Starting phenix.real_space_refine on Tue Sep 15 11:16:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ppi_20437/09_2026/6ppi_20437.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ppi_20437/09_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_20437/09_2026/6ppi_20437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ppi_20437/09_2026/6ppi_20437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ppi_20437/09_2026/6ppi_20437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ppi_20437/09_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-2.2.1-6174/lib/python3.11/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: 5.31, per 1000 atoms: 0.13 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: 3.12 Conformation dependent library (CDL) restraints added in 1.6 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: 1.28 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: 9.04 Time building geometry restraints manager: 4.29 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: 0.15 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: 0.560 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: 0.050 Extract box with map and model: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 32.880 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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/Z covalent geometry : bond 0.00321 / 0.17 (40380) covalent geometry : angle 0.71375 / 0.40 (54852) hydrogen bonds : bond 0.31430 / 20.91 ( 1452) hydrogen bonds : angle 9.89434 / 6.85 ( 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 : 0.078 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: 0.0733 time to fit residues: 22.5640 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 : 0.075 ------------------------------------------------------------------------------- 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... ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN A 113 HIS A 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 = 0.3555 r_free = 0.3555 target = 0.114690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.094372 restraints weight = 8252.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.097577 restraints weight = 5122.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099914 restraints weight = 3603.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.101916 restraints weight = 2738.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103427 restraints weight = 2157.729| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4357 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 : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.27 % Allowed : 2.40 % 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: -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 L 84 TYR 0.018 0.002 TYR B 477 PHE 0.010 0.002 PHE I 217 TRP 0.013 0.002 TRP L 103 HIS 0.005 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (40380) covalent geometry : angle 0.66086 / 0.36 (54852) hydrogen bonds : bond 0.04514 / 3.01 ( 1452) hydrogen bonds : angle 5.58713 / 3.81 ( 4284) *********************** REFINEMENT MACRO_CYCLE 2 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 248 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 ILE cc_start: 0.8481 (tt) cc_final: 0.8135 (mm) REVERT: G 25 GLU cc_start: 0.9387 (tm-30) cc_final: 0.9175 (tm-30) REVERT: G 32 SER cc_start: 0.9104 (t) cc_final: 0.8815 (m) REVERT: G 37 GLN cc_start: 0.8800 (mm110) cc_final: 0.8150 (mm110) REVERT: G 49 PHE cc_start: 0.9548 (t80) cc_final: 0.8965 (t80) REVERT: G 51 ARG cc_start: 0.9467 (mtt90) cc_final: 0.9182 (mtt-85) REVERT: G 53 LEU cc_start: 0.9446 (mt) cc_final: 0.8983 (mt) REVERT: G 60 ASN cc_start: 0.9460 (m-40) cc_final: 0.9175 (m-40) REVERT: G 68 ASP cc_start: 0.9534 (m-30) cc_final: 0.9026 (p0) REVERT: G 69 HIS cc_start: 0.9205 (m90) cc_final: 0.8683 (m90) REVERT: G 73 ASP cc_start: 0.9215 (p0) cc_final: 0.8775 (p0) REVERT: G 88 LYS cc_start: 0.9574 (mmtp) cc_final: 0.9162 (mttt) REVERT: G 97 ARG cc_start: 0.8881 (mtp85) cc_final: 0.8448 (mmp-170) REVERT: G 101 ASP cc_start: 0.9522 (t70) cc_final: 0.9159 (t70) REVERT: G 105 GLN cc_start: 0.9213 (mm-40) cc_final: 0.9000 (mm-40) REVERT: G 132 GLU cc_start: 0.9462 (mt-10) cc_final: 0.8878 (mt-10) REVERT: G 146 VAL cc_start: 0.9105 (t) cc_final: 0.8161 (t) REVERT: G 154 LYS cc_start: 0.9471 (tttt) cc_final: 0.9073 (tppt) REVERT: G 164 MET cc_start: 0.8866 (mmm) cc_final: 0.8545 (mpp) REVERT: G 169 ARG cc_start: 0.8694 (tpm170) cc_final: 0.8487 (tpp-160) REVERT: G 180 ILE cc_start: 0.8954 (mp) cc_final: 0.8267 (mp) REVERT: G 237 LEU cc_start: 0.9090 (tp) cc_final: 0.8829 (tp) REVERT: G 248 GLN cc_start: 0.9477 (tp40) cc_final: 0.9266 (tp40) REVERT: G 251 TYR cc_start: 0.8879 (t80) cc_final: 0.8503 (t80) REVERT: G 254 ILE cc_start: 0.9172 (mt) cc_final: 0.8949 (mp) REVERT: G 256 SER cc_start: 0.9093 (t) cc_final: 0.8728 (p) REVERT: G 423 GLN cc_start: 0.9445 (mt0) cc_final: 0.9243 (mt0) REVERT: G 427 ARG cc_start: 0.9169 (mmt180) cc_final: 0.8652 (tpt-90) REVERT: G 433 LEU cc_start: 0.9208 (mt) cc_final: 0.8987 (mt) REVERT: G 460 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8457 (mm-30) REVERT: G 469 TRP cc_start: 0.8908 (m100) cc_final: 0.8487 (m100) REVERT: G 472 GLU cc_start: 0.9310 (tp30) cc_final: 0.8642 (tp30) REVERT: G 473 MET cc_start: 0.9506 (mmp) cc_final: 0.8976 (mmp) REVERT: G 490 LEU cc_start: 0.8798 (mt) cc_final: 0.8541 (mp) REVERT: G 496 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: G 515 GLN cc_start: 0.9189 (mp10) cc_final: 0.8874 (pm20) REVERT: G 523 PHE cc_start: 0.9656 (m-10) cc_final: 0.9294 (m-80) REVERT: G 534 TYR cc_start: 0.9024 (t80) cc_final: 0.8767 (t80) outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.0669 time to fit residues: 19.8310 Evaluate side-chains 180 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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: 9.9990 chunk 233 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 306 optimal weight: 1.9990 chunk 172 optimal weight: 20.0000 chunk 319 optimal weight: 9.9990 chunk 324 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 164 optimal weight: 20.0000 chunk 124 optimal weight: 0.0020 chunk 73 optimal weight: 9.9990 overall best weight: 4.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN G 268 GLN G 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 = 0.3500 r_free = 0.3500 target = 0.110776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.091998 restraints weight = 8537.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.095274 restraints weight = 5076.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.097736 restraints weight = 3480.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.099521 restraints weight = 2557.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101031 restraints weight = 2000.883| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 40380 Z= 0.172 Angle : 0.621 6.547 54852 Z= 0.333 Chirality : 0.043 0.233 6336 Planarity : 0.006 0.067 6852 Dihedral : 5.112 25.181 5436 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % 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: -1.94 (0.11), residues: 4908 helix: -1.12 (0.09), residues: 2700 sheet: -0.32 (0.40), residues: 168 loop : -1.42 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 459 TYR 0.015 0.002 TYR E 95 PHE 0.012 0.002 PHE F 50 TRP 0.033 0.002 TRP H 85 HIS 0.006 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (40380) covalent geometry : angle 0.62103 / 0.33 (54852) hydrogen bonds : bond 0.03754 / 2.52 ( 1452) hydrogen bonds : angle 5.46512 / 3.74 ( 4284) *********************** REFINEMENT MACRO_CYCLE 3 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 244 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 0.110 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: 0.8435 (tt) cc_final: 0.8097 (mm) REVERT: C 32 SER cc_start: 0.9087 (t) cc_final: 0.8817 (m) REVERT: C 37 GLN cc_start: 0.8926 (mm110) cc_final: 0.8453 (mm110) REVERT: C 43 LEU cc_start: 0.9500 (tp) cc_final: 0.9280 (tp) REVERT: C 49 PHE cc_start: 0.9497 (t80) cc_final: 0.8948 (t80) REVERT: C 50 PHE cc_start: 0.9608 (m-80) cc_final: 0.9406 (m-80) REVERT: C 51 ARG cc_start: 0.9421 (mtt90) cc_final: 0.9155 (mtt-85) REVERT: C 53 LEU cc_start: 0.9404 (mt) cc_final: 0.8925 (mt) REVERT: C 60 ASN cc_start: 0.9541 (m-40) cc_final: 0.9277 (m-40) REVERT: C 68 ASP cc_start: 0.9522 (m-30) cc_final: 0.9097 (p0) REVERT: C 77 TYR cc_start: 0.9232 (t80) cc_final: 0.9008 (t80) REVERT: C 78 GLU cc_start: 0.9100 (tt0) cc_final: 0.8888 (tt0) REVERT: C 86 PRO cc_start: 0.9381 (Cg_exo) cc_final: 0.8545 (Cg_endo) REVERT: C 87 GLU cc_start: 0.9082 (pt0) cc_final: 0.8675 (pm20) REVERT: C 88 LYS cc_start: 0.9581 (mmtp) cc_final: 0.9218 (mttp) REVERT: C 91 GLN cc_start: 0.9206 (pp30) cc_final: 0.8808 (tm-30) REVERT: C 97 ARG cc_start: 0.9103 (mtp85) cc_final: 0.8391 (mmp-170) REVERT: C 101 ASP cc_start: 0.9536 (t70) cc_final: 0.9245 (t70) REVERT: C 113 HIS cc_start: 0.9322 (t-90) cc_final: 0.8953 (t-90) REVERT: C 146 VAL cc_start: 0.9144 (t) cc_final: 0.8235 (t) REVERT: C 154 LYS cc_start: 0.9463 (tttt) cc_final: 0.9068 (tppt) REVERT: C 164 MET cc_start: 0.8918 (mmm) cc_final: 0.8646 (mpp) REVERT: C 224 LYS cc_start: 0.9437 (mmtm) cc_final: 0.9196 (mmtm) REVERT: C 228 VAL cc_start: 0.8982 (t) cc_final: 0.8757 (t) REVERT: C 232 THR cc_start: 0.9097 (p) cc_final: 0.8741 (t) REVERT: C 254 ILE cc_start: 0.9310 (mt) cc_final: 0.9037 (mt) REVERT: C 268 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7641 (mm-40) REVERT: C 423 GLN cc_start: 0.9320 (mt0) cc_final: 0.9083 (mt0) REVERT: C 427 ARG cc_start: 0.9055 (mmt180) cc_final: 0.8688 (tpt-90) REVERT: C 460 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8970 (tp30) REVERT: C 463 LYS cc_start: 0.9196 (ptmt) cc_final: 0.8988 (ptmt) REVERT: C 464 ASP cc_start: 0.9017 (m-30) cc_final: 0.8810 (m-30) REVERT: C 469 TRP cc_start: 0.9029 (m100) cc_final: 0.8577 (m100) REVERT: C 477 TYR cc_start: 0.9364 (m-10) cc_final: 0.8927 (m-10) REVERT: C 515 GLN cc_start: 0.9226 (mp10) cc_final: 0.8807 (pm20) REVERT: C 523 PHE cc_start: 0.9627 (m-10) cc_final: 0.9372 (m-80) REVERT: C 537 GLN cc_start: 0.9109 (mp10) cc_final: 0.8892 (mp10) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.0634 time to fit residues: 18.7037 Evaluate side-chains 195 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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: 0.0970 chunk 411 optimal weight: 10.0000 chunk 456 optimal weight: 20.0000 chunk 476 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 482 optimal weight: 8.9990 chunk 336 optimal weight: 0.8980 chunk 215 optimal weight: 20.0000 chunk 338 optimal weight: 0.0030 chunk 477 optimal weight: 0.9980 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 HIS ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN C 488 GLN C 521 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.114071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.094446 restraints weight = 8249.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.097770 restraints weight = 5043.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.100237 restraints weight = 3514.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102069 restraints weight = 2628.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.103575 restraints weight = 2073.796| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 40380 Z= 0.127 Angle : 0.593 5.211 54852 Z= 0.316 Chirality : 0.042 0.236 6336 Planarity : 0.007 0.118 6852 Dihedral : 4.914 24.213 5436 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.27 % Allowed : 1.07 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.21 (0.12), residues: 4908 helix: -0.48 (0.10), residues: 2616 sheet: -0.38 (0.43), residues: 168 loop : -1.13 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 459 TYR 0.043 0.002 TYR E 67 PHE 0.008 0.001 PHE D 50 TRP 0.011 0.002 TRP H 137 HIS 0.007 0.001 HIS H 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (40380) covalent geometry : angle 0.59334 / 0.32 (54852) hydrogen bonds : bond 0.03379 / 2.27 ( 1452) hydrogen bonds : angle 5.16037 / 3.53 ( 4284) *********************** REFINEMENT MACRO_CYCLE 4 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 239 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 12 ILE cc_start: 0.8430 (tt) cc_final: 0.8073 (mm) REVERT: L 25 GLU cc_start: 0.9390 (tm-30) cc_final: 0.8931 (tm-30) REVERT: L 26 ILE cc_start: 0.9724 (mt) cc_final: 0.9522 (mt) REVERT: L 28 GLN cc_start: 0.9403 (mp10) cc_final: 0.9190 (mp10) REVERT: L 32 SER cc_start: 0.9103 (t) cc_final: 0.8845 (m) REVERT: L 49 PHE cc_start: 0.9483 (t80) cc_final: 0.8852 (t80) REVERT: L 50 PHE cc_start: 0.9591 (m-80) cc_final: 0.9382 (m-80) REVERT: L 51 ARG cc_start: 0.9371 (mtt90) cc_final: 0.9102 (mtt-85) REVERT: L 53 LEU cc_start: 0.9353 (mt) cc_final: 0.8896 (mt) REVERT: L 60 ASN cc_start: 0.9530 (m-40) cc_final: 0.9255 (m110) REVERT: L 68 ASP cc_start: 0.9419 (m-30) cc_final: 0.9065 (p0) REVERT: L 77 TYR cc_start: 0.9117 (t80) cc_final: 0.8635 (t80) REVERT: L 79 SER cc_start: 0.9693 (t) cc_final: 0.9243 (p) REVERT: L 83 THR cc_start: 0.9504 (p) cc_final: 0.9204 (p) REVERT: L 86 PRO cc_start: 0.9308 (Cg_exo) cc_final: 0.8713 (Cg_endo) REVERT: L 87 GLU cc_start: 0.9027 (pt0) cc_final: 0.8584 (pm20) REVERT: L 88 LYS cc_start: 0.9549 (mmtp) cc_final: 0.9244 (mttp) REVERT: L 91 GLN cc_start: 0.9008 (pp30) cc_final: 0.8720 (tm-30) REVERT: L 97 ARG cc_start: 0.9119 (mtp85) cc_final: 0.8442 (mmp-170) REVERT: L 101 ASP cc_start: 0.9539 (t70) cc_final: 0.9292 (t70) REVERT: L 113 HIS cc_start: 0.9322 (t-90) cc_final: 0.8944 (t-90) REVERT: L 154 LYS cc_start: 0.9490 (tttt) cc_final: 0.9004 (tppt) REVERT: L 169 ARG cc_start: 0.8911 (tpm170) cc_final: 0.8690 (tpp-160) REVERT: L 203 TYR cc_start: 0.9021 (t80) cc_final: 0.8640 (t80) REVERT: L 224 LYS cc_start: 0.9410 (mmtm) cc_final: 0.9130 (mmtm) REVERT: L 232 THR cc_start: 0.9146 (p) cc_final: 0.8786 (t) REVERT: L 237 LEU cc_start: 0.9147 (tp) cc_final: 0.8833 (tp) REVERT: L 241 VAL cc_start: 0.9625 (m) cc_final: 0.9413 (p) REVERT: L 248 GLN cc_start: 0.9532 (tp40) cc_final: 0.9319 (tp40) REVERT: L 254 ILE cc_start: 0.9313 (mt) cc_final: 0.9110 (mt) REVERT: L 256 SER cc_start: 0.9302 (t) cc_final: 0.8978 (p) REVERT: L 268 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7351 (mm-40) REVERT: L 423 GLN cc_start: 0.9338 (mt0) cc_final: 0.9109 (mt0) REVERT: L 427 ARG cc_start: 0.9042 (mmt180) cc_final: 0.8662 (tpt-90) REVERT: L 460 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8886 (tp30) REVERT: L 463 LYS cc_start: 0.9255 (ptmt) cc_final: 0.8837 (ptmt) REVERT: L 464 ASP cc_start: 0.9112 (m-30) cc_final: 0.8910 (m-30) REVERT: L 465 LEU cc_start: 0.9448 (mt) cc_final: 0.9230 (mp) REVERT: L 473 MET cc_start: 0.9531 (mmp) cc_final: 0.8945 (mmp) REVERT: L 477 TYR cc_start: 0.9325 (m-10) cc_final: 0.8677 (m-10) REVERT: L 515 GLN cc_start: 0.9212 (mp10) cc_final: 0.8816 (pm20) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.0596 time to fit residues: 17.1492 Evaluate side-chains 190 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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: 20.0000 chunk 327 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 206 optimal weight: 0.2980 chunk 164 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 297 optimal weight: 10.0000 chunk 266 optimal weight: 0.0050 chunk 404 optimal weight: 0.0670 chunk 310 optimal weight: 20.0000 chunk 227 optimal weight: 0.7980 overall best weight: 2.2334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 15 HIS L 37 GLN ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 HIS L 190 ASN L 268 GLN L 488 GLN L 521 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.115929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096288 restraints weight = 8550.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.099668 restraints weight = 5184.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.102054 restraints weight = 3591.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.104009 restraints weight = 2708.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105376 restraints weight = 2119.925| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.6069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 40380 Z= 0.127 Angle : 0.600 5.543 54852 Z= 0.322 Chirality : 0.043 0.227 6336 Planarity : 0.008 0.142 6852 Dihedral : 4.924 23.764 5436 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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: -1.19 (0.12), residues: 4908 helix: -0.31 (0.10), residues: 2628 sheet: -0.94 (0.38), residues: 168 loop : -1.29 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 459 TYR 0.018 0.002 TYR H 203 PHE 0.013 0.001 PHE E 54 TRP 0.034 0.002 TRP L 85 HIS 0.010 0.001 HIS H 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (40380) covalent geometry : angle 0.60024 / 0.32 (54852) hydrogen bonds : bond 0.03358 / 2.25 ( 1452) hydrogen bonds : angle 5.29192 / 3.61 ( 4284) *********************** REFINEMENT MACRO_CYCLE 5 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 226 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 ILE cc_start: 0.8394 (tt) cc_final: 0.8047 (mm) REVERT: F 28 GLN cc_start: 0.9373 (mp10) cc_final: 0.9130 (mp10) REVERT: F 32 SER cc_start: 0.9089 (t) cc_final: 0.8827 (m) REVERT: F 49 PHE cc_start: 0.9448 (t80) cc_final: 0.8745 (t80) REVERT: F 50 PHE cc_start: 0.9623 (m-80) cc_final: 0.9369 (m-80) REVERT: F 51 ARG cc_start: 0.9389 (mtt90) cc_final: 0.9116 (mtt-85) REVERT: F 53 LEU cc_start: 0.9373 (mt) cc_final: 0.8942 (mt) REVERT: F 60 ASN cc_start: 0.9599 (m-40) cc_final: 0.9110 (p0) REVERT: F 77 TYR cc_start: 0.9123 (t80) cc_final: 0.8900 (t80) REVERT: F 87 GLU cc_start: 0.8924 (pt0) cc_final: 0.8492 (pm20) REVERT: F 89 GLU cc_start: 0.8620 (mp0) cc_final: 0.8153 (mp0) REVERT: F 96 ARG cc_start: 0.8687 (mmt90) cc_final: 0.8184 (mmt-90) REVERT: F 97 ARG cc_start: 0.9098 (mtp85) cc_final: 0.8458 (mmp-170) REVERT: F 113 HIS cc_start: 0.9318 (t-90) cc_final: 0.8962 (t-90) REVERT: F 133 ARG cc_start: 0.9030 (mtt-85) cc_final: 0.8302 (mtp180) REVERT: F 169 ARG cc_start: 0.8926 (tpm170) cc_final: 0.8718 (tpp-160) REVERT: F 191 LEU cc_start: 0.9541 (tp) cc_final: 0.9126 (tp) REVERT: F 203 TYR cc_start: 0.9033 (t80) cc_final: 0.8724 (t80) REVERT: F 224 LYS cc_start: 0.9430 (mmtm) cc_final: 0.9114 (mmtm) REVERT: F 232 THR cc_start: 0.9283 (p) cc_final: 0.8975 (t) REVERT: F 237 LEU cc_start: 0.9113 (tp) cc_final: 0.8791 (tp) REVERT: F 241 VAL cc_start: 0.9611 (m) cc_final: 0.9384 (p) REVERT: F 248 GLN cc_start: 0.9467 (tp40) cc_final: 0.9257 (tp40) REVERT: F 251 TYR cc_start: 0.8944 (t80) cc_final: 0.8547 (t80) REVERT: F 427 ARG cc_start: 0.9015 (mmt180) cc_final: 0.8566 (tpt-90) REVERT: F 460 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8777 (mm-30) REVERT: F 463 LYS cc_start: 0.9228 (ptmt) cc_final: 0.8748 (ptmt) REVERT: F 464 ASP cc_start: 0.9162 (m-30) cc_final: 0.8928 (m-30) REVERT: F 473 MET cc_start: 0.9463 (mmp) cc_final: 0.8991 (mmp) REVERT: F 477 TYR cc_start: 0.9349 (m-10) cc_final: 0.8788 (m-10) REVERT: F 523 PHE cc_start: 0.9537 (m-10) cc_final: 0.9311 (m-80) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.0599 time to fit residues: 16.3981 Evaluate side-chains 210 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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: 4.9990 chunk 443 optimal weight: 4.9990 chunk 292 optimal weight: 20.0000 chunk 346 optimal weight: 2.9990 chunk 454 optimal weight: 30.0000 chunk 428 optimal weight: 20.0000 chunk 149 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 491 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 15 HIS F 37 GLN F 40 HIS ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 162 GLN F 190 ASN F 268 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.110614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.090801 restraints weight = 8663.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.094142 restraints weight = 5373.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.096636 restraints weight = 3757.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098528 restraints weight = 2822.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099980 restraints weight = 2230.131| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40380 Z= 0.163 Angle : 0.622 6.095 54852 Z= 0.331 Chirality : 0.043 0.232 6336 Planarity : 0.006 0.076 6852 Dihedral : 5.019 23.356 5436 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.94 (0.12), residues: 4908 helix: -0.12 (0.10), residues: 2580 sheet: -1.20 (0.37), residues: 168 loop : -1.09 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 459 TYR 0.016 0.002 TYR H 203 PHE 0.018 0.002 PHE G 506 TRP 0.013 0.002 TRP L 74 HIS 0.010 0.001 HIS G 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (40380) covalent geometry : angle 0.62154 / 0.33 (54852) hydrogen bonds : bond 0.03524 / 2.37 ( 1452) hydrogen bonds : angle 5.42082 / 3.70 ( 4284) *********************** REFINEMENT MACRO_CYCLE 6 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 222 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 ILE cc_start: 0.8402 (tt) cc_final: 0.8029 (mm) REVERT: F 25 GLU cc_start: 0.9412 (tm-30) cc_final: 0.8953 (tm-30) REVERT: F 26 ILE cc_start: 0.9652 (mt) cc_final: 0.9405 (mt) REVERT: F 43 LEU cc_start: 0.9607 (tp) cc_final: 0.9399 (tp) REVERT: F 49 PHE cc_start: 0.9491 (t80) cc_final: 0.8786 (t80) REVERT: F 50 PHE cc_start: 0.9628 (m-80) cc_final: 0.9364 (m-80) REVERT: F 51 ARG cc_start: 0.9394 (mtt90) cc_final: 0.9069 (mtt180) REVERT: F 53 LEU cc_start: 0.9417 (mt) cc_final: 0.9028 (mt) REVERT: F 59 LYS cc_start: 0.9477 (tttt) cc_final: 0.9144 (tmtt) REVERT: F 60 ASN cc_start: 0.9579 (m-40) cc_final: 0.9355 (m110) REVERT: F 68 ASP cc_start: 0.9327 (m-30) cc_final: 0.8947 (p0) REVERT: F 78 GLU cc_start: 0.9185 (mp0) cc_final: 0.8777 (mp0) REVERT: F 87 GLU cc_start: 0.8934 (pt0) cc_final: 0.8656 (pm20) REVERT: F 89 GLU cc_start: 0.8220 (mp0) cc_final: 0.7998 (mp0) REVERT: F 96 ARG cc_start: 0.8799 (mmt90) cc_final: 0.8252 (mmt-90) REVERT: F 97 ARG cc_start: 0.9086 (mtp85) cc_final: 0.8512 (mmp-170) REVERT: F 113 HIS cc_start: 0.9322 (t-90) cc_final: 0.8987 (t-90) REVERT: F 133 ARG cc_start: 0.9141 (mtt-85) cc_final: 0.8373 (mtp180) REVERT: F 154 LYS cc_start: 0.9524 (tttt) cc_final: 0.9036 (tppt) REVERT: F 203 TYR cc_start: 0.9050 (t80) cc_final: 0.8710 (t80) REVERT: F 224 LYS cc_start: 0.9422 (mmtm) cc_final: 0.9119 (mmtm) REVERT: F 232 THR cc_start: 0.9284 (p) cc_final: 0.8969 (t) REVERT: F 237 LEU cc_start: 0.9130 (tp) cc_final: 0.8813 (tp) REVERT: F 241 VAL cc_start: 0.9591 (m) cc_final: 0.9390 (p) REVERT: F 254 ILE cc_start: 0.9466 (mp) cc_final: 0.9263 (mp) REVERT: F 256 SER cc_start: 0.9319 (t) cc_final: 0.9030 (p) REVERT: F 257 CYS cc_start: 0.8811 (t) cc_final: 0.8585 (t) REVERT: F 427 ARG cc_start: 0.9039 (mmt180) cc_final: 0.8661 (tpt-90) REVERT: F 460 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8790 (mm-30) REVERT: F 463 LYS cc_start: 0.9225 (ptmt) cc_final: 0.8568 (ptmt) REVERT: F 469 TRP cc_start: 0.8949 (m100) cc_final: 0.8467 (m100) REVERT: F 473 MET cc_start: 0.9400 (mmp) cc_final: 0.8816 (mmp) REVERT: F 477 TYR cc_start: 0.9285 (m-10) cc_final: 0.8562 (m-10) REVERT: F 523 PHE cc_start: 0.9581 (m-10) cc_final: 0.9239 (m-80) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.0585 time to fit residues: 15.7546 Evaluate side-chains 188 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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: 1.9990 chunk 433 optimal weight: 20.0000 chunk 182 optimal weight: 0.2980 chunk 78 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 196 optimal weight: 8.9990 chunk 364 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 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 = 0.3557 r_free = 0.3557 target = 0.114320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.093541 restraints weight = 8626.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.096965 restraints weight = 5429.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.099533 restraints weight = 3847.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.101474 restraints weight = 2910.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102876 restraints weight = 2310.683| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.6571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 40380 Z= 0.116 Angle : 0.587 5.344 54852 Z= 0.311 Chirality : 0.043 0.220 6336 Planarity : 0.005 0.067 6852 Dihedral : 4.806 22.086 5436 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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: -1.19 (0.12), residues: 4908 helix: -0.11 (0.10), residues: 2676 sheet: -1.99 (0.28), residues: 288 loop : -1.46 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 459 TYR 0.016 0.002 TYR E 67 PHE 0.013 0.001 PHE D 54 TRP 0.013 0.002 TRP E 137 HIS 0.005 0.001 HIS K 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (40380) covalent geometry : angle 0.58677 / 0.31 (54852) hydrogen bonds : bond 0.03406 / 2.29 ( 1452) hydrogen bonds : angle 5.28984 / 3.61 ( 4284) *********************** REFINEMENT MACRO_CYCLE 7 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 234 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.123 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: 0.8460 (tt) cc_final: 0.8077 (mm) REVERT: L 25 GLU cc_start: 0.9384 (tm-30) cc_final: 0.8897 (tm-30) REVERT: L 26 ILE cc_start: 0.9659 (mt) cc_final: 0.9365 (mt) REVERT: L 49 PHE cc_start: 0.9484 (t80) cc_final: 0.8703 (t80) REVERT: L 50 PHE cc_start: 0.9626 (m-80) cc_final: 0.9361 (m-80) REVERT: L 51 ARG cc_start: 0.9436 (mtt90) cc_final: 0.8756 (mtp85) REVERT: L 53 LEU cc_start: 0.9411 (mt) cc_final: 0.8964 (mt) REVERT: L 59 LYS cc_start: 0.9514 (tttt) cc_final: 0.9201 (tmtt) REVERT: L 60 ASN cc_start: 0.9613 (m-40) cc_final: 0.9175 (p0) REVERT: L 68 ASP cc_start: 0.9352 (m-30) cc_final: 0.8927 (p0) REVERT: L 69 HIS cc_start: 0.9004 (m90) cc_final: 0.8652 (m90) REVERT: L 87 GLU cc_start: 0.8881 (pt0) cc_final: 0.8431 (pm20) REVERT: L 96 ARG cc_start: 0.8771 (mmt90) cc_final: 0.8179 (mmt-90) REVERT: L 97 ARG cc_start: 0.9099 (mtp85) cc_final: 0.8399 (mmp-170) REVERT: L 101 ASP cc_start: 0.9566 (t70) cc_final: 0.9245 (t70) REVERT: L 113 HIS cc_start: 0.9339 (t-90) cc_final: 0.9000 (t-90) REVERT: L 133 ARG cc_start: 0.9051 (mtt-85) cc_final: 0.8325 (mtp180) REVERT: L 154 LYS cc_start: 0.9501 (tttt) cc_final: 0.8987 (tppt) REVERT: L 169 ARG cc_start: 0.8869 (tpm170) cc_final: 0.8595 (tpp-160) REVERT: L 191 LEU cc_start: 0.9545 (tp) cc_final: 0.9207 (tp) REVERT: L 203 TYR cc_start: 0.9016 (t80) cc_final: 0.8389 (t80) REVERT: L 224 LYS cc_start: 0.9442 (mmtm) cc_final: 0.9120 (mmtm) REVERT: L 232 THR cc_start: 0.9282 (p) cc_final: 0.8922 (t) REVERT: L 237 LEU cc_start: 0.9086 (tp) cc_final: 0.8757 (tp) REVERT: L 248 GLN cc_start: 0.9451 (tp40) cc_final: 0.9210 (tp40) REVERT: L 251 TYR cc_start: 0.9012 (t80) cc_final: 0.8650 (t80) REVERT: L 256 SER cc_start: 0.9314 (t) cc_final: 0.9020 (p) REVERT: L 257 CYS cc_start: 0.8802 (t) cc_final: 0.8576 (t) REVERT: L 268 GLN cc_start: 0.7926 (mm110) cc_final: 0.7643 (mm-40) REVERT: L 423 GLN cc_start: 0.9361 (mt0) cc_final: 0.9104 (mt0) REVERT: L 427 ARG cc_start: 0.9041 (mmt180) cc_final: 0.8656 (tpt-90) REVERT: L 460 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8903 (mm-30) REVERT: L 463 LYS cc_start: 0.9178 (ptmt) cc_final: 0.8514 (ptmt) REVERT: L 469 TRP cc_start: 0.9024 (m100) cc_final: 0.8622 (m100) REVERT: L 473 MET cc_start: 0.9446 (mmp) cc_final: 0.9171 (mmp) REVERT: L 476 THR cc_start: 0.9427 (t) cc_final: 0.8715 (t) REVERT: L 515 GLN cc_start: 0.9169 (mp10) cc_final: 0.8743 (pm20) REVERT: L 523 PHE cc_start: 0.9547 (m-10) cc_final: 0.9085 (m-80) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.0568 time to fit residues: 16.2232 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 : 0.112 ------------------------------------------------------------------------------- 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: 1.9990 chunk 144 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 27 optimal weight: 0.0770 chunk 81 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 291 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 448 optimal weight: 6.9990 chunk 411 optimal weight: 9.9990 chunk 172 optimal weight: 0.0970 overall best weight: 2.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 40 HIS ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 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 = 0.3562 r_free = 0.3562 target = 0.114926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.093976 restraints weight = 8655.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.097214 restraints weight = 5515.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.099852 restraints weight = 3986.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.101805 restraints weight = 3025.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103389 restraints weight = 2417.808| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.6795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 40380 Z= 0.120 Angle : 0.611 8.509 54852 Z= 0.324 Chirality : 0.044 0.223 6336 Planarity : 0.006 0.080 6852 Dihedral : 4.833 21.898 5436 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: -0.93 (0.12), residues: 4908 helix: 0.06 (0.10), residues: 2580 sheet: -1.62 (0.29), residues: 288 loop : -1.24 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 84 TYR 0.023 0.002 TYR J 67 PHE 0.007 0.001 PHE A 49 TRP 0.014 0.002 TRP A 137 HIS 0.007 0.001 HIS I 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (40380) covalent geometry : angle 0.61059 / 0.32 (54852) hydrogen bonds : bond 0.03234 / 2.18 ( 1452) hydrogen bonds : angle 5.17889 / 3.53 ( 4284) *********************** REFINEMENT MACRO_CYCLE 8 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 229 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.099 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: symmetry clash revert: symmetry clash REVERT: L 12 ILE cc_start: 0.8429 (tt) cc_final: 0.8064 (mm) REVERT: L 15 HIS cc_start: 0.8016 (t-90) cc_final: 0.7652 (m170) REVERT: L 25 GLU cc_start: 0.9387 (tm-30) cc_final: 0.8933 (tm-30) REVERT: L 26 ILE cc_start: 0.9586 (mt) cc_final: 0.9335 (mt) REVERT: L 49 PHE cc_start: 0.9467 (t80) cc_final: 0.8771 (t80) REVERT: L 50 PHE cc_start: 0.9622 (m-10) cc_final: 0.9359 (m-80) REVERT: L 51 ARG cc_start: 0.9365 (mtt90) cc_final: 0.9153 (mtt-85) REVERT: L 52 GLN cc_start: 0.9751 (tt0) cc_final: 0.9380 (tp40) REVERT: L 53 LEU cc_start: 0.9385 (mt) cc_final: 0.8944 (mt) REVERT: L 59 LYS cc_start: 0.9537 (tttt) cc_final: 0.9212 (tmtt) REVERT: L 60 ASN cc_start: 0.9591 (m-40) cc_final: 0.9171 (p0) REVERT: L 69 HIS cc_start: 0.8936 (m90) cc_final: 0.8636 (m90) REVERT: L 83 THR cc_start: 0.9442 (p) cc_final: 0.9121 (p) REVERT: L 91 GLN cc_start: 0.9088 (pp30) cc_final: 0.8731 (tm-30) REVERT: L 96 ARG cc_start: 0.8777 (mmt90) cc_final: 0.8381 (mmt-90) REVERT: L 97 ARG cc_start: 0.9106 (mtp85) cc_final: 0.8444 (mmp-170) REVERT: L 100 PHE cc_start: 0.9330 (t80) cc_final: 0.9129 (t80) REVERT: L 101 ASP cc_start: 0.9567 (t70) cc_final: 0.9296 (t70) REVERT: L 113 HIS cc_start: 0.9379 (t-90) cc_final: 0.9062 (t-90) REVERT: L 133 ARG cc_start: 0.9049 (mtt-85) cc_final: 0.8316 (mtp180) REVERT: L 154 LYS cc_start: 0.9515 (tttt) cc_final: 0.8969 (tppt) REVERT: L 169 ARG cc_start: 0.8872 (tpm170) cc_final: 0.8609 (tpp-160) REVERT: L 191 LEU cc_start: 0.9534 (tp) cc_final: 0.9193 (tp) REVERT: L 199 TYR cc_start: 0.8574 (t80) cc_final: 0.8369 (t80) REVERT: L 203 TYR cc_start: 0.9018 (t80) cc_final: 0.8413 (t80) REVERT: L 224 LYS cc_start: 0.9434 (mmtm) cc_final: 0.9079 (mmtm) REVERT: L 232 THR cc_start: 0.9279 (p) cc_final: 0.8952 (t) REVERT: L 237 LEU cc_start: 0.9001 (tp) cc_final: 0.8738 (tp) REVERT: L 256 SER cc_start: 0.9326 (t) cc_final: 0.9021 (p) REVERT: L 268 GLN cc_start: 0.7862 (mm110) cc_final: 0.7499 (mm-40) REVERT: L 423 GLN cc_start: 0.9365 (mt0) cc_final: 0.9127 (mt0) REVERT: L 427 ARG cc_start: 0.9039 (mmt180) cc_final: 0.8660 (tpt-90) REVERT: L 463 LYS cc_start: 0.9208 (ptmt) cc_final: 0.8827 (pttm) REVERT: L 469 TRP cc_start: 0.8914 (m100) cc_final: 0.8527 (m100) REVERT: L 473 MET cc_start: 0.9454 (mmp) cc_final: 0.9210 (mmp) REVERT: L 476 THR cc_start: 0.9140 (t) cc_final: 0.8836 (t) REVERT: L 515 GLN cc_start: 0.9235 (mp10) cc_final: 0.8736 (pm20) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.0571 time to fit residues: 15.9790 Evaluate side-chains 194 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.076 ------------------------------------------------------------------------------- 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: 10.0000 chunk 359 optimal weight: 6.9990 chunk 418 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 467 optimal weight: 5.9990 chunk 324 optimal weight: 0.1980 chunk 248 optimal weight: 0.0070 chunk 179 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 461 optimal weight: 0.8980 chunk 316 optimal weight: 9.9990 overall best weight: 2.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 56 HIS L 60 ASN ** L 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.115179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.094240 restraints weight = 8644.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.097582 restraints weight = 5564.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.100102 restraints weight = 3991.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.102132 restraints weight = 3054.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.103698 restraints weight = 2422.959| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40380 Z= 0.133 Angle : 0.640 5.636 54852 Z= 0.341 Chirality : 0.045 0.223 6336 Planarity : 0.005 0.078 6852 Dihedral : 4.962 25.125 5436 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.06 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: -0.79 (0.12), residues: 4908 helix: 0.02 (0.10), residues: 2592 sheet: -1.16 (0.37), residues: 168 loop : -1.06 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 489 TYR 0.020 0.002 TYR J 67 PHE 0.008 0.001 PHE A 49 TRP 0.017 0.002 TRP E 137 HIS 0.003 0.001 HIS J 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (40380) covalent geometry : angle 0.64002 / 0.34 (54852) hydrogen bonds : bond 0.03474 / 2.36 ( 1452) hydrogen bonds : angle 5.40583 / 3.70 ( 4284) *********************** REFINEMENT MACRO_CYCLE 9 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 225 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.123 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: C 12 ILE cc_start: 0.8397 (tt) cc_final: 0.8042 (mm) REVERT: C 15 HIS cc_start: 0.8038 (t-90) cc_final: 0.7679 (m170) REVERT: C 25 GLU cc_start: 0.9419 (tm-30) cc_final: 0.8959 (tm-30) REVERT: C 26 ILE cc_start: 0.9583 (mt) cc_final: 0.9339 (mt) REVERT: C 49 PHE cc_start: 0.9480 (t80) cc_final: 0.8750 (t80) REVERT: C 50 PHE cc_start: 0.9622 (m-10) cc_final: 0.9360 (m-80) REVERT: C 51 ARG cc_start: 0.9363 (mtt90) cc_final: 0.9057 (mtt180) REVERT: C 53 LEU cc_start: 0.9462 (mt) cc_final: 0.9033 (mt) REVERT: C 60 ASN cc_start: 0.9569 (m-40) cc_final: 0.9333 (m-40) REVERT: C 68 ASP cc_start: 0.9414 (m-30) cc_final: 0.8967 (p0) REVERT: C 69 HIS cc_start: 0.8952 (m90) cc_final: 0.8628 (m90) REVERT: C 78 GLU cc_start: 0.9242 (mp0) cc_final: 0.8982 (mp0) REVERT: C 87 GLU cc_start: 0.8666 (pm20) cc_final: 0.8398 (pm20) REVERT: C 96 ARG cc_start: 0.8779 (mmt90) cc_final: 0.8072 (mmt-90) REVERT: C 97 ARG cc_start: 0.9098 (mtp85) cc_final: 0.8496 (mmp-170) REVERT: C 101 ASP cc_start: 0.9564 (t70) cc_final: 0.9290 (t70) REVERT: C 113 HIS cc_start: 0.9357 (t-90) cc_final: 0.9062 (t-90) REVERT: C 169 ARG cc_start: 0.8843 (tpm170) cc_final: 0.8587 (tpp-160) REVERT: C 203 TYR cc_start: 0.8994 (t80) cc_final: 0.8434 (t80) REVERT: C 224 LYS cc_start: 0.9405 (mmtm) cc_final: 0.9072 (mmtm) REVERT: C 232 THR cc_start: 0.9283 (p) cc_final: 0.9017 (t) REVERT: C 237 LEU cc_start: 0.8994 (tp) cc_final: 0.8738 (tp) REVERT: C 251 TYR cc_start: 0.8989 (t80) cc_final: 0.8674 (t80) REVERT: C 256 SER cc_start: 0.9320 (t) cc_final: 0.9030 (p) REVERT: C 268 GLN cc_start: 0.7887 (mm110) cc_final: 0.7504 (mm-40) REVERT: C 423 GLN cc_start: 0.9375 (mt0) cc_final: 0.9124 (mt0) REVERT: C 427 ARG cc_start: 0.9053 (mmt180) cc_final: 0.8642 (tpt-90) REVERT: C 459 ARG cc_start: 0.8519 (mtt90) cc_final: 0.8284 (ttm110) REVERT: C 460 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8810 (tp30) REVERT: C 463 LYS cc_start: 0.9243 (ptmt) cc_final: 0.8837 (ptmt) REVERT: C 469 TRP cc_start: 0.8977 (m100) cc_final: 0.8713 (m100) REVERT: C 473 MET cc_start: 0.9412 (mmp) cc_final: 0.8698 (mmp) REVERT: C 476 THR cc_start: 0.9249 (t) cc_final: 0.8625 (t) REVERT: C 477 TYR cc_start: 0.9005 (m-80) cc_final: 0.8456 (m-80) REVERT: C 515 GLN cc_start: 0.9185 (mp10) cc_final: 0.8874 (pm20) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.0567 time to fit residues: 15.5583 Evaluate side-chains 184 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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: 0.4980 chunk 279 optimal weight: 0.0070 chunk 281 optimal weight: 0.5980 chunk 426 optimal weight: 0.2980 chunk 123 optimal weight: 20.0000 chunk 358 optimal weight: 20.0000 chunk 416 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 355 optimal weight: 0.0570 chunk 216 optimal weight: 9.9990 chunk 186 optimal weight: 0.5980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 40 HIS C 56 HIS C 60 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.118589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.097617 restraints weight = 8330.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.100910 restraints weight = 5300.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103456 restraints weight = 3795.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.105340 restraints weight = 2902.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106951 restraints weight = 2330.521| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.7140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40380 Z= 0.131 Angle : 0.664 7.142 54852 Z= 0.352 Chirality : 0.045 0.225 6336 Planarity : 0.006 0.079 6852 Dihedral : 4.832 21.192 5436 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.95 (0.12), residues: 4908 helix: -0.03 (0.10), residues: 2580 sheet: -1.50 (0.27), residues: 288 loop : -1.15 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 84 TYR 0.036 0.002 TYR J 67 PHE 0.014 0.001 PHE C 54 TRP 0.021 0.002 TRP I 74 HIS 0.015 0.001 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (40380) covalent geometry : angle 0.66443 / 0.35 (54852) hydrogen bonds : bond 0.03519 / 2.39 ( 1452) hydrogen bonds : angle 5.42447 / 3.70 ( 4284) ********************** REFINEMENT MACRO_CYCLE 10 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 213 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.080 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: symmetry clash REVERT: L 12 ILE cc_start: 0.8484 (tt) cc_final: 0.8137 (mm) REVERT: L 15 HIS cc_start: 0.7854 (t-90) cc_final: 0.7610 (m-70) REVERT: L 25 GLU cc_start: 0.9395 (tm-30) cc_final: 0.8921 (tm-30) REVERT: L 26 ILE cc_start: 0.9526 (mt) cc_final: 0.9246 (mt) REVERT: L 43 LEU cc_start: 0.9541 (tp) cc_final: 0.9265 (tp) REVERT: L 49 PHE cc_start: 0.9480 (t80) cc_final: 0.8679 (t80) REVERT: L 50 PHE cc_start: 0.9562 (m-10) cc_final: 0.9314 (m-80) REVERT: L 51 ARG cc_start: 0.9349 (mtt90) cc_final: 0.9058 (mtt180) REVERT: L 53 LEU cc_start: 0.9237 (mt) cc_final: 0.8855 (mt) REVERT: L 59 LYS cc_start: 0.9529 (tttt) cc_final: 0.9138 (tmtt) REVERT: L 68 ASP cc_start: 0.9390 (m-30) cc_final: 0.9006 (p0) REVERT: L 87 GLU cc_start: 0.8426 (pm20) cc_final: 0.8171 (pm20) REVERT: L 96 ARG cc_start: 0.8845 (mmt90) cc_final: 0.8221 (tpp80) REVERT: L 97 ARG cc_start: 0.9068 (mtp85) cc_final: 0.8392 (mmp-170) REVERT: L 101 ASP cc_start: 0.9565 (t70) cc_final: 0.9309 (t70) REVERT: L 113 HIS cc_start: 0.9369 (t-90) cc_final: 0.9067 (t-90) REVERT: L 133 ARG cc_start: 0.8987 (mtt-85) cc_final: 0.8316 (mtp180) REVERT: L 169 ARG cc_start: 0.8818 (tpm170) cc_final: 0.8614 (tpp-160) REVERT: L 200 ILE cc_start: 0.9006 (mt) cc_final: 0.8732 (tt) REVERT: L 203 TYR cc_start: 0.8990 (t80) cc_final: 0.8711 (t80) REVERT: L 224 LYS cc_start: 0.9372 (mmtm) cc_final: 0.8996 (mmtm) REVERT: L 237 LEU cc_start: 0.8949 (tp) cc_final: 0.8685 (tp) REVERT: L 247 ILE cc_start: 0.9547 (mt) cc_final: 0.9343 (mt) REVERT: L 256 SER cc_start: 0.9314 (t) cc_final: 0.9027 (p) REVERT: L 268 GLN cc_start: 0.7856 (mm110) cc_final: 0.7468 (mm-40) REVERT: L 423 GLN cc_start: 0.9365 (mt0) cc_final: 0.9111 (mt0) REVERT: L 427 ARG cc_start: 0.9035 (mmt180) cc_final: 0.8520 (tpt-90) REVERT: L 463 LYS cc_start: 0.9268 (ptmt) cc_final: 0.8847 (pttm) REVERT: L 473 MET cc_start: 0.9421 (mmp) cc_final: 0.9182 (mmp) REVERT: L 515 GLN cc_start: 0.9101 (mp10) cc_final: 0.8851 (pm20) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.0617 time to fit residues: 15.8673 Evaluate side-chains 193 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.122 ------------------------------------------------------------------------------- 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: 0.0970 chunk 234 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 377 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 395 optimal weight: 0.0370 chunk 115 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 overall best weight: 2.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN L 153 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 = 0.3611 r_free = 0.3611 target = 0.118127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.096910 restraints weight = 8411.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.100101 restraints weight = 5329.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.102723 restraints weight = 3846.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.104681 restraints weight = 2927.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106255 restraints weight = 2341.752| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.7326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40380 Z= 0.124 Angle : 0.624 6.187 54852 Z= 0.330 Chirality : 0.044 0.233 6336 Planarity : 0.005 0.079 6852 Dihedral : 4.816 21.456 5436 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.99 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: -0.99 (0.12), residues: 4908 helix: -0.03 (0.10), residues: 2604 sheet: -1.48 (0.26), residues: 288 loop : -1.25 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 84 TYR 0.013 0.002 TYR B 477 PHE 0.017 0.001 PHE F 54 TRP 0.018 0.002 TRP A 74 HIS 0.004 0.001 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (40380) covalent geometry : angle 0.62449 / 0.33 (54852) hydrogen bonds : bond 0.03512 / 2.37 ( 1452) hydrogen bonds : angle 5.44877 / 3.72 ( 4284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2448.41 seconds wall clock time: 45 minutes 13.82 seconds (2713.82 seconds total)