Starting phenix.real_space_refine on Sun Jun 29 15:03:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ttn_26120/06_2025/7ttn_26120.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ttn_26120/06_2025/7ttn_26120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ttn_26120/06_2025/7ttn_26120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ttn_26120/06_2025/7ttn_26120.map" model { file = "/net/cci-nas-00/data/ceres_data/7ttn_26120/06_2025/7ttn_26120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ttn_26120/06_2025/7ttn_26120.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 8 Type Number sf(0) Gaussians Al 8 5.89 5 P 16 5.49 5 Mg 8 5.21 5 S 209 5.16 5 C 21598 2.51 5 N 6000 2.21 5 O 6700 1.98 5 F 24 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34563 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2119 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain breaks: 3 Chain: "B" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4029 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "C" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4003 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 15, 'TRANS': 505} Chain breaks: 1 Chain: "D" Number of atoms: 4072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4072 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 18, 'TRANS': 509} Chain: "E" Number of atoms: 3974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3974 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 11, 'TRANS': 516} Chain: "F" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3924 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "G" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4063 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 14, 'TRANS': 520} Chain: "H" Number of atoms: 4064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4064 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 16, 'TRANS': 506} Chain: "I" Number of atoms: 4051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4051 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 14, 'TRANS': 513} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 18.56, per 1000 atoms: 0.54 Number of scatterers: 34563 At special positions: 0 Unit cell: (180.4, 183.7, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 209 16.00 P 16 15.00 Al 8 13.00 Mg 8 11.99 F 24 9.00 O 6700 8.00 N 6000 7.00 C 21598 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.70 Conformation dependent library (CDL) restraints added in 4.3 seconds 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8340 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 50 sheets defined 52.7% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.523A pdb=" N LYS A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 27 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 72 removed outlier: 3.624A pdb=" N THR A 72 " --> pdb=" O GLU A 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 69 through 72' Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 108 through 113 removed outlier: 4.257A pdb=" N LEU A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 108 through 113' Processing helix chain 'A' and resid 113 through 127 removed outlier: 3.944A pdb=" N ASP A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 159 removed outlier: 3.795A pdb=" N MET A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 194 removed outlier: 3.860A pdb=" N LEU A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU A 194 " --> pdb=" O HIS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 removed outlier: 3.642A pdb=" N PHE A 378 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 382 " --> pdb=" O PHE A 378 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 404 through 422 removed outlier: 4.008A pdb=" N PHE A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 14 Processing helix chain 'B' and resid 28 through 44 removed outlier: 3.722A pdb=" N GLN B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 40 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 41 " --> pdb=" O LYS B 37 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 80 through 97 removed outlier: 3.676A pdb=" N MET B 85 " --> pdb=" O PRO B 81 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN B 95 " --> pdb=" O HIS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 121 removed outlier: 3.898A pdb=" N VAL B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 143 removed outlier: 3.501A pdb=" N GLU B 141 " --> pdb=" O ARG B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 147 removed outlier: 3.577A pdb=" N VAL B 147 " --> pdb=" O PRO B 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 147' Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.559A pdb=" N ALA B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 181 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 261 through 285 removed outlier: 3.560A pdb=" N LEU B 265 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS B 270 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 removed outlier: 3.658A pdb=" N TYR B 304 " --> pdb=" O MET B 300 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 3.538A pdb=" N LYS B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 405 removed outlier: 3.617A pdb=" N ASP B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 429 removed outlier: 3.790A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 444 Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 459 through 474 removed outlier: 3.842A pdb=" N VAL B 463 " --> pdb=" O LYS B 459 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 496 removed outlier: 3.666A pdb=" N ALA B 495 " --> pdb=" O ASP B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 520 removed outlier: 3.511A pdb=" N TRP B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 518 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 519 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 520 " --> pdb=" O VAL B 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 27 removed outlier: 3.635A pdb=" N ASN C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 36 removed outlier: 3.997A pdb=" N ILE C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 76 through 90 removed outlier: 3.671A pdb=" N VAL C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 107 removed outlier: 3.899A pdb=" N LEU C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 114 Processing helix chain 'C' and resid 117 through 139 removed outlier: 3.791A pdb=" N ILE C 121 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 164 removed outlier: 4.171A pdb=" N LEU C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 184 removed outlier: 3.631A pdb=" N LYS C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET C 178 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 208 removed outlier: 3.925A pdb=" N SER C 208 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 removed outlier: 3.980A pdb=" N GLN C 228 " --> pdb=" O PHE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 284 removed outlier: 3.563A pdb=" N ALA C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 305 removed outlier: 3.538A pdb=" N ASP C 305 " --> pdb=" O GLN C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 removed outlier: 3.770A pdb=" N ARG C 321 " --> pdb=" O GLU C 317 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 325 " --> pdb=" O ARG C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 342 removed outlier: 3.601A pdb=" N VAL C 341 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 342 " --> pdb=" O ALA C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 338 through 342' Processing helix chain 'C' and resid 378 through 402 removed outlier: 3.610A pdb=" N ASP C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA C 392 " --> pdb=" O SER C 388 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET C 394 " --> pdb=" O HIS C 390 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS C 401 " --> pdb=" O ARG C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 425 removed outlier: 3.709A pdb=" N GLU C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 430 No H-bonds generated for 'chain 'C' and resid 428 through 430' Processing helix chain 'C' and resid 431 through 440 removed outlier: 3.590A pdb=" N ALA C 437 " --> pdb=" O LEU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 454 removed outlier: 3.603A pdb=" N ALA C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.505A pdb=" N ILE C 460 " --> pdb=" O ASP C 456 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C 470 " --> pdb=" O ALA C 466 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 525 removed outlier: 3.608A pdb=" N ASN C 511 " --> pdb=" O MET C 507 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA C 512 " --> pdb=" O VAL C 508 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 525 " --> pdb=" O CYS C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 29 through 48 removed outlier: 3.599A pdb=" N ALA D 33 " --> pdb=" O MET D 29 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 removed outlier: 3.517A pdb=" N LEU D 78 " --> pdb=" O GLY D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 100 removed outlier: 3.721A pdb=" N GLN D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP D 100 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.514A pdb=" N GLU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 149 removed outlier: 3.960A pdb=" N GLU D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN D 139 " --> pdb=" O ASP D 135 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 146 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 173 removed outlier: 3.895A pdb=" N THR D 171 " --> pdb=" O GLN D 167 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 192 removed outlier: 3.952A pdb=" N ALA D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.763A pdb=" N THR D 222 " --> pdb=" O LEU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 295 removed outlier: 3.633A pdb=" N TYR D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D 286 " --> pdb=" O LYS D 282 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 317 removed outlier: 4.106A pdb=" N HIS D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 338 removed outlier: 3.666A pdb=" N ILE D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 332 " --> pdb=" O PRO D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 415 removed outlier: 3.566A pdb=" N ILE D 395 " --> pdb=" O ASN D 391 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU D 396 " --> pdb=" O LYS D 392 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 438 through 440 No H-bonds generated for 'chain 'D' and resid 438 through 440' Processing helix chain 'D' and resid 444 through 455 Processing helix chain 'D' and resid 456 through 467 removed outlier: 3.509A pdb=" N MET D 460 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU D 464 " --> pdb=" O MET D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 484 removed outlier: 3.508A pdb=" N THR D 475 " --> pdb=" O ILE D 471 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 510 through 529 removed outlier: 3.509A pdb=" N GLN D 516 " --> pdb=" O GLY D 512 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 517 " --> pdb=" O LYS D 513 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA D 520 " --> pdb=" O GLN D 516 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET D 523 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 40 removed outlier: 4.150A pdb=" N LEU E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 39 " --> pdb=" O ILE E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 43 No H-bonds generated for 'chain 'E' and resid 41 through 43' Processing helix chain 'E' and resid 68 through 74 Processing helix chain 'E' and resid 80 through 95 removed outlier: 4.277A pdb=" N LEU E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 118 removed outlier: 3.772A pdb=" N LEU E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU E 116 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 143 removed outlier: 3.874A pdb=" N GLU E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA E 133 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 167 removed outlier: 3.910A pdb=" N GLN E 157 " --> pdb=" O VAL E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.769A pdb=" N HIS E 174 " --> pdb=" O LEU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 189 removed outlier: 4.467A pdb=" N LYS E 181 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU E 182 " --> pdb=" O HIS E 178 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA E 186 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.774A pdb=" N SER E 212 " --> pdb=" O LEU E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 284 removed outlier: 3.616A pdb=" N VAL E 264 " --> pdb=" O SER E 260 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA E 265 " --> pdb=" O THR E 261 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS E 276 " --> pdb=" O LYS E 272 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 307 removed outlier: 3.720A pdb=" N GLN E 302 " --> pdb=" O ASN E 298 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 303 " --> pdb=" O TYR E 299 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA E 307 " --> pdb=" O LEU E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 321 Processing helix chain 'E' and resid 322 through 327 Processing helix chain 'E' and resid 379 through 403 removed outlier: 3.531A pdb=" N LEU E 383 " --> pdb=" O THR E 379 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP E 392 " --> pdb=" O ARG E 388 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 393 " --> pdb=" O SER E 389 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN E 399 " --> pdb=" O CYS E 395 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR E 400 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS E 402 " --> pdb=" O ALA E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 426 removed outlier: 3.582A pdb=" N ALA E 420 " --> pdb=" O LEU E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 444 removed outlier: 3.525A pdb=" N SER E 438 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR E 439 " --> pdb=" O ALA E 435 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG E 444 " --> pdb=" O ALA E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 454 removed outlier: 3.810A pdb=" N ALA E 454 " --> pdb=" O ILE E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 470 removed outlier: 4.002A pdb=" N ALA E 463 " --> pdb=" O ALA E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 492 removed outlier: 3.503A pdb=" N GLY E 492 " --> pdb=" O MET E 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 488 through 492' Processing helix chain 'E' and resid 497 through 516 removed outlier: 3.646A pdb=" N LEU E 504 " --> pdb=" O LYS E 500 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA E 511 " --> pdb=" O ALA E 507 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 48 removed outlier: 3.518A pdb=" N SER F 39 " --> pdb=" O PHE F 35 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE F 48 " --> pdb=" O VAL F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 81 removed outlier: 3.592A pdb=" N LEU F 78 " --> pdb=" O GLY F 74 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 102 removed outlier: 3.552A pdb=" N MET F 90 " --> pdb=" O PRO F 86 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU F 93 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN F 98 " --> pdb=" O LEU F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 126 removed outlier: 3.919A pdb=" N VAL F 110 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP F 118 " --> pdb=" O GLY F 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS F 120 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LYS F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 150 removed outlier: 3.557A pdb=" N ILE F 133 " --> pdb=" O HIS F 129 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU F 146 " --> pdb=" O GLU F 142 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP F 150 " --> pdb=" O GLU F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 170 removed outlier: 3.683A pdb=" N LEU F 163 " --> pdb=" O ASP F 159 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 179 through 193 removed outlier: 3.817A pdb=" N SER F 184 " --> pdb=" O SER F 180 " (cutoff:3.500A) Proline residue: F 185 - end of helix removed outlier: 3.555A pdb=" N ALA F 190 " --> pdb=" O MET F 186 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL F 191 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS F 193 " --> pdb=" O ASN F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 206 No H-bonds generated for 'chain 'F' and resid 204 through 206' Processing helix chain 'F' and resid 217 through 221 Processing helix chain 'F' and resid 269 through 293 removed outlier: 4.366A pdb=" N ASP F 273 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG F 274 " --> pdb=" O ALA F 270 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU F 276 " --> pdb=" O MET F 272 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR F 293 " --> pdb=" O GLN F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 319 removed outlier: 3.724A pdb=" N LYS F 319 " --> pdb=" O HIS F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 341 Processing helix chain 'F' and resid 347 through 351 Processing helix chain 'F' and resid 394 through 418 removed outlier: 3.563A pdb=" N GLU F 399 " --> pdb=" O LYS F 395 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 416 " --> pdb=" O ILE F 412 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS F 417 " --> pdb=" O ARG F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 443 removed outlier: 3.812A pdb=" N ILE F 430 " --> pdb=" O GLY F 426 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU F 431 " --> pdb=" O ALA F 427 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR F 437 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU F 438 " --> pdb=" O LEU F 434 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG F 441 " --> pdb=" O THR F 437 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR F 442 " --> pdb=" O GLU F 438 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU F 443 " --> pdb=" O TYR F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 458 removed outlier: 3.924A pdb=" N CYS F 450 " --> pdb=" O MET F 446 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG F 452 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET F 458 " --> pdb=" O PHE F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 469 removed outlier: 3.700A pdb=" N ALA F 466 " --> pdb=" O PRO F 462 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA F 469 " --> pdb=" O LEU F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 504 through 507 Processing helix chain 'F' and resid 512 through 530 removed outlier: 3.804A pdb=" N LEU F 519 " --> pdb=" O SER F 515 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU F 521 " --> pdb=" O SER F 517 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA F 522 " --> pdb=" O ALA F 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARG G 18 " --> pdb=" O GLY G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 32 removed outlier: 3.743A pdb=" N ILE G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL G 32 " --> pdb=" O ILE G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 35 No H-bonds generated for 'chain 'G' and resid 33 through 35' Processing helix chain 'G' and resid 57 through 65 removed outlier: 3.507A pdb=" N ILE G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 86 removed outlier: 3.840A pdb=" N VAL G 74 " --> pdb=" O PRO G 70 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS G 84 " --> pdb=" O ASP G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 110 removed outlier: 3.739A pdb=" N ILE G 95 " --> pdb=" O THR G 91 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE G 96 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU G 106 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU G 107 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 135 removed outlier: 3.584A pdb=" N VAL G 117 " --> pdb=" O HIS G 113 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE G 132 " --> pdb=" O ALA G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 142 removed outlier: 3.540A pdb=" N ASP G 141 " --> pdb=" O VAL G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 155 removed outlier: 3.793A pdb=" N SER G 155 " --> pdb=" O ALA G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 177 removed outlier: 4.428A pdb=" N ASN G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET G 171 " --> pdb=" O PHE G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 204 through 208 removed outlier: 3.768A pdb=" N SER G 208 " --> pdb=" O GLN G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 259 Processing helix chain 'G' and resid 260 through 266 Processing helix chain 'G' and resid 269 through 280 Processing helix chain 'G' and resid 298 through 303 removed outlier: 3.872A pdb=" N GLU G 302 " --> pdb=" O LYS G 298 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA G 303 " --> pdb=" O TYR G 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 298 through 303' Processing helix chain 'G' and resid 312 through 324 removed outlier: 3.816A pdb=" N ARG G 318 " --> pdb=" O ARG G 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 405 removed outlier: 3.515A pdb=" N GLU G 387 " --> pdb=" O PHE G 383 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG G 390 " --> pdb=" O ASP G 386 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA G 395 " --> pdb=" O SER G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 427 removed outlier: 3.550A pdb=" N ALA G 417 " --> pdb=" O GLY G 413 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE G 421 " --> pdb=" O ALA G 417 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU G 424 " --> pdb=" O SER G 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN G 425 " --> pdb=" O ILE G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 428 through 430 No H-bonds generated for 'chain 'G' and resid 428 through 430' Processing helix chain 'G' and resid 433 through 446 removed outlier: 4.112A pdb=" N ALA G 437 " --> pdb=" O ARG G 433 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU G 446 " --> pdb=" O ALA G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 456 removed outlier: 3.823A pdb=" N ASN G 450 " --> pdb=" O LEU G 446 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN G 455 " --> pdb=" O THR G 451 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 476 removed outlier: 3.633A pdb=" N GLU G 473 " --> pdb=" O ALA G 469 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN G 475 " --> pdb=" O HIS G 471 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL G 476 " --> pdb=" O ASN G 472 " (cutoff:3.500A) Processing helix chain 'G' and resid 481 through 485 removed outlier: 4.121A pdb=" N LYS G 484 " --> pdb=" O LYS G 481 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TRP G 485 " --> pdb=" O ASN G 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 481 through 485' Processing helix chain 'G' and resid 497 through 502 Processing helix chain 'G' and resid 507 through 526 removed outlier: 3.524A pdb=" N ILE G 524 " --> pdb=" O ALA G 520 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 38 removed outlier: 4.076A pdb=" N GLN H 23 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 68 removed outlier: 3.766A pdb=" N LEU H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 91 removed outlier: 3.729A pdb=" N SER H 79 " --> pdb=" O PRO H 75 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N MET H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER H 84 " --> pdb=" O MET H 80 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG H 85 " --> pdb=" O ILE H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 108 Processing helix chain 'H' and resid 109 through 114 Processing helix chain 'H' and resid 118 through 138 removed outlier: 3.783A pdb=" N VAL H 122 " --> pdb=" O HIS H 118 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER H 124 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA H 125 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP H 131 " --> pdb=" O ARG H 127 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP H 132 " --> pdb=" O LYS H 128 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER H 135 " --> pdb=" O ASP H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 161 removed outlier: 3.686A pdb=" N MET H 152 " --> pdb=" O ASP H 148 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE H 156 " --> pdb=" O MET H 152 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER H 159 " --> pdb=" O ILE H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'H' and resid 168 through 184 removed outlier: 4.535A pdb=" N ASN H 174 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP H 178 " --> pdb=" O ASN H 174 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA H 179 " --> pdb=" O ILE H 175 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET H 182 " --> pdb=" O ASP H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 208 through 212 Processing helix chain 'H' and resid 262 through 284 removed outlier: 3.705A pdb=" N GLU H 271 " --> pdb=" O ILE H 267 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE H 275 " --> pdb=" O GLU H 271 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE H 282 " --> pdb=" O LEU H 278 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN H 284 " --> pdb=" O GLU H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 306 removed outlier: 3.537A pdb=" N GLN H 301 " --> pdb=" O SER H 297 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS H 302 " --> pdb=" O ASP H 298 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU H 304 " --> pdb=" O ALA H 300 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG H 306 " --> pdb=" O HIS H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 318 through 327 removed outlier: 3.626A pdb=" N ILE H 323 " --> pdb=" O ASP H 319 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA H 324 " --> pdb=" O ASN H 320 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG H 325 " --> pdb=" O ASN H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 404 removed outlier: 3.555A pdb=" N GLU H 386 " --> pdb=" O GLU H 382 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN H 396 " --> pdb=" O GLN H 392 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU H 402 " --> pdb=" O CYS H 398 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 424 removed outlier: 3.633A pdb=" N MET H 416 " --> pdb=" O GLY H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 425 through 429 removed outlier: 3.628A pdb=" N ALA H 428 " --> pdb=" O LYS H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 443 removed outlier: 3.773A pdb=" N VAL H 440 " --> pdb=" O PRO H 436 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA H 441 " --> pdb=" O TYR H 437 " (cutoff:3.500A) Processing helix chain 'H' and resid 446 through 454 removed outlier: 3.595A pdb=" N LEU H 451 " --> pdb=" O ILE H 447 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE H 452 " --> pdb=" O PRO H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 468 Processing helix chain 'H' and resid 469 through 472 removed outlier: 3.886A pdb=" N GLN H 472 " --> pdb=" O LYS H 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 469 through 472' Processing helix chain 'H' and resid 490 through 494 Processing helix chain 'H' and resid 499 through 517 removed outlier: 3.546A pdb=" N GLU H 511 " --> pdb=" O LYS H 507 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 8 Processing helix chain 'I' and resid 17 through 35 removed outlier: 3.582A pdb=" N VAL I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN I 23 " --> pdb=" O ALA I 19 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 38 No H-bonds generated for 'chain 'I' and resid 36 through 38' Processing helix chain 'I' and resid 59 through 65 Processing helix chain 'I' and resid 72 through 86 removed outlier: 3.755A pdb=" N LEU I 76 " --> pdb=" O PRO I 72 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE I 77 " --> pdb=" O THR I 73 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP I 86 " --> pdb=" O THR I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 111 removed outlier: 3.922A pdb=" N VAL I 96 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS I 104 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU I 108 " --> pdb=" O LYS I 104 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR I 109 " --> pdb=" O GLN I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 135 removed outlier: 4.054A pdb=" N ILE I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY I 122 " --> pdb=" O ILE I 118 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU I 135 " --> pdb=" O LEU I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 155 removed outlier: 3.765A pdb=" N ASP I 150 " --> pdb=" O GLU I 146 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER I 155 " --> pdb=" O VAL I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 179 removed outlier: 3.517A pdb=" N ASP I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU I 170 " --> pdb=" O ASP I 166 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA I 171 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER I 175 " --> pdb=" O ALA I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 204 removed outlier: 3.812A pdb=" N ASP I 203 " --> pdb=" O SER I 200 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR I 204 " --> pdb=" O GLU I 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 200 through 204' Processing helix chain 'I' and resid 253 through 261 removed outlier: 3.790A pdb=" N GLU I 257 " --> pdb=" O ALA I 253 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU I 259 " --> pdb=" O GLU I 255 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS I 261 " --> pdb=" O GLU I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 282 removed outlier: 4.061A pdb=" N ARG I 270 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL I 271 " --> pdb=" O ILE I 267 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE I 274 " --> pdb=" O ARG I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 305 Processing helix chain 'I' and resid 319 through 328 removed outlier: 4.345A pdb=" N THR I 325 " --> pdb=" O MET I 321 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU I 326 " --> pdb=" O GLU I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 344 removed outlier: 3.572A pdb=" N LEU I 344 " --> pdb=" O PRO I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 404 removed outlier: 3.512A pdb=" N THR I 385 " --> pdb=" O LYS I 381 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL I 398 " --> pdb=" O GLY I 394 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA I 401 " --> pdb=" O ALA I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 425 removed outlier: 3.595A pdb=" N ILE I 423 " --> pdb=" O ALA I 419 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS I 424 " --> pdb=" O GLU I 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 430 through 432 No H-bonds generated for 'chain 'I' and resid 430 through 432' Processing helix chain 'I' and resid 433 through 444 removed outlier: 3.700A pdb=" N VAL I 437 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU I 444 " --> pdb=" O PHE I 440 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 455 removed outlier: 3.560A pdb=" N LYS I 449 " --> pdb=" O LEU I 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 458 through 469 removed outlier: 3.946A pdb=" N LEU I 463 " --> pdb=" O LEU I 459 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS I 465 " --> pdb=" O GLU I 461 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU I 469 " --> pdb=" O LYS I 465 " (cutoff:3.500A) Processing helix chain 'I' and resid 490 through 492 No H-bonds generated for 'chain 'I' and resid 490 through 492' Processing helix chain 'I' and resid 498 through 516 removed outlier: 3.640A pdb=" N THR I 509 " --> pdb=" O LEU I 505 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL I 510 " --> pdb=" O HIS I 506 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA I 512 " --> pdb=" O CYS I 508 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU I 516 " --> pdb=" O ALA I 512 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 8.449A pdb=" N VAL A 91 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU A 65 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU A 3 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY A 132 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 5 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLN A 131 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ASN A 165 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE A 133 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 198 " --> pdb=" O MET A 164 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR A 199 " --> pdb=" O PHE A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 23 removed outlier: 4.752A pdb=" N VAL B 521 " --> pdb=" O MET I 44 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N MET I 46 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN B 523 " --> pdb=" O MET I 46 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL I 48 " --> pdb=" O GLN B 523 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 525 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS I 45 " --> pdb=" O THR I 57 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR I 57 " --> pdb=" O LYS I 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 66 removed outlier: 3.705A pdb=" N THR B 66 " --> pdb=" O LYS B 54 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 54 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN B 53 " --> pdb=" O GLU C 528 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ILE C 530 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N MET B 55 " --> pdb=" O ILE C 530 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 202 through 208 removed outlier: 6.465A pdb=" N ARG B 203 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU B 377 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N CYS B 205 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLY B 379 " --> pdb=" O CYS B 205 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE B 207 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 222 through 223 Processing sheet with id=AA7, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.584A pdb=" N VAL B 290 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 256 through 257 removed outlier: 6.473A pdb=" N THR B 256 " --> pdb=" O TYR I 250 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 408 through 410 Processing sheet with id=AB1, first strand: chain 'C' and resid 56 through 59 removed outlier: 3.551A pdb=" N ILE C 49 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASP C 46 " --> pdb=" O ILE D 530 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP D 532 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D 535 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 195 through 201 removed outlier: 3.781A pdb=" N GLY C 376 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 371 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 215 through 217 removed outlier: 3.620A pdb=" N GLU C 349 " --> pdb=" O PHE C 360 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 237 through 240 Processing sheet with id=AB5, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.341A pdb=" N ILE C 255 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASP D 267 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL C 257 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ARG E 255 " --> pdb=" O HIS D 264 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU D 266 " --> pdb=" O ARG E 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 405 through 407 Processing sheet with id=AB7, first strand: chain 'C' and resid 485 through 488 removed outlier: 3.731A pdb=" N ALA C 495 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C 493 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 68 through 71 removed outlier: 6.583A pdb=" N ASP D 58 " --> pdb=" O VAL E 517 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASN E 519 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 209 through 213 Processing sheet with id=AC1, first strand: chain 'D' and resid 228 through 230 Processing sheet with id=AC2, first strand: chain 'D' and resid 248 through 250 removed outlier: 6.334A pdb=" N ALA D 249 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA D 300 " --> pdb=" O VAL D 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 418 through 419 Processing sheet with id=AC4, first strand: chain 'E' and resid 61 through 64 removed outlier: 3.724A pdb=" N THR E 64 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASP E 49 " --> pdb=" O ASP F 533 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL F 535 " --> pdb=" O ASP E 49 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE E 51 " --> pdb=" O VAL F 535 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASN F 537 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU E 53 " --> pdb=" O ASN F 537 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 146 through 147 Processing sheet with id=AC6, first strand: chain 'E' and resid 199 through 205 removed outlier: 4.093A pdb=" N GLY E 377 " --> pdb=" O LYS E 204 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 218 through 220 removed outlier: 3.667A pdb=" N ASP E 357 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL E 365 " --> pdb=" O CYS E 346 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS E 346 " --> pdb=" O VAL E 365 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE E 349 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE E 232 " --> pdb=" O ILE E 349 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 310 through 312 removed outlier: 9.097A pdb=" N ALA E 332 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE E 239 " --> pdb=" O ALA E 332 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 476 through 478 Processing sheet with id=AD1, first strand: chain 'F' and resid 68 through 71 removed outlier: 7.058A pdb=" N ASP F 58 " --> pdb=" O ASP G 528 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU G 530 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET F 60 " --> pdb=" O LEU G 530 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS G 532 " --> pdb=" O MET F 60 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN F 62 " --> pdb=" O LYS G 532 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AD3, first strand: chain 'F' and resid 208 through 214 removed outlier: 6.437A pdb=" N LYS F 209 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL F 390 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL F 211 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N GLY F 392 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LYS F 213 " --> pdb=" O GLY F 392 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 387 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU F 222 " --> pdb=" O VAL F 389 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 227 through 229 removed outlier: 6.338A pdb=" N CYS F 379 " --> pdb=" O ALA F 359 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA F 359 " --> pdb=" O CYS F 379 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL F 297 " --> pdb=" O LYS F 245 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP F 327 " --> pdb=" O ILE F 300 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 240 through 242 removed outlier: 9.193A pdb=" N VAL F 345 " --> pdb=" O ILE F 246 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU F 248 " --> pdb=" O VAL F 345 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 264 through 266 removed outlier: 6.172A pdb=" N ILE F 264 " --> pdb=" O GLN G 251 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL G 253 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL F 266 " --> pdb=" O VAL G 253 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 491 through 493 removed outlier: 3.529A pdb=" N SER F 501 " --> pdb=" O GLY F 492 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 52 through 55 removed outlier: 7.610A pdb=" N ASP G 42 " --> pdb=" O ASP H 521 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N VAL H 523 " --> pdb=" O ASP G 42 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N MET G 44 " --> pdb=" O VAL H 523 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 196 through 199 removed outlier: 5.969A pdb=" N ASN G 196 " --> pdb=" O ILE G 375 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU G 377 " --> pdb=" O ASN G 196 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU G 198 " --> pdb=" O LEU G 377 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER G 374 " --> pdb=" O ILE G 211 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET G 209 " --> pdb=" O ILE G 376 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 213 through 216 removed outlier: 3.553A pdb=" N VAL G 352 " --> pdb=" O LEU G 363 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU G 350 " --> pdb=" O LYS G 365 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 234 through 237 removed outlier: 6.612A pdb=" N ILE G 286 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 408 through 410 Processing sheet with id=AE4, first strand: chain 'H' and resid 59 through 60 removed outlier: 3.578A pdb=" N LYS H 48 " --> pdb=" O THR H 60 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N MET H 47 " --> pdb=" O ASP I 519 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE I 521 " --> pdb=" O MET H 47 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET H 49 " --> pdb=" O ILE I 521 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 142 through 143 Processing sheet with id=AE6, first strand: chain 'H' and resid 199 through 205 removed outlier: 4.016A pdb=" N GLY H 378 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS H 213 " --> pdb=" O LEU H 375 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 218 through 220 Processing sheet with id=AE8, first strand: chain 'H' and resid 238 through 241 Processing sheet with id=AE9, first strand: chain 'H' and resid 478 through 480 Processing sheet with id=AF1, first strand: chain 'I' and resid 192 through 196 removed outlier: 6.128A pdb=" N GLU I 192 " --> pdb=" O LEU I 374 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE I 376 " --> pdb=" O GLU I 192 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N MET I 194 " --> pdb=" O ILE I 376 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 210 through 212 removed outlier: 3.560A pdb=" N TYR I 351 " --> pdb=" O PHE I 362 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU I 349 " --> pdb=" O GLU I 364 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 228 through 233 removed outlier: 3.507A pdb=" N VAL I 311 " --> pdb=" O PHE I 289 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 407 through 409 removed outlier: 3.515A pdb=" N VAL I 408 " --> pdb=" O ASP I 496 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 477 through 479 1492 hydrogen bonds defined for protein. 4323 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: 13.12 Time building geometry restraints manager: 9.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 6030 1.28 - 1.41: 7278 1.41 - 1.55: 21254 1.55 - 1.68: 48 1.68 - 1.81: 361 Bond restraints: 34971 Sorted by residual: bond pdb=" F1 AF3 D 603 " pdb="AL AF3 D 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" F1 AF3 C 603 " pdb="AL AF3 C 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" F2 AF3 B 601 " pdb="AL AF3 B 601 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" F1 AF3 I 603 " pdb="AL AF3 I 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.68e+01 ... (remaining 34966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 46492 2.19 - 4.38: 594 4.38 - 6.58: 125 6.58 - 8.77: 10 8.77 - 10.96: 5 Bond angle restraints: 47226 Sorted by residual: angle pdb=" N SER F 181 " pdb=" CA SER F 181 " pdb=" C SER F 181 " ideal model delta sigma weight residual 113.02 103.87 9.15 1.20e+00 6.94e-01 5.81e+01 angle pdb=" N GLU D 444 " pdb=" CA GLU D 444 " pdb=" C GLU D 444 " ideal model delta sigma weight residual 114.31 104.97 9.34 1.29e+00 6.01e-01 5.25e+01 angle pdb=" C THR D 252 " pdb=" N CYS D 253 " pdb=" CA CYS D 253 " ideal model delta sigma weight residual 120.68 131.64 -10.96 1.52e+00 4.33e-01 5.20e+01 angle pdb=" N LEU F 117 " pdb=" CA LEU F 117 " pdb=" C LEU F 117 " ideal model delta sigma weight residual 111.82 104.81 7.01 1.16e+00 7.43e-01 3.65e+01 angle pdb=" C GLU D 444 " pdb=" N GLN D 445 " pdb=" CA GLN D 445 " ideal model delta sigma weight residual 120.28 112.16 8.12 1.44e+00 4.82e-01 3.18e+01 ... (remaining 47221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.09: 20792 34.09 - 68.17: 729 68.17 - 102.26: 44 102.26 - 136.34: 1 136.34 - 170.43: 6 Dihedral angle restraints: 21572 sinusoidal: 8687 harmonic: 12885 Sorted by residual: dihedral pdb=" C5' ADP C 602 " pdb=" O5' ADP C 602 " pdb=" PA ADP C 602 " pdb=" O2A ADP C 602 " ideal model delta sinusoidal sigma weight residual -60.00 110.43 -170.43 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2A ADP C 602 " pdb=" O3A ADP C 602 " pdb=" PA ADP C 602 " pdb=" PB ADP C 602 " ideal model delta sinusoidal sigma weight residual -60.00 102.40 -162.40 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" O1B ADP B 603 " pdb=" O3A ADP B 603 " pdb=" PB ADP B 603 " pdb=" PA ADP B 603 " ideal model delta sinusoidal sigma weight residual 300.00 148.61 151.39 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 21569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 5237 0.089 - 0.178: 351 0.178 - 0.267: 9 0.267 - 0.356: 3 0.356 - 0.445: 1 Chirality restraints: 5601 Sorted by residual: chirality pdb=" CB VAL I 160 " pdb=" CA VAL I 160 " pdb=" CG1 VAL I 160 " pdb=" CG2 VAL I 160 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CA SER E 168 " pdb=" N SER E 168 " pdb=" C SER E 168 " pdb=" CB SER E 168 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA ASP C 61 " pdb=" N ASP C 61 " pdb=" C ASP C 61 " pdb=" CB ASP C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 5598 not shown) Planarity restraints: 6039 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 441 " -0.027 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" C PRO D 441 " 0.088 2.00e-02 2.50e+03 pdb=" O PRO D 441 " -0.032 2.00e-02 2.50e+03 pdb=" N THR D 442 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN G 187 " -0.079 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO G 188 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO G 188 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO G 188 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 178 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C GLN F 178 " 0.077 2.00e-02 2.50e+03 pdb=" O GLN F 178 " -0.029 2.00e-02 2.50e+03 pdb=" N TYR F 179 " -0.026 2.00e-02 2.50e+03 ... (remaining 6036 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 143 2.48 - 3.08: 21537 3.08 - 3.69: 48440 3.69 - 4.29: 70434 4.29 - 4.90: 120299 Nonbonded interactions: 260853 Sorted by model distance: nonbonded pdb="MG MG E 601 " pdb=" F1 AF3 E 603 " model vdw 1.873 2.120 nonbonded pdb="MG MG D 601 " pdb=" O1B ADP D 602 " model vdw 1.913 2.170 nonbonded pdb=" OD1 ASP C 92 " pdb="MG MG C 601 " model vdw 1.914 2.170 nonbonded pdb="MG MG H 601 " pdb=" F1 AF3 H 603 " model vdw 1.950 2.120 nonbonded pdb="MG MG C 601 " pdb=" O1A ADP C 602 " model vdw 1.968 2.170 ... (remaining 260848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.040 Extract box with map and model: 1.370 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 72.350 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 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 : 0.006 0.361 34973 Z= 0.345 Angle : 0.681 10.959 47226 Z= 0.402 Chirality : 0.044 0.445 5601 Planarity : 0.004 0.116 6039 Dihedral : 16.384 170.425 13232 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.14 % Favored : 96.75 % Rotamer: Outliers : 0.48 % Allowed : 17.50 % Favored : 82.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.11), residues: 4455 helix: -2.46 (0.09), residues: 2082 sheet: -0.94 (0.23), residues: 542 loop : -1.58 (0.13), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 319 HIS 0.008 0.001 HIS I 71 PHE 0.017 0.001 PHE H 185 TYR 0.027 0.001 TYR F 179 ARG 0.005 0.000 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.33453 ( 1490) hydrogen bonds : angle 8.53487 ( 4323) covalent geometry : bond 0.00530 (34971) covalent geometry : angle 0.68149 (47226) Misc. bond : bond 0.25637 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 245 time to evaluate : 4.288 Fit side-chains revert: symmetry clash REVERT: A 379 LYS cc_start: 0.8463 (mmtp) cc_final: 0.7527 (ptmt) REVERT: C 123 ARG cc_start: 0.8411 (mtp85) cc_final: 0.7934 (ttp-110) REVERT: F 60 MET cc_start: 0.8982 (tmm) cc_final: 0.8582 (ppp) REVERT: F 343 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7792 (mmmt) REVERT: F 458 MET cc_start: 0.8979 (mmp) cc_final: 0.8605 (mmt) REVERT: G 171 MET cc_start: 0.8244 (mtp) cc_final: 0.7520 (ttm) REVERT: I 190 MET cc_start: 0.8119 (mmp) cc_final: 0.7891 (mmt) REVERT: I 418 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8317 (mtt) outliers start: 18 outliers final: 3 residues processed: 260 average time/residue: 0.5122 time to fit residues: 229.2419 Evaluate side-chains 229 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 225 time to evaluate : 5.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 418 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 374 optimal weight: 10.0000 chunk 335 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 347 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 258 optimal weight: 8.9990 chunk 402 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS C 511 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN G 103 ASN H 390 ASN ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 380 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.092202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.079870 restraints weight = 72332.539| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.50 r_work: 0.3052 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 34973 Z= 0.201 Angle : 0.641 8.518 47226 Z= 0.329 Chirality : 0.045 0.166 5601 Planarity : 0.004 0.073 6039 Dihedral : 7.801 175.770 4855 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.86 % Favored : 96.03 % Rotamer: Outliers : 1.87 % Allowed : 15.68 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.12), residues: 4455 helix: -0.87 (0.11), residues: 2125 sheet: -0.76 (0.22), residues: 580 loop : -1.60 (0.13), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 271 HIS 0.011 0.001 HIS I 71 PHE 0.016 0.001 PHE H 185 TYR 0.017 0.002 TYR F 282 ARG 0.003 0.000 ARG F 527 Details of bonding type rmsd hydrogen bonds : bond 0.07381 ( 1490) hydrogen bonds : angle 4.89361 ( 4323) covalent geometry : bond 0.00469 (34971) covalent geometry : angle 0.64117 (47226) Misc. bond : bond 0.00373 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 232 time to evaluate : 4.491 Fit side-chains REVERT: A 139 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 379 LYS cc_start: 0.8106 (mmtp) cc_final: 0.7233 (ptmt) REVERT: B 319 TRP cc_start: 0.7318 (m-90) cc_final: 0.6884 (m-90) REVERT: F 343 LYS cc_start: 0.8187 (mmmt) cc_final: 0.7757 (mptt) REVERT: G 44 MET cc_start: 0.8410 (ttm) cc_final: 0.8196 (ttp) REVERT: G 171 MET cc_start: 0.8259 (mtp) cc_final: 0.7570 (ttm) REVERT: G 206 MET cc_start: 0.9100 (mmm) cc_final: 0.8894 (mtt) REVERT: I 121 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7879 (mp0) outliers start: 70 outliers final: 36 residues processed: 294 average time/residue: 0.4755 time to fit residues: 241.0206 Evaluate side-chains 255 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 3.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 183 ASP Chi-restraints excluded: chain I residue 463 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 438 optimal weight: 8.9990 chunk 254 optimal weight: 0.4980 chunk 369 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 302 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 295 optimal weight: 0.4980 chunk 435 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.095248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.082805 restraints weight = 71757.869| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.53 r_work: 0.3108 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 34973 Z= 0.100 Angle : 0.513 8.553 47226 Z= 0.253 Chirality : 0.041 0.151 5601 Planarity : 0.003 0.055 6039 Dihedral : 7.289 167.346 4851 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.56 % Favored : 97.33 % Rotamer: Outliers : 1.52 % Allowed : 16.06 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.12), residues: 4455 helix: 0.01 (0.11), residues: 2150 sheet: -0.56 (0.22), residues: 576 loop : -1.51 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 435 HIS 0.017 0.001 HIS A 190 PHE 0.010 0.001 PHE B 268 TYR 0.013 0.001 TYR F 282 ARG 0.003 0.000 ARG F 435 Details of bonding type rmsd hydrogen bonds : bond 0.04959 ( 1490) hydrogen bonds : angle 4.19198 ( 4323) covalent geometry : bond 0.00198 (34971) covalent geometry : angle 0.51305 (47226) Misc. bond : bond 0.00029 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 242 time to evaluate : 4.834 Fit side-chains revert: symmetry clash REVERT: A 190 HIS cc_start: 0.7451 (OUTLIER) cc_final: 0.6383 (t-90) REVERT: A 379 LYS cc_start: 0.8019 (mmtp) cc_final: 0.7103 (ptpt) REVERT: B 319 TRP cc_start: 0.7397 (m-90) cc_final: 0.6929 (m-90) REVERT: B 464 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8170 (mp) REVERT: C 413 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7750 (mp0) REVERT: G 44 MET cc_start: 0.8034 (ttm) cc_final: 0.7800 (ttp) REVERT: G 171 MET cc_start: 0.7884 (mtp) cc_final: 0.7572 (ttm) REVERT: G 206 MET cc_start: 0.8939 (mmm) cc_final: 0.8673 (mtt) REVERT: I 143 MET cc_start: 0.6099 (mmt) cc_final: 0.4942 (mmt) REVERT: I 238 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7215 (mt-10) outliers start: 57 outliers final: 27 residues processed: 290 average time/residue: 0.4458 time to fit residues: 221.2883 Evaluate side-chains 252 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 3.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 528 ASP Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 479 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 397 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 396 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 374 optimal weight: 2.9990 chunk 427 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 257 optimal weight: 4.9990 chunk 217 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN G 435 GLN ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.094247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.081839 restraints weight = 71873.797| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.52 r_work: 0.3090 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34973 Z= 0.116 Angle : 0.517 8.431 47226 Z= 0.253 Chirality : 0.042 0.179 5601 Planarity : 0.003 0.046 6039 Dihedral : 6.916 150.337 4851 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.21 % Favored : 96.68 % Rotamer: Outliers : 2.30 % Allowed : 15.74 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 4455 helix: 0.47 (0.12), residues: 2155 sheet: -0.44 (0.22), residues: 607 loop : -1.43 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 324 HIS 0.006 0.001 HIS A 396 PHE 0.011 0.001 PHE H 185 TYR 0.013 0.001 TYR I 250 ARG 0.003 0.000 ARG H 313 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 1490) hydrogen bonds : angle 3.94978 ( 4323) covalent geometry : bond 0.00266 (34971) covalent geometry : angle 0.51708 (47226) Misc. bond : bond 0.00065 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 233 time to evaluate : 5.891 Fit side-chains revert: symmetry clash REVERT: A 379 LYS cc_start: 0.8004 (mmtp) cc_final: 0.7071 (ptpt) REVERT: B 319 TRP cc_start: 0.7713 (m-90) cc_final: 0.7180 (m-90) REVERT: B 464 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8041 (mp) REVERT: C 130 GLN cc_start: 0.8495 (mt0) cc_final: 0.8269 (mt0) REVERT: C 413 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7798 (mp0) REVERT: D 91 MET cc_start: 0.8899 (mmp) cc_final: 0.8468 (mmp) REVERT: E 275 MET cc_start: 0.8605 (tpp) cc_final: 0.8227 (tpp) REVERT: F 456 ASP cc_start: 0.7541 (t0) cc_final: 0.7284 (t0) REVERT: G 171 MET cc_start: 0.7935 (mtp) cc_final: 0.7654 (ttm) REVERT: G 206 MET cc_start: 0.8915 (mmm) cc_final: 0.8689 (mtt) REVERT: I 143 MET cc_start: 0.6197 (mmt) cc_final: 0.5088 (mmt) outliers start: 86 outliers final: 42 residues processed: 308 average time/residue: 0.5437 time to fit residues: 292.8887 Evaluate side-chains 264 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 528 ASP Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 479 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 81 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 232 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 328 optimal weight: 10.0000 chunk 286 optimal weight: 0.2980 chunk 128 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 17 optimal weight: 0.0010 chunk 26 optimal weight: 9.9990 chunk 284 optimal weight: 0.7980 overall best weight: 2.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.093587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.081165 restraints weight = 71825.187| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.51 r_work: 0.3082 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34973 Z= 0.124 Angle : 0.515 8.832 47226 Z= 0.251 Chirality : 0.042 0.151 5601 Planarity : 0.003 0.042 6039 Dihedral : 6.805 149.664 4850 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.23 % Favored : 96.68 % Rotamer: Outliers : 2.08 % Allowed : 16.22 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 4455 helix: 0.71 (0.12), residues: 2154 sheet: -0.39 (0.22), residues: 622 loop : -1.41 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 324 HIS 0.004 0.001 HIS I 71 PHE 0.011 0.001 PHE H 185 TYR 0.013 0.001 TYR F 282 ARG 0.003 0.000 ARG H 313 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 1490) hydrogen bonds : angle 3.86729 ( 4323) covalent geometry : bond 0.00288 (34971) covalent geometry : angle 0.51485 (47226) Misc. bond : bond 0.00067 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 225 time to evaluate : 8.113 Fit side-chains revert: symmetry clash REVERT: A 147 MET cc_start: 0.6632 (tpp) cc_final: 0.6279 (tpt) REVERT: A 267 MET cc_start: 0.7058 (ppp) cc_final: 0.5416 (ptp) REVERT: B 319 TRP cc_start: 0.7869 (m-90) cc_final: 0.7288 (m-90) REVERT: B 464 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8106 (mp) REVERT: C 130 GLN cc_start: 0.8512 (mt0) cc_final: 0.8291 (mt0) REVERT: C 249 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: C 382 MET cc_start: 0.8548 (mmm) cc_final: 0.7947 (mmt) REVERT: C 413 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7750 (mp0) REVERT: D 91 MET cc_start: 0.8941 (mmp) cc_final: 0.8521 (mmp) REVERT: F 301 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8467 (tt0) REVERT: F 456 ASP cc_start: 0.7674 (t0) cc_final: 0.7404 (t0) REVERT: G 171 MET cc_start: 0.7915 (mtp) cc_final: 0.7661 (ttm) REVERT: G 206 MET cc_start: 0.8869 (mmm) cc_final: 0.8649 (mtt) REVERT: H 49 MET cc_start: 0.8462 (ptp) cc_final: 0.8171 (ptp) REVERT: I 143 MET cc_start: 0.6209 (mmt) cc_final: 0.5203 (mmt) outliers start: 78 outliers final: 48 residues processed: 294 average time/residue: 0.7326 time to fit residues: 382.4047 Evaluate side-chains 269 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 218 time to evaluate : 6.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 301 GLN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 528 ASP Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 183 ASP Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 479 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 43 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 321 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 20 optimal weight: 0.0060 chunk 140 optimal weight: 0.3980 chunk 191 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 388 optimal weight: 0.6980 chunk 196 optimal weight: 9.9990 overall best weight: 2.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 GLN G 353 GLN ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.093832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.081409 restraints weight = 71848.987| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.51 r_work: 0.3082 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34973 Z= 0.116 Angle : 0.510 8.945 47226 Z= 0.248 Chirality : 0.042 0.150 5601 Planarity : 0.003 0.040 6039 Dihedral : 6.684 146.800 4850 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.25 % Favored : 96.66 % Rotamer: Outliers : 2.08 % Allowed : 16.51 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.13), residues: 4455 helix: 0.90 (0.12), residues: 2152 sheet: -0.32 (0.22), residues: 630 loop : -1.36 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 319 HIS 0.011 0.001 HIS I 71 PHE 0.011 0.001 PHE H 185 TYR 0.012 0.001 TYR F 282 ARG 0.002 0.000 ARG H 127 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 1490) hydrogen bonds : angle 3.77279 ( 4323) covalent geometry : bond 0.00271 (34971) covalent geometry : angle 0.51011 (47226) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 230 time to evaluate : 3.948 Fit side-chains revert: symmetry clash REVERT: A 147 MET cc_start: 0.6623 (tpp) cc_final: 0.6288 (tpt) REVERT: A 267 MET cc_start: 0.7031 (ppp) cc_final: 0.5481 (ptp) REVERT: B 319 TRP cc_start: 0.8009 (m-90) cc_final: 0.7373 (m-90) REVERT: B 464 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8037 (mp) REVERT: C 130 GLN cc_start: 0.8496 (mt0) cc_final: 0.8291 (mt0) REVERT: C 249 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7339 (tt0) REVERT: C 382 MET cc_start: 0.8512 (mmm) cc_final: 0.8248 (mmt) REVERT: C 413 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7778 (mp0) REVERT: D 91 MET cc_start: 0.8956 (mmp) cc_final: 0.8496 (mmp) REVERT: F 301 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: F 414 CYS cc_start: 0.8066 (m) cc_final: 0.7519 (m) REVERT: F 456 ASP cc_start: 0.7611 (t0) cc_final: 0.7360 (t0) REVERT: G 171 MET cc_start: 0.7888 (mtp) cc_final: 0.7660 (ttm) REVERT: G 206 MET cc_start: 0.8895 (mmm) cc_final: 0.8634 (mtt) REVERT: I 143 MET cc_start: 0.6211 (mmt) cc_final: 0.5313 (mmt) outliers start: 78 outliers final: 50 residues processed: 299 average time/residue: 0.4097 time to fit residues: 212.3045 Evaluate side-chains 273 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 GLN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 479 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 320 optimal weight: 0.6980 chunk 429 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 206 optimal weight: 0.0060 chunk 71 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 361 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 258 HIS ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.094464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.082086 restraints weight = 71903.504| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.50 r_work: 0.3093 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34973 Z= 0.103 Angle : 0.502 10.248 47226 Z= 0.242 Chirality : 0.041 0.149 5601 Planarity : 0.002 0.038 6039 Dihedral : 6.547 143.218 4850 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.88 % Rotamer: Outliers : 2.00 % Allowed : 16.94 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.13), residues: 4455 helix: 1.10 (0.12), residues: 2158 sheet: -0.24 (0.22), residues: 622 loop : -1.29 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 319 HIS 0.008 0.001 HIS C 258 PHE 0.014 0.001 PHE G 8 TYR 0.012 0.001 TYR I 250 ARG 0.002 0.000 ARG F 391 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 1490) hydrogen bonds : angle 3.68097 ( 4323) covalent geometry : bond 0.00234 (34971) covalent geometry : angle 0.50170 (47226) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 235 time to evaluate : 4.322 Fit side-chains revert: symmetry clash REVERT: A 147 MET cc_start: 0.6615 (tpp) cc_final: 0.6301 (tpt) REVERT: A 267 MET cc_start: 0.7024 (ppp) cc_final: 0.5462 (ptp) REVERT: B 54 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8636 (mttp) REVERT: B 464 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8104 (mp) REVERT: C 130 GLN cc_start: 0.8463 (mt0) cc_final: 0.8245 (mt0) REVERT: C 249 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: C 382 MET cc_start: 0.8534 (mmm) cc_final: 0.8319 (mmt) REVERT: C 413 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7752 (mp0) REVERT: D 91 MET cc_start: 0.8943 (mmp) cc_final: 0.8498 (mmp) REVERT: F 301 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8669 (tt0) REVERT: G 171 MET cc_start: 0.7849 (mtp) cc_final: 0.7517 (ttm) REVERT: G 206 MET cc_start: 0.8888 (mmm) cc_final: 0.8675 (mtt) REVERT: I 143 MET cc_start: 0.6224 (mmt) cc_final: 0.5339 (mmt) outliers start: 75 outliers final: 55 residues processed: 301 average time/residue: 0.4146 time to fit residues: 216.4461 Evaluate side-chains 277 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 GLN Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 479 VAL Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 59 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 321 optimal weight: 7.9990 chunk 381 optimal weight: 0.0040 chunk 19 optimal weight: 20.0000 chunk 206 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 214 optimal weight: 9.9990 chunk 213 optimal weight: 0.7980 chunk 316 optimal weight: 0.7980 chunk 326 optimal weight: 7.9990 overall best weight: 2.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 ASN ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.093623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.081258 restraints weight = 71684.740| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.50 r_work: 0.3079 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34973 Z= 0.120 Angle : 0.516 7.908 47226 Z= 0.250 Chirality : 0.042 0.164 5601 Planarity : 0.003 0.037 6039 Dihedral : 6.534 140.250 4850 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.39 % Favored : 96.52 % Rotamer: Outliers : 2.19 % Allowed : 17.02 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.13), residues: 4455 helix: 1.19 (0.12), residues: 2155 sheet: -0.25 (0.22), residues: 627 loop : -1.29 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 324 HIS 0.007 0.001 HIS A 396 PHE 0.011 0.001 PHE H 185 TYR 0.011 0.001 TYR F 282 ARG 0.002 0.000 ARG E 293 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 1490) hydrogen bonds : angle 3.69867 ( 4323) covalent geometry : bond 0.00280 (34971) covalent geometry : angle 0.51562 (47226) Misc. bond : bond 0.00053 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 222 time to evaluate : 4.591 Fit side-chains revert: symmetry clash REVERT: A 147 MET cc_start: 0.6615 (tpp) cc_final: 0.6302 (tpt) REVERT: A 267 MET cc_start: 0.6948 (ppp) cc_final: 0.5336 (ptp) REVERT: B 464 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8058 (mp) REVERT: C 130 GLN cc_start: 0.8487 (mt0) cc_final: 0.8278 (mt0) REVERT: C 249 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: C 382 MET cc_start: 0.8543 (mmm) cc_final: 0.8247 (mmt) REVERT: C 413 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7738 (mp0) REVERT: D 91 MET cc_start: 0.8952 (mmp) cc_final: 0.8506 (mmp) REVERT: F 301 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: F 456 ASP cc_start: 0.7543 (t0) cc_final: 0.7256 (t0) REVERT: G 171 MET cc_start: 0.7866 (mtp) cc_final: 0.7516 (ttm) REVERT: G 206 MET cc_start: 0.8884 (mmm) cc_final: 0.8624 (mtt) REVERT: I 84 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: I 143 MET cc_start: 0.6130 (mmt) cc_final: 0.5360 (mmt) outliers start: 82 outliers final: 59 residues processed: 294 average time/residue: 0.4173 time to fit residues: 213.6750 Evaluate side-chains 279 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 216 time to evaluate : 4.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 GLN Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 429 MET Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 84 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 479 VAL Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 267 optimal weight: 5.9990 chunk 371 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 175 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 382 optimal weight: 1.9990 chunk 379 optimal weight: 1.9990 chunk 385 optimal weight: 5.9990 chunk 305 optimal weight: 8.9990 chunk 277 optimal weight: 8.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.093522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.081159 restraints weight = 71911.795| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.50 r_work: 0.3078 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34973 Z= 0.118 Angle : 0.517 8.719 47226 Z= 0.250 Chirality : 0.042 0.164 5601 Planarity : 0.003 0.036 6039 Dihedral : 6.500 136.979 4850 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.63 % Rotamer: Outliers : 1.87 % Allowed : 17.47 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 4455 helix: 1.27 (0.12), residues: 2155 sheet: -0.20 (0.22), residues: 635 loop : -1.27 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 324 HIS 0.007 0.001 HIS A 396 PHE 0.015 0.001 PHE G 8 TYR 0.012 0.001 TYR I 250 ARG 0.002 0.000 ARG H 313 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 1490) hydrogen bonds : angle 3.69342 ( 4323) covalent geometry : bond 0.00278 (34971) covalent geometry : angle 0.51656 (47226) Misc. bond : bond 0.00057 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 223 time to evaluate : 4.139 Fit side-chains revert: symmetry clash REVERT: A 147 MET cc_start: 0.6625 (tpp) cc_final: 0.6313 (tpt) REVERT: A 267 MET cc_start: 0.6949 (ppp) cc_final: 0.5351 (ptp) REVERT: B 344 MET cc_start: 0.8636 (mmm) cc_final: 0.8378 (mtm) REVERT: B 464 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8071 (mp) REVERT: C 130 GLN cc_start: 0.8495 (mt0) cc_final: 0.8287 (mt0) REVERT: C 249 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7347 (tt0) REVERT: C 382 MET cc_start: 0.8554 (mmm) cc_final: 0.8261 (mmt) REVERT: C 413 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7748 (mp0) REVERT: D 91 MET cc_start: 0.8959 (mmp) cc_final: 0.8519 (mmp) REVERT: F 301 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8424 (tt0) REVERT: F 456 ASP cc_start: 0.7556 (t0) cc_final: 0.7265 (t0) REVERT: G 171 MET cc_start: 0.7866 (mtp) cc_final: 0.7526 (ttm) REVERT: G 206 MET cc_start: 0.8888 (mmm) cc_final: 0.8630 (mtt) REVERT: I 84 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: I 143 MET cc_start: 0.6159 (mmt) cc_final: 0.5388 (mmt) REVERT: I 190 MET cc_start: 0.8244 (mmp) cc_final: 0.8034 (mmt) outliers start: 70 outliers final: 62 residues processed: 284 average time/residue: 0.4137 time to fit residues: 205.1388 Evaluate side-chains 285 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 219 time to evaluate : 4.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 GLN Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 429 MET Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 84 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 479 VAL Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 250 optimal weight: 3.9990 chunk 368 optimal weight: 3.9990 chunk 342 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 187 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 chunk 341 optimal weight: 2.9990 chunk 234 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.080960 restraints weight = 71599.300| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.49 r_work: 0.3075 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34973 Z= 0.121 Angle : 0.522 8.759 47226 Z= 0.253 Chirality : 0.042 0.165 5601 Planarity : 0.003 0.036 6039 Dihedral : 6.486 134.703 4850 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.61 % Favored : 96.32 % Rotamer: Outliers : 1.90 % Allowed : 17.55 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.13), residues: 4455 helix: 1.33 (0.12), residues: 2156 sheet: -0.22 (0.22), residues: 602 loop : -1.24 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 324 HIS 0.007 0.001 HIS A 396 PHE 0.011 0.001 PHE H 185 TYR 0.012 0.001 TYR I 250 ARG 0.002 0.000 ARG H 313 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 1490) hydrogen bonds : angle 3.69400 ( 4323) covalent geometry : bond 0.00286 (34971) covalent geometry : angle 0.52199 (47226) Misc. bond : bond 0.00048 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 222 time to evaluate : 3.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.6677 (tpp) cc_final: 0.6357 (tpt) REVERT: A 267 MET cc_start: 0.7189 (ppp) cc_final: 0.5630 (ptp) REVERT: A 379 LYS cc_start: 0.7965 (mmtp) cc_final: 0.7029 (ptpt) REVERT: B 193 ASP cc_start: 0.6748 (m-30) cc_final: 0.6514 (m-30) REVERT: B 344 MET cc_start: 0.8652 (mmm) cc_final: 0.8392 (mtm) REVERT: B 464 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8054 (mp) REVERT: C 130 GLN cc_start: 0.8474 (mt0) cc_final: 0.8249 (mt0) REVERT: C 249 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: C 382 MET cc_start: 0.8547 (mmm) cc_final: 0.7966 (mmt) REVERT: C 413 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7743 (mp0) REVERT: D 91 MET cc_start: 0.8965 (mmp) cc_final: 0.8535 (mmp) REVERT: F 301 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: F 456 ASP cc_start: 0.7410 (t0) cc_final: 0.7141 (t0) REVERT: G 171 MET cc_start: 0.7874 (mtp) cc_final: 0.7519 (ttm) REVERT: G 206 MET cc_start: 0.8923 (mmm) cc_final: 0.8678 (mtt) REVERT: I 84 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: I 143 MET cc_start: 0.6148 (mmt) cc_final: 0.5385 (mmt) REVERT: I 190 MET cc_start: 0.8290 (mmp) cc_final: 0.8086 (mmt) outliers start: 71 outliers final: 62 residues processed: 284 average time/residue: 0.4156 time to fit residues: 204.7031 Evaluate side-chains 282 residues out of total 3743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 216 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 GLN Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 429 MET Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 84 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 479 VAL Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 368 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 213 optimal weight: 7.9990 chunk 408 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 chunk 420 optimal weight: 7.9990 chunk 200 optimal weight: 0.2980 chunk 262 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 242 optimal weight: 0.8980 chunk 328 optimal weight: 9.9990 overall best weight: 4.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 ASN I 65 HIS ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.090526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.078253 restraints weight = 72750.276| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.48 r_work: 0.3025 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 34973 Z= 0.217 Angle : 0.603 7.933 47226 Z= 0.298 Chirality : 0.045 0.175 5601 Planarity : 0.003 0.036 6039 Dihedral : 6.770 138.403 4850 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.35 % Favored : 95.58 % Rotamer: Outliers : 1.82 % Allowed : 17.71 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.13), residues: 4455 helix: 1.05 (0.12), residues: 2171 sheet: -0.30 (0.22), residues: 594 loop : -1.35 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 324 HIS 0.007 0.001 HIS I 71 PHE 0.018 0.001 PHE G 8 TYR 0.013 0.001 TYR D 280 ARG 0.004 0.000 ARG I 315 Details of bonding type rmsd hydrogen bonds : bond 0.05272 ( 1490) hydrogen bonds : angle 3.99563 ( 4323) covalent geometry : bond 0.00527 (34971) covalent geometry : angle 0.60337 (47226) Misc. bond : bond 0.00090 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14758.46 seconds wall clock time: 263 minutes 11.21 seconds (15791.21 seconds total)