT: C 241 VAL cc_start: 0.9581 (m) cc_final: 0.9270 (p) REVERT: C 248 GLN cc_start: 0.9422 (tp40) cc_final: 0.9200 (tp40) REVERT: C 251 TYR cc_start: 0.8955 (t80) cc_final: 0.8464 (t80) REVERT: C 254 ILE cc_start: 0.9283 (mt) cc_final: 0.9047 (mt) REVERT: C 427 ARG cc_start: 0.8954 (mmt180) cc_final: 0.8500 (tpt-90) REVERT: C 463 LYS cc_start: 0.9234 (ptmt) cc_final: 0.9015 (pttm) REVERT: C 469 TRP cc_start: 0.8977 (m100) cc_final: 0.8548 (m100) REVERT: C 473 MET cc_start: 0.9463 (mmp) cc_final: 0.8759 (mmp) REVERT: C 476 THR cc_start: 0.9261 (t) cc_final: 0.8626 (t) REVERT: C 477 TYR cc_start: 0.9068 (m-80) cc_final: 0.8502 (m-80) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.0614 time to fit residues: 16.2936 Evaluate side-chains 192 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 86 optimal weight: 0.8980 chunk 433 optimal weight: 20.0000 chunk 182 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 chunk 72 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 196 optimal weight: 5.9990 chunk 364 optimal weight: 0.0470 chunk 282 optimal weight: 0.0030 chunk 176 optimal weight: 9.9990 overall best weight: 0.4688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS C 434 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.121573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100578 restraints weight = 8430.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.104043 restraints weight = 5363.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106594 restraints weight = 3815.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.108650 restraints weight = 2911.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.110220 restraints weight = 2303.665| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 40380 Z= 0.118 Angle : 0.619 7.744 54852 Z= 0.321 Chirality : 0.043 0.214 6336 Planarity : 0.008 0.155 6852 Dihedral : 4.998 23.604 5436 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.11), residues: 4908 helix: -0.45 (0.10), residues: 2652 sheet: -1.72 (0.31), residues: 288 loop : -1.69 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 84 TYR 0.027 0.002 TYR L 199 PHE 0.011 0.001 PHE G 54 TRP 0.017 0.001 TRP H 137 HIS 0.005 0.001 HIS I 69 Details of bonding type rmsd covalent geometry : bond 0.00255 (40380) covalent geometry : angle 0.61867 (54852) hydrogen bonds : bond 0.03075 ( 1452) hydrogen bonds : angle 4.89950 ( 4284) *********************** REFINEMENT MACRO_CYCLE 7 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 220 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 ILE cc_start: 0.8461 (tt) cc_final: 0.8089 (mm) REVERT: C 15 HIS cc_start: 0.7926 (t-90) cc_final: 0.7584 (m170) REVERT: C 25 GLU cc_start: 0.9356 (tm-30) cc_final: 0.8861 (tm-30) REVERT: C 26 ILE cc_start: 0.9534 (mt) cc_final: 0.9298 (mt) REVERT: C 35 ARG cc_start: 0.8486 (ttp-170) cc_final: 0.7684 (mmt180) REVERT: C 49 PHE cc_start: 0.9342 (t80) cc_final: 0.8669 (t80) REVERT: C 50 PHE cc_start: 0.9610 (m-80) cc_final: 0.9351 (m-80) REVERT: C 51 ARG cc_start: 0.9281 (mtt90) cc_final: 0.9077 (mtt180) REVERT: C 52 GLN cc_start: 0.9709 (tt0) cc_final: 0.9499 (tp40) REVERT: C 53 LEU cc_start: 0.9204 (mt) cc_final: 0.8705 (mt) REVERT: C 60 ASN cc_start: 0.9390 (m110) cc_final: 0.9100 (m110) REVERT: C 68 ASP cc_start: 0.9211 (p0) cc_final: 0.8905 (p0) REVERT: C 84 ARG cc_start: 0.7033 (ttt180) cc_final: 0.6715 (tpt90) REVERT: C 88 LYS cc_start: 0.9656 (mmtp) cc_final: 0.9306 (mttt) REVERT: C 97 ARG cc_start: 0.9139 (mtp85) cc_final: 0.8468 (mmp-170) REVERT: C 113 HIS cc_start: 0.9297 (t70) cc_final: 0.9035 (t70) REVERT: C 133 ARG cc_start: 0.9034 (mtt-85) cc_final: 0.8294 (mtp180) REVERT: C 169 ARG cc_start: 0.8717 (tpm170) cc_final: 0.8441 (tpm170) REVERT: C 200 ILE cc_start: 0.9171 (mt) cc_final: 0.8837 (tt) REVERT: C 203 TYR cc_start: 0.9082 (t80) cc_final: 0.8467 (t80) REVERT: C 224 LYS cc_start: 0.9368 (mmtm) cc_final: 0.9039 (mmtm) REVERT: C 237 LEU cc_start: 0.9070 (tp) cc_final: 0.8728 (tp) REVERT: C 241 VAL cc_start: 0.9579 (m) cc_final: 0.9249 (p) REVERT: C 251 TYR cc_start: 0.8935 (t80) cc_final: 0.8535 (t80) REVERT: C 254 ILE cc_start: 0.9244 (mt) cc_final: 0.9029 (mt) REVERT: C 256 SER cc_start: 0.9353 (t) cc_final: 0.9084 (p) REVERT: C 423 GLN cc_start: 0.9285 (mt0) cc_final: 0.8951 (mt0) REVERT: C 427 ARG cc_start: 0.8955 (mmt180) cc_final: 0.8476 (tpt-90) REVERT: C 433 LEU cc_start: 0.9471 (mt) cc_final: 0.9216 (mt) REVERT: C 463 LYS cc_start: 0.9324 (ptmt) cc_final: 0.9006 (pttm) REVERT: C 469 TRP cc_start: 0.8962 (m100) cc_final: 0.8537 (m100) REVERT: C 473 MET cc_start: 0.9440 (mmp) cc_final: 0.8689 (mmp) REVERT: C 476 THR cc_start: 0.9212 (t) cc_final: 0.8549 (t) REVERT: C 477 TYR cc_start: 0.8857 (m-80) cc_final: 0.8450 (m-80) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.0646 time to fit residues: 16.9346 Evaluate side-chains 196 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 394 optimal weight: 4.9990 chunk 144 optimal weight: 0.0470 chunk 88 optimal weight: 7.9990 chunk 27 optimal weight: 0.0170 chunk 81 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 448 optimal weight: 0.0670 chunk 411 optimal weight: 0.5980 chunk 172 optimal weight: 7.9990 overall best weight: 0.9456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.121534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.100653 restraints weight = 8538.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.103997 restraints weight = 5512.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106553 restraints weight = 3946.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108536 restraints weight = 3012.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.109970 restraints weight = 2399.861| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.7000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 40380 Z= 0.114 Angle : 0.594 5.401 54852 Z= 0.315 Chirality : 0.044 0.223 6336 Planarity : 0.005 0.038 6852 Dihedral : 4.936 23.252 5436 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.11), residues: 4908 helix: -0.58 (0.10), residues: 2652 sheet: -2.04 (0.28), residues: 288 loop : -1.59 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 459 TYR 0.019 0.001 TYR J 199 PHE 0.012 0.001 PHE H 54 TRP 0.009 0.001 TRP H 137 HIS 0.007 0.001 HIS I 40 Details of bonding type rmsd covalent geometry : bond 0.00242 (40380) covalent geometry : angle 0.59410 (54852) hydrogen bonds : bond 0.03130 ( 1452) hydrogen bonds : angle 4.99983 ( 4284) *********************** REFINEMENT MACRO_CYCLE 8 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 204 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 ILE cc_start: 0.8465 (tt) cc_final: 0.8100 (mm) REVERT: C 15 HIS cc_start: 0.7884 (t-90) cc_final: 0.7614 (m170) REVERT: C 25 GLU cc_start: 0.9367 (tm-30) cc_final: 0.8886 (tm-30) REVERT: C 26 ILE cc_start: 0.9504 (mt) cc_final: 0.9273 (mt) REVERT: C 35 ARG cc_start: 0.8512 (ttp-170) cc_final: 0.7686 (mmt180) REVERT: C 49 PHE cc_start: 0.9394 (t80) cc_final: 0.8656 (t80) REVERT: C 50 PHE cc_start: 0.9607 (m-80) cc_final: 0.9351 (m-80) REVERT: C 51 ARG cc_start: 0.9315 (mtt90) cc_final: 0.9103 (mtt-85) REVERT: C 53 LEU cc_start: 0.9286 (mt) cc_final: 0.8686 (mt) REVERT: C 58 TYR cc_start: 0.9261 (t80) cc_final: 0.9030 (t80) REVERT: C 59 LYS cc_start: 0.9568 (tttt) cc_final: 0.9155 (tmtt) REVERT: C 60 ASN cc_start: 0.9385 (m110) cc_final: 0.9129 (m110) REVERT: C 78 GLU cc_start: 0.9373 (mm-30) cc_final: 0.9170 (mm-30) REVERT: C 87 GLU cc_start: 0.8431 (pt0) cc_final: 0.8175 (pm20) REVERT: C 88 LYS cc_start: 0.9644 (mmtp) cc_final: 0.9352 (mttt) REVERT: C 97 ARG cc_start: 0.9115 (mtp85) cc_final: 0.8469 (mmp-170) REVERT: C 113 HIS cc_start: 0.9283 (t70) cc_final: 0.9039 (t70) REVERT: C 169 ARG cc_start: 0.8721 (tpm170) cc_final: 0.8456 (tpm170) REVERT: C 200 ILE cc_start: 0.9115 (mt) cc_final: 0.8840 (tt) REVERT: C 203 TYR cc_start: 0.9085 (t80) cc_final: 0.8422 (t80) REVERT: C 224 LYS cc_start: 0.9318 (mmtm) cc_final: 0.8987 (mmtm) REVERT: C 232 THR cc_start: 0.9328 (p) cc_final: 0.9023 (t) REVERT: C 237 LEU cc_start: 0.9078 (tp) cc_final: 0.8748 (tp) REVERT: C 241 VAL cc_start: 0.9491 (m) cc_final: 0.9105 (p) REVERT: C 251 TYR cc_start: 0.8945 (t80) cc_final: 0.8581 (t80) REVERT: C 256 SER cc_start: 0.9312 (t) cc_final: 0.9027 (p) REVERT: C 423 GLN cc_start: 0.9331 (mt0) cc_final: 0.9036 (mt0) REVERT: C 427 ARG cc_start: 0.8945 (mmt180) cc_final: 0.8478 (tpt-90) REVERT: C 434 GLN cc_start: 0.8869 (mm110) cc_final: 0.8565 (mm110) REVERT: C 463 LYS cc_start: 0.9283 (ptmt) cc_final: 0.9057 (pttm) REVERT: C 469 TRP cc_start: 0.8933 (m100) cc_final: 0.8560 (m100) REVERT: C 473 MET cc_start: 0.9444 (mmp) cc_final: 0.8612 (mmp) REVERT: C 477 TYR cc_start: 0.8875 (m-80) cc_final: 0.8443 (m-80) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.0664 time to fit residues: 16.1170 Evaluate side-chains 189 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 262 optimal weight: 5.9990 chunk 359 optimal weight: 7.9990 chunk 418 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 467 optimal weight: 0.9980 chunk 324 optimal weight: 0.8980 chunk 248 optimal weight: 0.0570 chunk 179 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 461 optimal weight: 20.0000 chunk 316 optimal weight: 8.9990 overall best weight: 3.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 HIS L 120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.097966 restraints weight = 8515.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.101261 restraints weight = 5503.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.103800 restraints weight = 3970.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.105774 restraints weight = 3041.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107245 restraints weight = 2432.784| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.7189 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= 0.125 Angle : 0.594 5.491 54852 Z= 0.315 Chirality : 0.043 0.226 6336 Planarity : 0.005 0.062 6852 Dihedral : 4.863 22.774 5436 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.39 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.12), residues: 4908 helix: -0.50 (0.10), residues: 2700 sheet: -2.03 (0.29), residues: 288 loop : -1.48 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 84 TYR 0.017 0.002 TYR L 199 PHE 0.010 0.001 PHE E 54 TRP 0.018 0.001 TRP F 137 HIS 0.004 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00271 (40380) covalent geometry : angle 0.59365 (54852) hydrogen bonds : bond 0.03093 ( 1452) hydrogen bonds : angle 4.96584 ( 4284) *********************** REFINEMENT MACRO_CYCLE 9 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 208 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 GLU cc_start: 0.9403 (tm-30) cc_final: 0.8918 (tm-30) REVERT: L 26 ILE cc_start: 0.9528 (mt) cc_final: 0.9296 (mt) REVERT: L 35 ARG cc_start: 0.8560 (ttp-170) cc_final: 0.7825 (tpp-160) REVERT: L 49 PHE cc_start: 0.9432 (t80) cc_final: 0.8724 (t80) REVERT: L 50 PHE cc_start: 0.9642 (m-80) cc_final: 0.9401 (m-80) REVERT: L 51 ARG cc_start: 0.9321 (mtt90) cc_final: 0.9041 (mtt180) REVERT: L 53 LEU cc_start: 0.9364 (mt) cc_final: 0.8883 (mt) REVERT: L 59 LYS cc_start: 0.9526 (tttt) cc_final: 0.9139 (tmtt) REVERT: L 60 ASN cc_start: 0.9372 (m110) cc_final: 0.9121 (m110) REVERT: L 87 GLU cc_start: 0.8530 (pt0) cc_final: 0.8288 (pm20) REVERT: L 97 ARG cc_start: 0.9136 (mtp85) cc_final: 0.8526 (mmp-170) REVERT: L 113 HIS cc_start: 0.9361 (t70) cc_final: 0.9086 (t70) REVERT: L 169 ARG cc_start: 0.8689 (tpm170) cc_final: 0.8440 (tpm170) REVERT: L 200 ILE cc_start: 0.9117 (mt) cc_final: 0.8839 (tt) REVERT: L 203 TYR cc_start: 0.9055 (t80) cc_final: 0.8356 (t80) REVERT: L 224 LYS cc_start: 0.9343 (mmtm) cc_final: 0.8979 (mmtm) REVERT: L 232 THR cc_start: 0.9284 (p) cc_final: 0.8983 (t) REVERT: L 237 LEU cc_start: 0.9081 (tp) cc_final: 0.8745 (tp) REVERT: L 241 VAL cc_start: 0.9447 (m) cc_final: 0.9205 (p) REVERT: L 251 TYR cc_start: 0.8941 (t80) cc_final: 0.8531 (t80) REVERT: L 254 ILE cc_start: 0.9273 (mt) cc_final: 0.9056 (mt) REVERT: L 423 GLN cc_start: 0.9381 (mt0) cc_final: 0.9063 (mt0) REVERT: L 427 ARG cc_start: 0.9025 (mmt180) cc_final: 0.8536 (tpt-90) REVERT: L 434 GLN cc_start: 0.8998 (mm110) cc_final: 0.8696 (mm110) REVERT: L 463 LYS cc_start: 0.9311 (ptmt) cc_final: 0.8791 (pttm) REVERT: L 469 TRP cc_start: 0.9037 (m100) cc_final: 0.8794 (m100) REVERT: L 473 MET cc_start: 0.9459 (mmp) cc_final: 0.9033 (mmp) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.0623 time to fit residues: 15.5837 Evaluate side-chains 191 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 465 optimal weight: 0.3980 chunk 279 optimal weight: 10.0000 chunk 281 optimal weight: 0.9990 chunk 426 optimal weight: 0.9980 chunk 123 optimal weight: 20.0000 chunk 358 optimal weight: 0.0470 chunk 416 optimal weight: 0.3980 chunk 62 optimal weight: 0.2980 chunk 355 optimal weight: 0.0570 chunk 216 optimal weight: 2.9990 chunk 186 optimal weight: 0.1980 overall best weight: 0.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 HIS L 69 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.123544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102698 restraints weight = 8287.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106025 restraints weight = 5282.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108588 restraints weight = 3795.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110601 restraints weight = 2888.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112184 restraints weight = 2300.702| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.7400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 40380 Z= 0.119 Angle : 0.618 7.057 54852 Z= 0.324 Chirality : 0.043 0.227 6336 Planarity : 0.004 0.044 6852 Dihedral : 4.751 22.109 5436 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.12), residues: 4908 helix: -0.65 (0.10), residues: 2712 sheet: -1.82 (0.29), residues: 288 loop : -1.48 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 459 TYR 0.016 0.002 TYR G 199 PHE 0.010 0.001 PHE B 54 TRP 0.011 0.002 TRP E 85 HIS 0.009 0.001 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00247 (40380) covalent geometry : angle 0.61781 (54852) hydrogen bonds : bond 0.03383 ( 1452) hydrogen bonds : angle 5.08394 ( 4284) ********************** REFINEMENT MACRO_CYCLE 10 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 202 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 GLU cc_start: 0.9337 (tm-30) cc_final: 0.8868 (tm-30) REVERT: L 26 ILE cc_start: 0.9463 (mt) cc_final: 0.9218 (mt) REVERT: L 35 ARG cc_start: 0.8453 (ttp-170) cc_final: 0.7744 (tpp-160) REVERT: L 49 PHE cc_start: 0.9407 (t80) cc_final: 0.8672 (t80) REVERT: L 50 PHE cc_start: 0.9623 (m-80) cc_final: 0.9380 (m-80) REVERT: L 51 ARG cc_start: 0.9357 (mtt90) cc_final: 0.8865 (mtp85) REVERT: L 53 LEU cc_start: 0.9372 (mt) cc_final: 0.8798 (mt) REVERT: L 59 LYS cc_start: 0.9519 (tttt) cc_final: 0.9113 (tmtt) REVERT: L 60 ASN cc_start: 0.9344 (m110) cc_final: 0.9132 (m110) REVERT: L 68 ASP cc_start: 0.9385 (m-30) cc_final: 0.9064 (p0) REVERT: L 78 GLU cc_start: 0.9014 (mp0) cc_final: 0.8737 (mp0) REVERT: L 97 ARG cc_start: 0.9088 (mtp85) cc_final: 0.8446 (mmp-170) REVERT: L 113 HIS cc_start: 0.9325 (t70) cc_final: 0.9025 (t70) REVERT: L 133 ARG cc_start: 0.8999 (mtt-85) cc_final: 0.8223 (mtp180) REVERT: L 169 ARG cc_start: 0.8731 (tpm170) cc_final: 0.8485 (tpm170) REVERT: L 200 ILE cc_start: 0.9095 (mt) cc_final: 0.8862 (tt) REVERT: L 203 TYR cc_start: 0.9049 (t80) cc_final: 0.8421 (t80) REVERT: L 232 THR cc_start: 0.9196 (p) cc_final: 0.8912 (t) REVERT: L 237 LEU cc_start: 0.9040 (tp) cc_final: 0.8687 (tp) REVERT: L 241 VAL cc_start: 0.9446 (m) cc_final: 0.9192 (p) REVERT: L 251 TYR cc_start: 0.8916 (t80) cc_final: 0.8595 (t80) REVERT: L 265 LYS cc_start: 0.5627 (pttt) cc_final: 0.5349 (tttt) REVERT: L 423 GLN cc_start: 0.9357 (mt0) cc_final: 0.9042 (mt0) REVERT: L 427 ARG cc_start: 0.8972 (mmt180) cc_final: 0.8513 (tpt-90) REVERT: L 434 GLN cc_start: 0.8876 (mm110) cc_final: 0.8587 (mm110) REVERT: L 469 TRP cc_start: 0.8951 (m100) cc_final: 0.8619 (m100) REVERT: L 473 MET cc_start: 0.9406 (mmp) cc_final: 0.9155 (mmp) REVERT: L 484 ASP cc_start: 0.8694 (m-30) cc_final: 0.7932 (p0) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.0616 time to fit residues: 14.8850 Evaluate side-chains 187 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 163 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 234 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 377 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 276 optimal weight: 20.0000 chunk 21 optimal weight: 0.4980 chunk 395 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.117560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.096629 restraints weight = 8760.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.099948 restraints weight = 5627.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.102566 restraints weight = 4040.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.104467 restraints weight = 3074.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106068 restraints weight = 2457.748| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.7534 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= 0.143 Angle : 0.639 6.721 54852 Z= 0.340 Chirality : 0.045 0.230 6336 Planarity : 0.005 0.037 6852 Dihedral : 4.756 22.359 5436 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.11), residues: 4908 helix: -0.50 (0.09), residues: 2772 sheet: -1.72 (0.28), residues: 288 loop : -1.80 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 75 TYR 0.014 0.002 TYR C 199 PHE 0.010 0.001 PHE D 54 TRP 0.018 0.002 TRP J 137 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd covalent geometry : bond 0.00303 (40380) covalent geometry : angle 0.63927 (54852) hydrogen bonds : bond 0.03451 ( 1452) hydrogen bonds : angle 5.16225 ( 4284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2169.75 seconds wall clock time: 40 minutes 27.60 seconds (2427.60 seconds total)