Starting phenix.real_space_refine on Sat Oct 31 03:42:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6e88_9004/10_2026/6e88_9004.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e88_9004/10_2026/6e88_9004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6e88_9004/10_2026/6e88_9004.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6e88_9004/10_2026/6e88_9004.cif" model { file = "/net/cci-nas-00/data/ceres_data/6e88_9004/10_2026/6e88_9004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e88_9004/10_2026/6e88_9004.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e88_9004/10_2026/6e88_9004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e88_9004/10_2026/6e88_9004.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 1.161 sd= 2.608 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 30 5.49 5 S 282 5.16 5 C 25710 2.51 5 N 6954 2.21 5 O 7932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40908 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3406 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "C" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3406 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain: "D" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "H" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3406 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain: "J" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "L" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3406 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain: "N" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "I" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3406 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain: "K" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "M" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3406 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain: "O" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.98, per 1000 atoms: 0.20 Number of scatterers: 40908 At special positions: 0 Unit cell: (152.403, 145.538, 215.561, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 282 16.00 P 30 15.00 O 7932 8.00 N 6954 7.00 C 25710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.7 seconds 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9540 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 36 sheets defined 49.8% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.540A pdb=" N ILE A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.837A pdb=" N THR A 41 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN A 42 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 removed outlier: 3.645A pdb=" N GLU A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.047A pdb=" N LYS A 83 " --> pdb=" O THR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 108 through 111 Processing helix chain 'A' and resid 112 through 125 removed outlier: 3.876A pdb=" N ASP A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 159 removed outlier: 3.806A pdb=" N PHE A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 191 removed outlier: 3.779A pdb=" N ILE A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 removed outlier: 3.504A pdb=" N ILE A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 242 removed outlier: 3.742A pdb=" N ARG A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 258 removed outlier: 3.667A pdb=" N GLN A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.621A pdb=" N ILE A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 336 removed outlier: 3.984A pdb=" N VAL A 326 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 removed outlier: 3.857A pdb=" N GLU A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 395 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET A 396 " --> pdb=" O LYS A 392 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.918A pdb=" N TRP A 405 " --> pdb=" O PHE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 434 removed outlier: 3.881A pdb=" N THR A 417 " --> pdb=" O GLU A 413 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 421 " --> pdb=" O THR A 417 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 27 removed outlier: 3.855A pdb=" N GLN B 15 " --> pdb=" O GLN B 11 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 44 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 79 removed outlier: 4.005A pdb=" N ASP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 76 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.760A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASN B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 124 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 4.392A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.511A pdb=" N THR B 186 " --> pdb=" O PRO B 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 187 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 4.067A pdb=" N TYR B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.524A pdb=" N ASN B 226 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.669A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.539A pdb=" N GLN B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.558A pdb=" N GLY B 308 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.938A pdb=" N LEU B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 374 through 389 removed outlier: 3.796A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 382 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 389 " --> pdb=" O PHE B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 405 through 426 removed outlier: 3.577A pdb=" N ALA B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 418 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 419 " --> pdb=" O MET B 415 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 removed outlier: 3.540A pdb=" N ILE C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 42 removed outlier: 3.836A pdb=" N THR C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN C 42 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 77 removed outlier: 3.646A pdb=" N GLU C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.048A pdb=" N LYS C 83 " --> pdb=" O THR C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 108 through 111 Processing helix chain 'C' and resid 112 through 125 removed outlier: 3.875A pdb=" N ASP C 118 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 159 removed outlier: 3.806A pdb=" N PHE C 147 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER C 156 " --> pdb=" O MET C 152 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 191 removed outlier: 3.779A pdb=" N ILE C 186 " --> pdb=" O PRO C 182 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 214 removed outlier: 3.504A pdb=" N ILE C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 242 removed outlier: 3.742A pdb=" N ARG C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 236 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 258 removed outlier: 3.667A pdb=" N GLN C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 294 removed outlier: 3.621A pdb=" N ILE C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN C 291 " --> pdb=" O SER C 287 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE C 294 " --> pdb=" O THR C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 336 removed outlier: 3.984A pdb=" N VAL C 326 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA C 331 " --> pdb=" O ASN C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 399 removed outlier: 3.857A pdb=" N GLU C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP C 394 " --> pdb=" O ASP C 390 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU C 395 " --> pdb=" O TYR C 391 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET C 396 " --> pdb=" O LYS C 392 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 406 removed outlier: 3.917A pdb=" N TRP C 405 " --> pdb=" O PHE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 434 removed outlier: 3.881A pdb=" N THR C 417 " --> pdb=" O GLU C 413 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 421 " --> pdb=" O THR C 417 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR C 430 " --> pdb=" O LEU C 426 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 27 removed outlier: 3.855A pdb=" N GLN D 15 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY D 17 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER D 18 " --> pdb=" O ASN D 14 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 23 " --> pdb=" O LYS D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 44 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 70 through 79 removed outlier: 4.005A pdb=" N ASP D 74 " --> pdb=" O PRO D 70 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D 76 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.759A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASN D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 removed outlier: 4.392A pdb=" N THR D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLU D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU D 158 " --> pdb=" O LYS D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.512A pdb=" N THR D 186 " --> pdb=" O PRO D 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 187 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN D 195 " --> pdb=" O GLN D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 removed outlier: 4.066A pdb=" N TYR D 208 " --> pdb=" O ASN D 204 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.524A pdb=" N ASN D 226 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 236 " --> pdb=" O THR D 232 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.670A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.540A pdb=" N GLN D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN D 292 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 308 removed outlier: 3.558A pdb=" N GLY D 308 " --> pdb=" O PRO D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.938A pdb=" N LEU D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 374 through 389 removed outlier: 3.796A pdb=" N PHE D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER D 382 " --> pdb=" O PHE D 378 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 383 " --> pdb=" O LYS D 379 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET D 388 " --> pdb=" O GLN D 384 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE D 389 " --> pdb=" O PHE D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 405 through 426 removed outlier: 3.576A pdb=" N ALA D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 418 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 419 " --> pdb=" O MET D 415 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 29 removed outlier: 3.540A pdb=" N ILE H 16 " --> pdb=" O ALA H 12 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU H 22 " --> pdb=" O ASN H 18 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU H 26 " --> pdb=" O GLU H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 42 removed outlier: 3.836A pdb=" N THR H 41 " --> pdb=" O THR H 38 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN H 42 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 77 removed outlier: 3.645A pdb=" N GLU H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE H 76 " --> pdb=" O VAL H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.048A pdb=" N LYS H 83 " --> pdb=" O THR H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 108 through 111 Processing helix chain 'H' and resid 112 through 125 removed outlier: 3.876A pdb=" N ASP H 118 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 159 removed outlier: 3.806A pdb=" N PHE H 147 " --> pdb=" O THR H 143 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR H 148 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU H 150 " --> pdb=" O GLY H 146 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER H 156 " --> pdb=" O MET H 152 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL H 157 " --> pdb=" O GLU H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 191 removed outlier: 3.779A pdb=" N ILE H 186 " --> pdb=" O PRO H 182 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 214 removed outlier: 3.504A pdb=" N ILE H 207 " --> pdb=" O ASP H 203 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE H 210 " --> pdb=" O ALA H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 242 removed outlier: 3.742A pdb=" N ARG H 227 " --> pdb=" O THR H 223 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE H 229 " --> pdb=" O LEU H 225 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL H 232 " --> pdb=" O ILE H 228 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE H 236 " --> pdb=" O VAL H 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR H 237 " --> pdb=" O VAL H 233 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER H 239 " --> pdb=" O SER H 235 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU H 240 " --> pdb=" O ILE H 236 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 258 removed outlier: 3.667A pdb=" N GLN H 254 " --> pdb=" O LEU H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 294 removed outlier: 3.621A pdb=" N ILE H 289 " --> pdb=" O SER H 285 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN H 291 " --> pdb=" O SER H 287 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE H 294 " --> pdb=" O THR H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 336 removed outlier: 3.984A pdb=" N VAL H 326 " --> pdb=" O VAL H 322 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA H 331 " --> pdb=" O ASN H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 399 removed outlier: 3.858A pdb=" N GLU H 384 " --> pdb=" O THR H 380 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG H 388 " --> pdb=" O GLU H 384 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU H 389 " --> pdb=" O ALA H 385 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS H 392 " --> pdb=" O ARG H 388 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP H 394 " --> pdb=" O ASP H 390 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU H 395 " --> pdb=" O TYR H 391 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET H 396 " --> pdb=" O LYS H 392 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS H 399 " --> pdb=" O LEU H 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 402 through 406 removed outlier: 3.918A pdb=" N TRP H 405 " --> pdb=" O PHE H 402 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 434 removed outlier: 3.880A pdb=" N THR H 417 " --> pdb=" O GLU H 413 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG H 420 " --> pdb=" O PHE H 416 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU H 421 " --> pdb=" O THR H 417 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA H 425 " --> pdb=" O GLU H 421 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU H 427 " --> pdb=" O LEU H 423 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR H 430 " --> pdb=" O LEU H 426 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU H 431 " --> pdb=" O GLU H 427 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 27 removed outlier: 3.856A pdb=" N GLN J 15 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY J 17 " --> pdb=" O GLY J 13 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER J 18 " --> pdb=" O ASN J 14 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU J 22 " --> pdb=" O SER J 18 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL J 23 " --> pdb=" O LYS J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 44 Processing helix chain 'J' and resid 47 through 49 No H-bonds generated for 'chain 'J' and resid 47 through 49' Processing helix chain 'J' and resid 70 through 79 removed outlier: 4.005A pdb=" N ASP J 74 " --> pdb=" O PRO J 70 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER J 75 " --> pdb=" O GLY J 71 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL J 76 " --> pdb=" O THR J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 88 No H-bonds generated for 'chain 'J' and resid 86 through 88' Processing helix chain 'J' and resid 100 through 106 Processing helix chain 'J' and resid 108 through 126 removed outlier: 3.759A pdb=" N LEU J 112 " --> pdb=" O GLU J 108 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP J 114 " --> pdb=" O ALA J 110 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASN J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL J 116 " --> pdb=" O LEU J 112 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP J 118 " --> pdb=" O ASP J 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL J 119 " --> pdb=" O ASN J 115 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY J 126 " --> pdb=" O LYS J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 159 removed outlier: 4.393A pdb=" N THR J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE J 152 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER J 153 " --> pdb=" O THR J 149 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS J 154 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG J 156 " --> pdb=" O ILE J 152 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLU J 157 " --> pdb=" O SER J 153 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU J 158 " --> pdb=" O LYS J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 196 removed outlier: 3.512A pdb=" N THR J 186 " --> pdb=" O PRO J 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU J 187 " --> pdb=" O TYR J 183 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER J 188 " --> pdb=" O ASN J 184 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN J 191 " --> pdb=" O LEU J 187 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU J 194 " --> pdb=" O HIS J 190 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN J 195 " --> pdb=" O GLN J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 214 removed outlier: 4.067A pdb=" N TYR J 208 " --> pdb=" O ASN J 204 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP J 209 " --> pdb=" O GLU J 205 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG J 213 " --> pdb=" O ASP J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 237 removed outlier: 3.525A pdb=" N ASN J 226 " --> pdb=" O TYR J 222 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY J 235 " --> pdb=" O LEU J 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL J 236 " --> pdb=" O THR J 232 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR J 237 " --> pdb=" O MET J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 242 removed outlier: 3.669A pdb=" N ARG J 241 " --> pdb=" O THR J 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 256 Processing helix chain 'J' and resid 285 through 294 removed outlier: 3.539A pdb=" N GLN J 291 " --> pdb=" O ALA J 287 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN J 292 " --> pdb=" O GLU J 288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET J 293 " --> pdb=" O LEU J 289 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE J 294 " --> pdb=" O THR J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 308 removed outlier: 3.558A pdb=" N GLY J 308 " --> pdb=" O PRO J 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 322 through 337 removed outlier: 3.938A pdb=" N LEU J 331 " --> pdb=" O ASP J 327 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN J 334 " --> pdb=" O MET J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 371 through 373 No H-bonds generated for 'chain 'J' and resid 371 through 373' Processing helix chain 'J' and resid 374 through 389 removed outlier: 3.796A pdb=" N PHE J 378 " --> pdb=" O ILE J 374 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE J 381 " --> pdb=" O LEU J 377 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER J 382 " --> pdb=" O PHE J 378 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU J 383 " --> pdb=" O LYS J 379 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN J 384 " --> pdb=" O ARG J 380 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET J 388 " --> pdb=" O GLN J 384 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE J 389 " --> pdb=" O PHE J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 394 through 398 Processing helix chain 'J' and resid 405 through 426 removed outlier: 3.578A pdb=" N ALA J 411 " --> pdb=" O GLU J 407 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU J 418 " --> pdb=" O ASN J 414 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE J 419 " --> pdb=" O MET J 415 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER J 420 " --> pdb=" O ASN J 416 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR J 422 " --> pdb=" O LEU J 418 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR J 425 " --> pdb=" O GLU J 421 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 29 removed outlier: 3.540A pdb=" N ILE L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU L 22 " --> pdb=" O ASN L 18 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU L 26 " --> pdb=" O GLU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.836A pdb=" N THR L 41 " --> pdb=" O THR L 38 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN L 42 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 77 removed outlier: 3.646A pdb=" N GLU L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE L 76 " --> pdb=" O VAL L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.048A pdb=" N LYS L 83 " --> pdb=" O THR L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 106 Processing helix chain 'L' and resid 108 through 111 Processing helix chain 'L' and resid 112 through 125 removed outlier: 3.875A pdb=" N ASP L 118 " --> pdb=" O ASP L 114 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG L 119 " --> pdb=" O THR L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 159 removed outlier: 3.806A pdb=" N PHE L 147 " --> pdb=" O THR L 143 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR L 148 " --> pdb=" O GLY L 144 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER L 156 " --> pdb=" O MET L 152 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL L 157 " --> pdb=" O GLU L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 191 removed outlier: 3.778A pdb=" N ILE L 186 " --> pdb=" O PRO L 182 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR L 191 " --> pdb=" O LEU L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 214 removed outlier: 3.505A pdb=" N ILE L 207 " --> pdb=" O ASP L 203 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE L 210 " --> pdb=" O ALA L 206 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 242 removed outlier: 3.742A pdb=" N ARG L 227 " --> pdb=" O THR L 223 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE L 229 " --> pdb=" O LEU L 225 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL L 232 " --> pdb=" O ILE L 228 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE L 236 " --> pdb=" O VAL L 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR L 237 " --> pdb=" O VAL L 233 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER L 239 " --> pdb=" O SER L 235 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU L 240 " --> pdb=" O ILE L 236 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 258 removed outlier: 3.668A pdb=" N GLN L 254 " --> pdb=" O LEU L 250 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 294 removed outlier: 3.620A pdb=" N ILE L 289 " --> pdb=" O SER L 285 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN L 291 " --> pdb=" O SER L 287 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE L 294 " --> pdb=" O THR L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 322 through 336 removed outlier: 3.984A pdb=" N VAL L 326 " --> pdb=" O VAL L 322 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA L 331 " --> pdb=" O ASN L 327 " (cutoff:3.500A) Processing helix chain 'L' and resid 380 through 399 removed outlier: 3.858A pdb=" N GLU L 384 " --> pdb=" O THR L 380 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG L 388 " --> pdb=" O GLU L 384 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU L 389 " --> pdb=" O ALA L 385 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS L 392 " --> pdb=" O ARG L 388 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP L 394 " --> pdb=" O ASP L 390 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU L 395 " --> pdb=" O TYR L 391 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET L 396 " --> pdb=" O LYS L 392 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS L 399 " --> pdb=" O LEU L 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 402 through 406 removed outlier: 3.918A pdb=" N TRP L 405 " --> pdb=" O PHE L 402 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 434 removed outlier: 3.881A pdb=" N THR L 417 " --> pdb=" O GLU L 413 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG L 420 " --> pdb=" O PHE L 416 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU L 421 " --> pdb=" O THR L 417 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA L 425 " --> pdb=" O GLU L 421 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU L 426 " --> pdb=" O ASP L 422 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU L 427 " --> pdb=" O LEU L 423 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR L 430 " --> pdb=" O LEU L 426 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU L 431 " --> pdb=" O GLU L 427 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 27 removed outlier: 3.855A pdb=" N GLN N 15 " --> pdb=" O GLN N 11 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY N 17 " --> pdb=" O GLY N 13 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER N 18 " --> pdb=" O ASN N 14 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS N 19 " --> pdb=" O GLN N 15 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU N 22 " --> pdb=" O SER N 18 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL N 23 " --> pdb=" O LYS N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 44 Processing helix chain 'N' and resid 47 through 49 No H-bonds generated for 'chain 'N' and resid 47 through 49' Processing helix chain 'N' and resid 70 through 79 removed outlier: 4.005A pdb=" N ASP N 74 " --> pdb=" O PRO N 70 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER N 75 " --> pdb=" O GLY N 71 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL N 76 " --> pdb=" O THR N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 88 No H-bonds generated for 'chain 'N' and resid 86 through 88' Processing helix chain 'N' and resid 100 through 106 Processing helix chain 'N' and resid 108 through 126 removed outlier: 3.759A pdb=" N LEU N 112 " --> pdb=" O GLU N 108 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASP N 114 " --> pdb=" O ALA N 110 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASN N 115 " --> pdb=" O GLU N 111 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL N 116 " --> pdb=" O LEU N 112 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP N 118 " --> pdb=" O ASP N 114 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL N 119 " --> pdb=" O ASN N 115 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA N 124 " --> pdb=" O ILE N 120 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY N 126 " --> pdb=" O LYS N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 159 removed outlier: 4.392A pdb=" N THR N 149 " --> pdb=" O SER N 145 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU N 150 " --> pdb=" O GLY N 146 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE N 152 " --> pdb=" O GLY N 148 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER N 153 " --> pdb=" O THR N 149 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS N 154 " --> pdb=" O LEU N 150 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG N 156 " --> pdb=" O ILE N 152 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLU N 157 " --> pdb=" O SER N 153 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU N 158 " --> pdb=" O LYS N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 196 removed outlier: 3.512A pdb=" N THR N 186 " --> pdb=" O PRO N 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU N 187 " --> pdb=" O TYR N 183 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER N 188 " --> pdb=" O ASN N 184 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN N 191 " --> pdb=" O LEU N 187 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU N 194 " --> pdb=" O HIS N 190 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN N 195 " --> pdb=" O GLN N 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 214 removed outlier: 4.066A pdb=" N TYR N 208 " --> pdb=" O ASN N 204 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP N 209 " --> pdb=" O GLU N 205 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG N 213 " --> pdb=" O ASP N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 237 removed outlier: 3.525A pdb=" N ASN N 226 " --> pdb=" O TYR N 222 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY N 235 " --> pdb=" O LEU N 231 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL N 236 " --> pdb=" O THR N 232 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR N 237 " --> pdb=" O MET N 233 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 242 removed outlier: 3.668A pdb=" N ARG N 241 " --> pdb=" O THR N 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 256 Processing helix chain 'N' and resid 285 through 294 removed outlier: 3.540A pdb=" N GLN N 291 " --> pdb=" O ALA N 287 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN N 292 " --> pdb=" O GLU N 288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET N 293 " --> pdb=" O LEU N 289 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE N 294 " --> pdb=" O THR N 290 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 308 removed outlier: 3.558A pdb=" N GLY N 308 " --> pdb=" O PRO N 305 " (cutoff:3.500A) Processing helix chain 'N' and resid 322 through 337 removed outlier: 3.939A pdb=" N LEU N 331 " --> pdb=" O ASP N 327 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN N 334 " --> pdb=" O MET N 330 " (cutoff:3.500A) Processing helix chain 'N' and resid 371 through 373 No H-bonds generated for 'chain 'N' and resid 371 through 373' Processing helix chain 'N' and resid 374 through 389 removed outlier: 3.795A pdb=" N PHE N 378 " --> pdb=" O ILE N 374 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE N 381 " --> pdb=" O LEU N 377 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER N 382 " --> pdb=" O PHE N 378 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU N 383 " --> pdb=" O LYS N 379 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN N 384 " --> pdb=" O ARG N 380 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET N 388 " --> pdb=" O GLN N 384 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE N 389 " --> pdb=" O PHE N 385 " (cutoff:3.500A) Processing helix chain 'N' and resid 394 through 398 Processing helix chain 'N' and resid 405 through 426 removed outlier: 3.577A pdb=" N ALA N 411 " --> pdb=" O GLU N 407 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU N 418 " --> pdb=" O ASN N 414 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE N 419 " --> pdb=" O MET N 415 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER N 420 " --> pdb=" O ASN N 416 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR N 422 " --> pdb=" O LEU N 418 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR N 425 " --> pdb=" O GLU N 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 removed outlier: 3.539A pdb=" N ILE I 16 " --> pdb=" O ALA I 12 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU I 22 " --> pdb=" O ASN I 18 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 42 removed outlier: 3.837A pdb=" N THR I 41 " --> pdb=" O THR I 38 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN I 42 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 77 removed outlier: 3.645A pdb=" N GLU I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE I 76 " --> pdb=" O VAL I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.049A pdb=" N LYS I 83 " --> pdb=" O THR I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 111 Processing helix chain 'I' and resid 112 through 125 removed outlier: 3.875A pdb=" N ASP I 118 " --> pdb=" O ASP I 114 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG I 119 " --> pdb=" O THR I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 159 removed outlier: 3.806A pdb=" N PHE I 147 " --> pdb=" O THR I 143 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR I 148 " --> pdb=" O GLY I 144 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU I 150 " --> pdb=" O GLY I 146 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER I 156 " --> pdb=" O MET I 152 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL I 157 " --> pdb=" O GLU I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 191 removed outlier: 3.779A pdb=" N ILE I 186 " --> pdb=" O PRO I 182 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 removed outlier: 3.504A pdb=" N ILE I 207 " --> pdb=" O ASP I 203 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 242 removed outlier: 3.742A pdb=" N ARG I 227 " --> pdb=" O THR I 223 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE I 229 " --> pdb=" O LEU I 225 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL I 232 " --> pdb=" O ILE I 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE I 236 " --> pdb=" O VAL I 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR I 237 " --> pdb=" O VAL I 233 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER I 239 " --> pdb=" O SER I 235 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU I 240 " --> pdb=" O ILE I 236 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE I 242 " --> pdb=" O ALA I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 258 removed outlier: 3.667A pdb=" N GLN I 254 " --> pdb=" O LEU I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 294 removed outlier: 3.620A pdb=" N ILE I 289 " --> pdb=" O SER I 285 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN I 291 " --> pdb=" O SER I 287 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE I 294 " --> pdb=" O THR I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 322 through 336 removed outlier: 3.983A pdb=" N VAL I 326 " --> pdb=" O VAL I 322 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA I 331 " --> pdb=" O ASN I 327 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 399 removed outlier: 3.858A pdb=" N GLU I 384 " --> pdb=" O THR I 380 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG I 388 " --> pdb=" O GLU I 384 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU I 389 " --> pdb=" O ALA I 385 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS I 392 " --> pdb=" O ARG I 388 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP I 394 " --> pdb=" O ASP I 390 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU I 395 " --> pdb=" O TYR I 391 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET I 396 " --> pdb=" O LYS I 392 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS I 399 " --> pdb=" O LEU I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 406 removed outlier: 3.918A pdb=" N TRP I 405 " --> pdb=" O PHE I 402 " (cutoff:3.500A) Processing helix chain 'I' and resid 413 through 434 removed outlier: 3.880A pdb=" N THR I 417 " --> pdb=" O GLU I 413 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG I 420 " --> pdb=" O PHE I 416 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU I 421 " --> pdb=" O THR I 417 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA I 425 " --> pdb=" O GLU I 421 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU I 426 " --> pdb=" O ASP I 422 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU I 427 " --> pdb=" O LEU I 423 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR I 430 " --> pdb=" O LEU I 426 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU I 431 " --> pdb=" O GLU I 427 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 27 removed outlier: 3.856A pdb=" N GLN K 15 " --> pdb=" O GLN K 11 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY K 17 " --> pdb=" O GLY K 13 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER K 18 " --> pdb=" O ASN K 14 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS K 19 " --> pdb=" O GLN K 15 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU K 22 " --> pdb=" O SER K 18 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL K 23 " --> pdb=" O LYS K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 44 Processing helix chain 'K' and resid 47 through 49 No H-bonds generated for 'chain 'K' and resid 47 through 49' Processing helix chain 'K' and resid 70 through 79 removed outlier: 4.005A pdb=" N ASP K 74 " --> pdb=" O PRO K 70 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER K 75 " --> pdb=" O GLY K 71 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL K 76 " --> pdb=" O THR K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 88 No H-bonds generated for 'chain 'K' and resid 86 through 88' Processing helix chain 'K' and resid 100 through 106 Processing helix chain 'K' and resid 108 through 126 removed outlier: 3.759A pdb=" N LEU K 112 " --> pdb=" O GLU K 108 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASP K 114 " --> pdb=" O ALA K 110 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASN K 115 " --> pdb=" O GLU K 111 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL K 116 " --> pdb=" O LEU K 112 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP K 118 " --> pdb=" O ASP K 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA K 124 " --> pdb=" O ILE K 120 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 159 removed outlier: 4.392A pdb=" N THR K 149 " --> pdb=" O SER K 145 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE K 152 " --> pdb=" O GLY K 148 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER K 153 " --> pdb=" O THR K 149 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS K 154 " --> pdb=" O LEU K 150 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG K 156 " --> pdb=" O ILE K 152 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLU K 157 " --> pdb=" O SER K 153 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU K 158 " --> pdb=" O LYS K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 196 removed outlier: 3.511A pdb=" N THR K 186 " --> pdb=" O PRO K 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU K 187 " --> pdb=" O TYR K 183 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER K 188 " --> pdb=" O ASN K 184 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN K 191 " --> pdb=" O LEU K 187 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU K 194 " --> pdb=" O HIS K 190 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN K 195 " --> pdb=" O GLN K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 214 removed outlier: 4.067A pdb=" N TYR K 208 " --> pdb=" O ASN K 204 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP K 209 " --> pdb=" O GLU K 205 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG K 213 " --> pdb=" O ASP K 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 237 removed outlier: 3.525A pdb=" N ASN K 226 " --> pdb=" O TYR K 222 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR K 232 " --> pdb=" O LEU K 228 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY K 235 " --> pdb=" O LEU K 231 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL K 236 " --> pdb=" O THR K 232 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR K 237 " --> pdb=" O MET K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 242 removed outlier: 3.669A pdb=" N ARG K 241 " --> pdb=" O THR K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 256 Processing helix chain 'K' and resid 285 through 294 removed outlier: 3.539A pdb=" N GLN K 291 " --> pdb=" O ALA K 287 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN K 292 " --> pdb=" O GLU K 288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET K 293 " --> pdb=" O LEU K 289 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE K 294 " --> pdb=" O THR K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 308 removed outlier: 3.557A pdb=" N GLY K 308 " --> pdb=" O PRO K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 322 through 337 removed outlier: 3.938A pdb=" N LEU K 331 " --> pdb=" O ASP K 327 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN K 334 " --> pdb=" O MET K 330 " (cutoff:3.500A) Processing helix chain 'K' and resid 371 through 373 No H-bonds generated for 'chain 'K' and resid 371 through 373' Processing helix chain 'K' and resid 374 through 389 removed outlier: 3.796A pdb=" N PHE K 378 " --> pdb=" O ILE K 374 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE K 381 " --> pdb=" O LEU K 377 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER K 382 " --> pdb=" O PHE K 378 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU K 383 " --> pdb=" O LYS K 379 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN K 384 " --> pdb=" O ARG K 380 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET K 388 " --> pdb=" O GLN K 384 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE K 389 " --> pdb=" O PHE K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 394 through 398 Processing helix chain 'K' and resid 405 through 426 removed outlier: 3.578A pdb=" N ALA K 411 " --> pdb=" O GLU K 407 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU K 418 " --> pdb=" O ASN K 414 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE K 419 " --> pdb=" O MET K 415 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER K 420 " --> pdb=" O ASN K 416 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR K 422 " --> pdb=" O LEU K 418 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR K 425 " --> pdb=" O GLU K 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 29 removed outlier: 3.540A pdb=" N ILE M 16 " --> pdb=" O ALA M 12 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU M 22 " --> pdb=" O ASN M 18 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU M 26 " --> pdb=" O GLU M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 42 removed outlier: 3.836A pdb=" N THR M 41 " --> pdb=" O THR M 38 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN M 42 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 77 removed outlier: 3.646A pdb=" N GLU M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE M 76 " --> pdb=" O VAL M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 4.048A pdb=" N LYS M 83 " --> pdb=" O THR M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 106 Processing helix chain 'M' and resid 108 through 111 Processing helix chain 'M' and resid 112 through 125 removed outlier: 3.875A pdb=" N ASP M 118 " --> pdb=" O ASP M 114 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG M 119 " --> pdb=" O THR M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 159 removed outlier: 3.806A pdb=" N PHE M 147 " --> pdb=" O THR M 143 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR M 148 " --> pdb=" O GLY M 144 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU M 150 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER M 156 " --> pdb=" O MET M 152 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL M 157 " --> pdb=" O GLU M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 191 removed outlier: 3.779A pdb=" N ILE M 186 " --> pdb=" O PRO M 182 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR M 191 " --> pdb=" O LEU M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 214 removed outlier: 3.505A pdb=" N ILE M 207 " --> pdb=" O ASP M 203 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE M 210 " --> pdb=" O ALA M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 242 removed outlier: 3.742A pdb=" N ARG M 227 " --> pdb=" O THR M 223 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE M 229 " --> pdb=" O LEU M 225 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL M 232 " --> pdb=" O ILE M 228 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE M 236 " --> pdb=" O VAL M 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR M 237 " --> pdb=" O VAL M 233 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER M 239 " --> pdb=" O SER M 235 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU M 240 " --> pdb=" O ILE M 236 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE M 242 " --> pdb=" O ALA M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 249 through 258 removed outlier: 3.668A pdb=" N GLN M 254 " --> pdb=" O LEU M 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 285 through 294 removed outlier: 3.621A pdb=" N ILE M 289 " --> pdb=" O SER M 285 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN M 291 " --> pdb=" O SER M 287 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) Processing helix chain 'M' and resid 322 through 336 removed outlier: 3.984A pdb=" N VAL M 326 " --> pdb=" O VAL M 322 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA M 331 " --> pdb=" O ASN M 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 380 through 399 removed outlier: 3.857A pdb=" N GLU M 384 " --> pdb=" O THR M 380 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG M 388 " --> pdb=" O GLU M 384 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU M 389 " --> pdb=" O ALA M 385 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS M 392 " --> pdb=" O ARG M 388 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP M 394 " --> pdb=" O ASP M 390 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU M 395 " --> pdb=" O TYR M 391 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET M 396 " --> pdb=" O LYS M 392 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS M 399 " --> pdb=" O LEU M 395 " (cutoff:3.500A) Processing helix chain 'M' and resid 402 through 406 removed outlier: 3.917A pdb=" N TRP M 405 " --> pdb=" O PHE M 402 " (cutoff:3.500A) Processing helix chain 'M' and resid 413 through 434 removed outlier: 3.880A pdb=" N THR M 417 " --> pdb=" O GLU M 413 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG M 420 " --> pdb=" O PHE M 416 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU M 421 " --> pdb=" O THR M 417 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA M 425 " --> pdb=" O GLU M 421 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU M 426 " --> pdb=" O ASP M 422 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU M 427 " --> pdb=" O LEU M 423 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR M 430 " --> pdb=" O LEU M 426 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU M 431 " --> pdb=" O GLU M 427 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 27 removed outlier: 3.854A pdb=" N GLN O 15 " --> pdb=" O GLN O 11 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY O 17 " --> pdb=" O GLY O 13 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER O 18 " --> pdb=" O ASN O 14 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS O 19 " --> pdb=" O GLN O 15 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU O 22 " --> pdb=" O SER O 18 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL O 23 " --> pdb=" O LYS O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 44 Processing helix chain 'O' and resid 47 through 49 No H-bonds generated for 'chain 'O' and resid 47 through 49' Processing helix chain 'O' and resid 70 through 79 removed outlier: 4.005A pdb=" N ASP O 74 " --> pdb=" O PRO O 70 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER O 75 " --> pdb=" O GLY O 71 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL O 76 " --> pdb=" O THR O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 88 No H-bonds generated for 'chain 'O' and resid 86 through 88' Processing helix chain 'O' and resid 100 through 106 Processing helix chain 'O' and resid 108 through 126 removed outlier: 3.759A pdb=" N LEU O 112 " --> pdb=" O GLU O 108 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASP O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASN O 115 " --> pdb=" O GLU O 111 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL O 116 " --> pdb=" O LEU O 112 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP O 118 " --> pdb=" O ASP O 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL O 119 " --> pdb=" O ASN O 115 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA O 124 " --> pdb=" O ILE O 120 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY O 126 " --> pdb=" O LYS O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 159 removed outlier: 4.391A pdb=" N THR O 149 " --> pdb=" O SER O 145 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU O 150 " --> pdb=" O GLY O 146 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE O 152 " --> pdb=" O GLY O 148 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER O 153 " --> pdb=" O THR O 149 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS O 154 " --> pdb=" O LEU O 150 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG O 156 " --> pdb=" O ILE O 152 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLU O 157 " --> pdb=" O SER O 153 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU O 158 " --> pdb=" O LYS O 154 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 196 removed outlier: 3.512A pdb=" N THR O 186 " --> pdb=" O PRO O 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU O 187 " --> pdb=" O TYR O 183 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER O 188 " --> pdb=" O ASN O 184 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN O 191 " --> pdb=" O LEU O 187 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU O 194 " --> pdb=" O HIS O 190 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN O 195 " --> pdb=" O GLN O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 214 removed outlier: 4.067A pdb=" N TYR O 208 " --> pdb=" O ASN O 204 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP O 209 " --> pdb=" O GLU O 205 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG O 213 " --> pdb=" O ASP O 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 221 through 237 removed outlier: 3.523A pdb=" N ASN O 226 " --> pdb=" O TYR O 222 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR O 232 " --> pdb=" O LEU O 228 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY O 235 " --> pdb=" O LEU O 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL O 236 " --> pdb=" O THR O 232 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR O 237 " --> pdb=" O MET O 233 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 242 removed outlier: 3.668A pdb=" N ARG O 241 " --> pdb=" O THR O 237 " (cutoff:3.500A) Processing helix chain 'O' and resid 249 through 256 Processing helix chain 'O' and resid 285 through 294 removed outlier: 3.539A pdb=" N GLN O 291 " --> pdb=" O ALA O 287 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN O 292 " --> pdb=" O GLU O 288 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET O 293 " --> pdb=" O LEU O 289 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE O 294 " --> pdb=" O THR O 290 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 308 removed outlier: 3.557A pdb=" N GLY O 308 " --> pdb=" O PRO O 305 " (cutoff:3.500A) Processing helix chain 'O' and resid 322 through 337 removed outlier: 3.938A pdb=" N LEU O 331 " --> pdb=" O ASP O 327 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN O 334 " --> pdb=" O MET O 330 " (cutoff:3.500A) Processing helix chain 'O' and resid 371 through 373 No H-bonds generated for 'chain 'O' and resid 371 through 373' Processing helix chain 'O' and resid 374 through 389 removed outlier: 3.795A pdb=" N PHE O 378 " --> pdb=" O ILE O 374 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE O 381 " --> pdb=" O LEU O 377 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER O 382 " --> pdb=" O PHE O 378 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU O 383 " --> pdb=" O LYS O 379 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN O 384 " --> pdb=" O ARG O 380 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET O 388 " --> pdb=" O GLN O 384 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE O 389 " --> pdb=" O PHE O 385 " (cutoff:3.500A) Processing helix chain 'O' and resid 394 through 398 Processing helix chain 'O' and resid 405 through 426 removed outlier: 3.578A pdb=" N ALA O 411 " --> pdb=" O GLU O 407 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU O 418 " --> pdb=" O ASN O 414 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE O 419 " --> pdb=" O MET O 415 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER O 420 " --> pdb=" O ASN O 416 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR O 422 " --> pdb=" O LEU O 418 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR O 425 " --> pdb=" O GLU O 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 7.930A pdb=" N ILE A 91 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE A 65 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N ILE A 64 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER A 6 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A 66 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N HIS A 8 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU A 3 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLY A 132 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 5 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU A 166 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 52 removed outlier: 3.662A pdb=" N VAL A 60 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.512A pdb=" N ALA A 372 " --> pdb=" O ARG A 318 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 316 " --> pdb=" O CYS A 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 378 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 312 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 350 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 315 " --> pdb=" O LYS A 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.512A pdb=" N ALA A 372 " --> pdb=" O ARG A 318 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 316 " --> pdb=" O CYS A 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 378 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 312 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ASN A 354 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR A 317 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.683A pdb=" N VAL B 91 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP B 67 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N HIS B 137 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N ILE B 163 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N SER B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE B 133 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR B 200 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER B 168 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE B 202 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 11.595A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.831A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 52 removed outlier: 3.912A pdb=" N VAL B 60 " --> pdb=" O ASN B 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 90 through 92 removed outlier: 7.929A pdb=" N ILE C 91 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE C 65 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE C 64 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER C 6 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL C 66 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N HIS C 8 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU C 3 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLY C 132 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 5 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU C 166 " --> pdb=" O PHE C 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 51 through 52 removed outlier: 3.662A pdb=" N VAL C 60 " --> pdb=" O SER C 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 268 through 271 removed outlier: 3.513A pdb=" N ALA C 372 " --> pdb=" O ARG C 318 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 316 " --> pdb=" O CYS C 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN C 378 " --> pdb=" O ALA C 312 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 312 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS C 350 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 315 " --> pdb=" O LYS C 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 268 through 271 removed outlier: 3.513A pdb=" N ALA C 372 " --> pdb=" O ARG C 318 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 316 " --> pdb=" O CYS C 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN C 378 " --> pdb=" O ALA C 312 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 312 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ASN C 354 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TYR C 317 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 90 through 92 removed outlier: 3.683A pdb=" N VAL D 91 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP D 67 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N HIS D 137 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA D 9 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N ILE D 163 " --> pdb=" O CYS D 129 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N SER D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE D 133 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL D 169 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N HIS D 137 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR D 200 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER D 168 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE D 202 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 11.595A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 13.831A pdb=" N ASP D 203 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL D 313 " --> pdb=" O LYS D 350 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ALA D 352 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA D 315 " --> pdb=" O ALA D 352 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N CYS D 354 " --> pdb=" O ALA D 315 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE D 317 " --> pdb=" O CYS D 354 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 51 through 52 removed outlier: 3.913A pdb=" N VAL D 60 " --> pdb=" O ASN D 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 90 through 92 removed outlier: 7.929A pdb=" N ILE H 91 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE H 65 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE H 64 " --> pdb=" O VAL H 4 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL H 66 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N HIS H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU H 3 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY H 132 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE H 5 " --> pdb=" O GLY H 132 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU H 166 " --> pdb=" O PHE H 200 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 51 through 52 removed outlier: 3.662A pdb=" N VAL H 60 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 268 through 271 removed outlier: 3.512A pdb=" N ALA H 372 " --> pdb=" O ARG H 318 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU H 316 " --> pdb=" O CYS H 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN H 378 " --> pdb=" O ALA H 312 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA H 312 " --> pdb=" O ASN H 378 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS H 350 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU H 315 " --> pdb=" O LYS H 350 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 268 through 271 removed outlier: 3.512A pdb=" N ALA H 372 " --> pdb=" O ARG H 318 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU H 316 " --> pdb=" O CYS H 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN H 378 " --> pdb=" O ALA H 312 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA H 312 " --> pdb=" O ASN H 378 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ASN H 354 " --> pdb=" O LEU H 315 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TYR H 317 " --> pdb=" O ASN H 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 90 through 92 removed outlier: 3.682A pdb=" N VAL J 91 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP J 67 " --> pdb=" O VAL J 91 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU J 3 " --> pdb=" O GLN J 131 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE J 133 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL J 5 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU J 135 " --> pdb=" O VAL J 5 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL J 7 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N HIS J 137 " --> pdb=" O VAL J 7 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA J 9 " --> pdb=" O HIS J 137 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N ILE J 163 " --> pdb=" O CYS J 129 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN J 131 " --> pdb=" O ILE J 163 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N SER J 165 " --> pdb=" O GLN J 131 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE J 133 " --> pdb=" O SER J 165 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N PHE J 167 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU J 135 " --> pdb=" O PHE J 167 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL J 169 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N HIS J 137 " --> pdb=" O VAL J 169 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR J 200 " --> pdb=" O SER J 166 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER J 168 " --> pdb=" O TYR J 200 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE J 202 " --> pdb=" O SER J 168 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR J 199 " --> pdb=" O PHE J 266 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N CYS J 201 " --> pdb=" O PRO J 268 " (cutoff:3.500A) removed outlier: 11.595A pdb=" N PHE J 270 " --> pdb=" O CYS J 201 " (cutoff:3.500A) removed outlier: 13.831A pdb=" N ASP J 203 " --> pdb=" O PHE J 270 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL J 313 " --> pdb=" O LYS J 350 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA J 352 " --> pdb=" O VAL J 313 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA J 315 " --> pdb=" O ALA J 352 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N CYS J 354 " --> pdb=" O ALA J 315 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE J 317 " --> pdb=" O CYS J 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 51 through 52 removed outlier: 3.912A pdb=" N VAL J 60 " --> pdb=" O ASN J 52 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 90 through 92 removed outlier: 7.929A pdb=" N ILE L 91 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE L 65 " --> pdb=" O ILE L 91 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE L 64 " --> pdb=" O VAL L 4 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER L 6 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL L 66 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N HIS L 8 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU L 3 " --> pdb=" O LEU L 130 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLY L 132 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE L 5 " --> pdb=" O GLY L 132 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU L 166 " --> pdb=" O PHE L 200 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 51 through 52 removed outlier: 3.661A pdb=" N VAL L 60 " --> pdb=" O SER L 52 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 268 through 271 removed outlier: 3.512A pdb=" N ALA L 372 " --> pdb=" O ARG L 318 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU L 316 " --> pdb=" O CYS L 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN L 378 " --> pdb=" O ALA L 312 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA L 312 " --> pdb=" O ASN L 378 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS L 350 " --> pdb=" O VAL L 313 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU L 315 " --> pdb=" O LYS L 350 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 268 through 271 removed outlier: 3.512A pdb=" N ALA L 372 " --> pdb=" O ARG L 318 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU L 316 " --> pdb=" O CYS L 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN L 378 " --> pdb=" O ALA L 312 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA L 312 " --> pdb=" O ASN L 378 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ASN L 354 " --> pdb=" O LEU L 315 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TYR L 317 " --> pdb=" O ASN L 354 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 90 through 92 removed outlier: 3.683A pdb=" N VAL N 91 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP N 67 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU N 3 " --> pdb=" O GLN N 131 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE N 133 " --> pdb=" O GLU N 3 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL N 5 " --> pdb=" O PHE N 133 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU N 135 " --> pdb=" O VAL N 5 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL N 7 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N HIS N 137 " --> pdb=" O VAL N 7 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA N 9 " --> pdb=" O HIS N 137 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N ILE N 163 " --> pdb=" O CYS N 129 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN N 131 " --> pdb=" O ILE N 163 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N SER N 165 " --> pdb=" O GLN N 131 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE N 133 " --> pdb=" O SER N 165 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE N 167 " --> pdb=" O PHE N 133 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU N 135 " --> pdb=" O PHE N 167 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL N 169 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N HIS N 137 " --> pdb=" O VAL N 169 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR N 200 " --> pdb=" O SER N 166 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER N 168 " --> pdb=" O TYR N 200 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE N 202 " --> pdb=" O SER N 168 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR N 199 " --> pdb=" O PHE N 266 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N CYS N 201 " --> pdb=" O PRO N 268 " (cutoff:3.500A) removed outlier: 11.594A pdb=" N PHE N 270 " --> pdb=" O CYS N 201 " (cutoff:3.500A) removed outlier: 13.831A pdb=" N ASP N 203 " --> pdb=" O PHE N 270 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL N 313 " --> pdb=" O LYS N 350 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA N 352 " --> pdb=" O VAL N 313 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA N 315 " --> pdb=" O ALA N 352 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N CYS N 354 " --> pdb=" O ALA N 315 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE N 317 " --> pdb=" O CYS N 354 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 51 through 52 removed outlier: 3.912A pdb=" N VAL N 60 " --> pdb=" O ASN N 52 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 90 through 92 removed outlier: 7.930A pdb=" N ILE I 91 " --> pdb=" O SER I 63 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE I 65 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N ILE I 64 " --> pdb=" O VAL I 4 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL I 66 " --> pdb=" O SER I 6 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N HIS I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU I 3 " --> pdb=" O LEU I 130 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLY I 132 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE I 5 " --> pdb=" O GLY I 132 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU I 166 " --> pdb=" O PHE I 200 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 51 through 52 removed outlier: 3.662A pdb=" N VAL I 60 " --> pdb=" O SER I 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 268 through 271 removed outlier: 3.512A pdb=" N ALA I 372 " --> pdb=" O ARG I 318 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU I 316 " --> pdb=" O CYS I 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN I 378 " --> pdb=" O ALA I 312 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA I 312 " --> pdb=" O ASN I 378 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS I 350 " --> pdb=" O VAL I 313 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU I 315 " --> pdb=" O LYS I 350 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 268 through 271 removed outlier: 3.512A pdb=" N ALA I 372 " --> pdb=" O ARG I 318 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU I 316 " --> pdb=" O CYS I 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN I 378 " --> pdb=" O ALA I 312 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA I 312 " --> pdb=" O ASN I 378 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ASN I 354 " --> pdb=" O LEU I 315 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR I 317 " --> pdb=" O ASN I 354 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 90 through 92 removed outlier: 3.682A pdb=" N VAL K 91 " --> pdb=" O LEU K 65 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP K 67 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU K 3 " --> pdb=" O GLN K 131 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE K 133 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL K 5 " --> pdb=" O PHE K 133 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU K 135 " --> pdb=" O VAL K 5 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL K 7 " --> pdb=" O LEU K 135 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N HIS K 137 " --> pdb=" O VAL K 7 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA K 9 " --> pdb=" O HIS K 137 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N ILE K 163 " --> pdb=" O CYS K 129 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN K 131 " --> pdb=" O ILE K 163 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N SER K 165 " --> pdb=" O GLN K 131 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE K 133 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N PHE K 167 " --> pdb=" O PHE K 133 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU K 135 " --> pdb=" O PHE K 167 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL K 169 " --> pdb=" O LEU K 135 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N HIS K 137 " --> pdb=" O VAL K 169 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR K 200 " --> pdb=" O SER K 166 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER K 168 " --> pdb=" O TYR K 200 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE K 202 " --> pdb=" O SER K 168 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR K 199 " --> pdb=" O PHE K 266 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N CYS K 201 " --> pdb=" O PRO K 268 " (cutoff:3.500A) removed outlier: 11.595A pdb=" N PHE K 270 " --> pdb=" O CYS K 201 " (cutoff:3.500A) removed outlier: 13.831A pdb=" N ASP K 203 " --> pdb=" O PHE K 270 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL K 313 " --> pdb=" O LYS K 350 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA K 352 " --> pdb=" O VAL K 313 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA K 315 " --> pdb=" O ALA K 352 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N CYS K 354 " --> pdb=" O ALA K 315 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE K 317 " --> pdb=" O CYS K 354 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 51 through 52 removed outlier: 3.913A pdb=" N VAL K 60 " --> pdb=" O ASN K 52 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 90 through 92 removed outlier: 7.930A pdb=" N ILE M 91 " --> pdb=" O SER M 63 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE M 65 " --> pdb=" O ILE M 91 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N ILE M 64 " --> pdb=" O VAL M 4 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER M 6 " --> pdb=" O ILE M 64 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL M 66 " --> pdb=" O SER M 6 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N HIS M 8 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU M 3 " --> pdb=" O LEU M 130 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLY M 132 " --> pdb=" O GLU M 3 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE M 5 " --> pdb=" O GLY M 132 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU M 166 " --> pdb=" O PHE M 200 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 51 through 52 removed outlier: 3.661A pdb=" N VAL M 60 " --> pdb=" O SER M 52 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 268 through 271 removed outlier: 3.512A pdb=" N ALA M 372 " --> pdb=" O ARG M 318 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU M 316 " --> pdb=" O CYS M 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN M 378 " --> pdb=" O ALA M 312 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA M 312 " --> pdb=" O ASN M 378 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS M 350 " --> pdb=" O VAL M 313 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU M 315 " --> pdb=" O LYS M 350 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 268 through 271 removed outlier: 3.512A pdb=" N ALA M 372 " --> pdb=" O ARG M 318 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU M 316 " --> pdb=" O CYS M 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN M 378 " --> pdb=" O ALA M 312 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA M 312 " --> pdb=" O ASN M 378 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASN M 354 " --> pdb=" O LEU M 315 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR M 317 " --> pdb=" O ASN M 354 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 90 through 92 removed outlier: 3.683A pdb=" N VAL O 91 " --> pdb=" O LEU O 65 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP O 67 " --> pdb=" O VAL O 91 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU O 3 " --> pdb=" O GLN O 131 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE O 133 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL O 5 " --> pdb=" O PHE O 133 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU O 135 " --> pdb=" O VAL O 5 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL O 7 " --> pdb=" O LEU O 135 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N HIS O 137 " --> pdb=" O VAL O 7 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA O 9 " --> pdb=" O HIS O 137 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N ILE O 163 " --> pdb=" O CYS O 129 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN O 131 " --> pdb=" O ILE O 163 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N SER O 165 " --> pdb=" O GLN O 131 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE O 133 " --> pdb=" O SER O 165 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N PHE O 167 " --> pdb=" O PHE O 133 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU O 135 " --> pdb=" O PHE O 167 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL O 169 " --> pdb=" O LEU O 135 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N HIS O 137 " --> pdb=" O VAL O 169 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR O 200 " --> pdb=" O SER O 166 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER O 168 " --> pdb=" O TYR O 200 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE O 202 " --> pdb=" O SER O 168 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR O 199 " --> pdb=" O PHE O 266 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N CYS O 201 " --> pdb=" O PRO O 268 " (cutoff:3.500A) removed outlier: 11.595A pdb=" N PHE O 270 " --> pdb=" O CYS O 201 " (cutoff:3.500A) removed outlier: 13.831A pdb=" N ASP O 203 " --> pdb=" O PHE O 270 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL O 313 " --> pdb=" O LYS O 350 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA O 352 " --> pdb=" O VAL O 313 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA O 315 " --> pdb=" O ALA O 352 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N CYS O 354 " --> pdb=" O ALA O 315 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE O 317 " --> pdb=" O CYS O 354 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 51 through 52 removed outlier: 3.913A pdb=" N VAL O 60 " --> pdb=" O ASN O 52 " (cutoff:3.500A) 1338 hydrogen bonds defined for protein. 3798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.95 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13501 1.34 - 1.46: 7954 1.46 - 1.57: 19891 1.57 - 1.69: 48 1.69 - 1.81: 456 Bond restraints: 41850 Sorted by residual: bond pdb=" C5 GDP J 501 " pdb=" C4 GDP J 501 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.59e+00 bond pdb=" C5 GDP N 501 " pdb=" C4 GDP N 501 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.53e+00 bond pdb=" C5 GDP B 501 " pdb=" C4 GDP B 501 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" C5 GDP O 501 " pdb=" C4 GDP O 501 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C5 GDP K 501 " pdb=" C4 GDP K 501 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.48e+00 ... (remaining 41845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 53239 1.41 - 2.83: 3069 2.83 - 4.24: 394 4.24 - 5.66: 100 5.66 - 7.07: 48 Bond angle restraints: 56850 Sorted by residual: angle pdb=" N VAL C 108 " pdb=" CA VAL C 108 " pdb=" C VAL C 108 " ideal model delta sigma weight residual 113.39 107.46 5.93 1.47e+00 4.63e-01 1.63e+01 angle pdb=" N VAL M 108 " pdb=" CA VAL M 108 " pdb=" C VAL M 108 " ideal model delta sigma weight residual 113.39 107.47 5.92 1.47e+00 4.63e-01 1.62e+01 angle pdb=" N VAL L 108 " pdb=" CA VAL L 108 " pdb=" C VAL L 108 " ideal model delta sigma weight residual 113.39 107.49 5.90 1.47e+00 4.63e-01 1.61e+01 angle pdb=" N VAL H 108 " pdb=" CA VAL H 108 " pdb=" C VAL H 108 " ideal model delta sigma weight residual 113.39 107.49 5.90 1.47e+00 4.63e-01 1.61e+01 angle pdb=" N VAL A 108 " pdb=" CA VAL A 108 " pdb=" C VAL A 108 " ideal model delta sigma weight residual 113.39 107.51 5.88 1.47e+00 4.63e-01 1.60e+01 ... (remaining 56845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 24691 35.06 - 70.12: 150 70.12 - 105.18: 18 105.18 - 140.24: 12 140.24 - 175.30: 17 Dihedral angle restraints: 24888 sinusoidal: 9984 harmonic: 14904 Sorted by residual: dihedral pdb=" O5' GTP C 501 " pdb=" O3A GTP C 501 " pdb=" PA GTP C 501 " pdb=" PB GTP C 501 " ideal model delta sinusoidal sigma weight residual -85.88 89.42 -175.30 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP I 501 " pdb=" O3A GTP I 501 " pdb=" PA GTP I 501 " pdb=" PB GTP I 501 " ideal model delta sinusoidal sigma weight residual -85.88 89.41 -175.29 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP M 501 " pdb=" O3A GTP M 501 " pdb=" PA GTP M 501 " pdb=" PB GTP M 501 " ideal model delta sinusoidal sigma weight residual -85.88 89.40 -175.28 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 24885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3335 0.033 - 0.066: 1797 0.066 - 0.099: 742 0.099 - 0.132: 286 0.132 - 0.166: 38 Chirality restraints: 6198 Sorted by residual: chirality pdb=" CB VAL M 342 " pdb=" CA VAL M 342 " pdb=" CG1 VAL M 342 " pdb=" CG2 VAL M 342 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CB VAL C 342 " pdb=" CA VAL C 342 " pdb=" CG1 VAL C 342 " pdb=" CG2 VAL C 342 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CB VAL I 342 " pdb=" CA VAL I 342 " pdb=" CG1 VAL I 342 " pdb=" CG2 VAL I 342 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 6195 not shown) Planarity restraints: 7410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 322 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO H 323 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO H 323 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 323 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 322 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO A 323 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 322 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO L 323 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO L 323 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 323 " -0.035 5.00e-02 4.00e+02 ... (remaining 7407 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 10192 2.79 - 3.32: 36005 3.32 - 3.84: 67293 3.84 - 4.37: 80359 4.37 - 4.90: 132287 Nonbonded interactions: 326136 Sorted by model distance: nonbonded pdb=" OE2 GLU C 181 " pdb=" O3' GTP C 501 " model vdw 2.258 3.040 nonbonded pdb=" O LEU K 192 " pdb=" OG1 THR K 196 " model vdw 2.265 3.040 nonbonded pdb=" O LEU N 192 " pdb=" OG1 THR N 196 " model vdw 2.266 3.040 nonbonded pdb=" O LEU J 192 " pdb=" OG1 THR J 196 " model vdw 2.266 3.040 nonbonded pdb=" O LEU D 192 " pdb=" OG1 THR D 196 " model vdw 2.266 3.040 ... (remaining 326131 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'H' selection = chain 'L' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'J' selection = chain 'N' selection = chain 'K' selection = chain 'O' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'H' selection = chain 'L' selection = chain 'I' selection = chain 'M' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'J' selection = chain 'N' selection = chain 'K' selection = chain 'O' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 35.590 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41850 Z= 0.169 Angle : 0.749 7.074 56850 Z= 0.414 Chirality : 0.048 0.166 6198 Planarity : 0.006 0.064 7410 Dihedral : 11.588 175.301 15348 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.27 % Allowed : 1.63 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.09), residues: 5136 helix: -3.76 (0.06), residues: 1848 sheet: -1.28 (0.19), residues: 714 loop : -2.37 (0.11), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 380 TYR 0.016 0.002 TYR H 59 PHE 0.023 0.002 PHE M 51 TRP 0.014 0.002 TRP O 397 HIS 0.007 0.002 HIS I 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (41850) covalent geometry : angle 0.74908 / 0.41 (56850) hydrogen bonds : bond 0.30233 / 20.08 ( 1290) hydrogen bonds : angle 10.14567 / 7.04 ( 3798) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6579 (ttt180) cc_final: 0.5620 (ttt180) REVERT: A 94 LYS cc_start: 0.8337 (mtmm) cc_final: 0.8119 (tmtt) REVERT: A 96 ASP cc_start: 0.7574 (t70) cc_final: 0.7371 (t0) REVERT: A 136 PHE cc_start: 0.7205 (m-10) cc_final: 0.6610 (m-10) REVERT: A 137 HIS cc_start: 0.6408 (p90) cc_final: 0.5717 (p90) REVERT: A 147 PHE cc_start: 0.7368 (t80) cc_final: 0.6682 (t80) REVERT: A 152 MET cc_start: 0.7798 (mmp) cc_final: 0.7403 (mmp) REVERT: A 170 TYR cc_start: 0.6869 (t80) cc_final: 0.6667 (t80) REVERT: A 231 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8520 (mm-40) REVERT: A 300 MET cc_start: 0.6876 (mmt) cc_final: 0.6323 (mmm) REVERT: A 316 LEU cc_start: 0.9249 (mp) cc_final: 0.8689 (mm) REVERT: A 368 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8055 (tttm) REVERT: A 374 CYS cc_start: 0.8589 (t) cc_final: 0.8352 (p) REVERT: A 416 PHE cc_start: 0.8030 (m-10) cc_final: 0.7047 (m-80) outliers start: 2 outliers final: 0 residues processed: 112 average time/residue: 0.0869 time to fit residues: 11.2827 Evaluate side-chains 61 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.133 Evaluate side-chains 115 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8342 (mt) cc_final: 0.8079 (tt) REVERT: B 199 THR cc_start: 0.7137 (p) cc_final: 0.6767 (t) REVERT: B 209 ASP cc_start: 0.5851 (m-30) cc_final: 0.4670 (m-30) REVERT: B 326 VAL cc_start: 0.9037 (t) cc_final: 0.8320 (t) REVERT: B 378 PHE cc_start: 0.8310 (m-80) cc_final: 0.7932 (m-80) REVERT: B 379 LYS cc_start: 0.9401 (mtpm) cc_final: 0.8769 (ttpp) REVERT: B 418 LEU cc_start: 0.8794 (tt) cc_final: 0.8510 (tt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0702 time to fit residues: 9.7651 Evaluate side-chains 65 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: [432, 197, 388, 455, 215, 20, 132, 494, 261, 248, 207] chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 0.0170 chunk 388 optimal weight: 30.0000 chunk 455 optimal weight: 0.0270 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 20.0000 chunk 494 optimal weight: 0.4980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0570 chunk 207 optimal weight: 2.9990 overall best weight: 0.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 HIS A 105 HIS A 298 ASN B 227 HIS ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 332 ASN ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.088349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.078981 restraints weight = 12651.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.080943 restraints weight = 8276.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.082360 restraints weight = 5857.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.083396 restraints weight = 4392.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.084175 restraints weight = 3431.391| |-----------------------------------------------------------------------------| r_work (final): 0.3583 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.084350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.076046 restraints weight = 13438.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.077874 restraints weight = 8680.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.079159 restraints weight = 6025.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.080138 restraints weight = 4452.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.080803 restraints weight = 3420.579| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41850 Z= 0.126 Angle : 0.627 8.435 56850 Z= 0.328 Chirality : 0.044 0.156 6198 Planarity : 0.005 0.054 7410 Dihedral : 11.598 176.770 5790 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.14 % Allowed : 1.63 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.10), residues: 5136 helix: -2.41 (0.08), residues: 2016 sheet: -1.03 (0.17), residues: 834 loop : -1.74 (0.12), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 219 TYR 0.040 0.002 TYR M 280 PHE 0.020 0.001 PHE K 294 TRP 0.013 0.001 TRP K 101 HIS 0.005 0.001 HIS L 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (41850) covalent geometry : angle 0.62701 / 0.33 (56850) hydrogen bonds : bond 0.04651 / 3.04 ( 1290) hydrogen bonds : angle 5.65919 / 3.91 ( 3798) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 TYR cc_start: 0.7291 (m-10) cc_final: 0.7060 (m-80) REVERT: H 90 MET cc_start: 0.9081 (mtp) cc_final: 0.8751 (ttp) REVERT: H 147 PHE cc_start: 0.7020 (t80) cc_final: 0.6805 (t80) REVERT: H 170 TYR cc_start: 0.6834 (t80) cc_final: 0.6620 (t80) REVERT: H 205 GLU cc_start: 0.7844 (tp30) cc_final: 0.7541 (mp0) REVERT: H 300 MET cc_start: 0.7356 (mmt) cc_final: 0.6853 (mmm) REVERT: H 314 CYS cc_start: 0.8399 (t) cc_final: 0.7817 (t) REVERT: H 376 LEU cc_start: 0.8324 (mp) cc_final: 0.8115 (mt) REVERT: H 426 LEU cc_start: 0.8729 (tt) cc_final: 0.8232 (mm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0794 time to fit residues: 7.3387 Evaluate side-chains 46 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.128 Evaluate side-chains 103 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 117 LEU cc_start: 0.8976 (tt) cc_final: 0.8702 (tt) REVERT: N 163 ILE cc_start: 0.8443 (pt) cc_final: 0.8179 (pt) REVERT: N 208 TYR cc_start: 0.7615 (m-10) cc_final: 0.7395 (m-80) REVERT: N 262 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7796 (ptm-80) REVERT: N 273 LEU cc_start: 0.7182 (mt) cc_final: 0.6834 (mt) REVERT: N 299 MET cc_start: 0.6767 (mmm) cc_final: 0.5802 (mmm) REVERT: N 328 GLU cc_start: 0.9057 (tt0) cc_final: 0.8841 (mm-30) REVERT: N 426 GLN cc_start: 0.5897 (tt0) cc_final: 0.4620 (tm-30) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.0813 time to fit residues: 9.6661 Evaluate side-chains 61 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: [157, 107, 385, 471, 502, 214, 237, 180, 226, 330, 74] chunk 157 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 385 optimal weight: 7.9990 chunk 471 optimal weight: 4.9990 chunk 502 optimal weight: 0.2980 chunk 214 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 180 optimal weight: 30.0000 chunk 226 optimal weight: 0.3980 chunk 330 optimal weight: 0.0980 chunk 74 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 HIS H 226 ASN H 291 ASN H 298 ASN H 378 ASN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 131 GLN N 256 ASN N 332 ASN N 396 HIS N 414 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.088948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.078693 restraints weight = 12565.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.080853 restraints weight = 8206.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.082480 restraints weight = 5813.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.083627 restraints weight = 4346.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.084612 restraints weight = 3404.284| |-----------------------------------------------------------------------------| r_work (final): 0.3578 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.084052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.074892 restraints weight = 13648.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.076895 restraints weight = 8712.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.078297 restraints weight = 6036.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.079382 restraints weight = 4432.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.080152 restraints weight = 3385.904| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 41850 Z= 0.130 Angle : 0.642 10.845 56850 Z= 0.330 Chirality : 0.044 0.153 6198 Planarity : 0.006 0.123 7410 Dihedral : 11.436 178.031 5790 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.11), residues: 5136 helix: -1.59 (0.10), residues: 1980 sheet: -0.73 (0.18), residues: 792 loop : -1.61 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG B 251 TYR 0.048 0.002 TYR K 212 PHE 0.016 0.001 PHE I 294 TRP 0.025 0.002 TRP M 21 HIS 0.007 0.001 HIS I 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (41850) covalent geometry : angle 0.64224 / 0.33 (56850) hydrogen bonds : bond 0.04149 / 2.69 ( 1290) hydrogen bonds : angle 5.22268 / 3.61 ( 3798) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 237 THR cc_start: 0.9373 (p) cc_final: 0.9135 (t) REVERT: L 300 MET cc_start: 0.7778 (mmt) cc_final: 0.6617 (mtt) REVERT: L 418 GLU cc_start: 0.6083 (mm-30) cc_final: 0.5309 (mm-30) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0804 time to fit residues: 8.9063 Evaluate side-chains 56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.119 Evaluate side-chains 81 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 163 ILE cc_start: 0.8132 (pt) cc_final: 0.7683 (pt) REVERT: N 183 TYR cc_start: 0.6445 (m-10) cc_final: 0.5590 (m-10) REVERT: N 262 ARG cc_start: 0.8277 (mtp85) cc_final: 0.7944 (ptm-80) REVERT: N 267 MET cc_start: 0.7190 (tmm) cc_final: 0.6763 (tmm) REVERT: N 299 MET cc_start: 0.6808 (mmm) cc_final: 0.6112 (mmm) REVERT: N 300 MET cc_start: 0.8428 (mtt) cc_final: 0.7753 (mtp) REVERT: N 323 MET cc_start: 0.7811 (pmm) cc_final: 0.7251 (pmm) REVERT: N 378 PHE cc_start: 0.7498 (m-80) cc_final: 0.7252 (m-80) REVERT: N 426 GLN cc_start: 0.5754 (tt0) cc_final: 0.4532 (tm-30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0838 time to fit residues: 7.9100 Evaluate side-chains 52 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: [278, 155, 442, 116, 483, 75, 92, 9, 29, 231, 87] chunk 278 optimal weight: 0.1980 chunk 155 optimal weight: 0.4980 chunk 442 optimal weight: 20.0000 chunk 116 optimal weight: 30.0000 chunk 483 optimal weight: 20.0000 chunk 75 optimal weight: 0.4980 chunk 92 optimal weight: 6.9990 chunk 9 optimal weight: 0.0270 chunk 29 optimal weight: 30.0000 chunk 231 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 226 ASN L 298 ASN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 131 GLN ** N 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 332 ASN N 337 ASN N 347 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.088553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.078195 restraints weight = 12397.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.080295 restraints weight = 8038.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.081868 restraints weight = 5667.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.083045 restraints weight = 4219.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.083919 restraints weight = 3280.649| |-----------------------------------------------------------------------------| r_work (final): 0.3562 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.082306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.073325 restraints weight = 15014.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075175 restraints weight = 9781.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.076446 restraints weight = 6879.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.077421 restraints weight = 5141.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.078113 restraints weight = 4009.258| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 41850 Z= 0.123 Angle : 0.647 12.552 56850 Z= 0.321 Chirality : 0.044 0.150 6198 Planarity : 0.005 0.061 7410 Dihedral : 11.083 178.603 5790 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.27 % Allowed : 2.86 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.11), residues: 5136 helix: -1.15 (0.10), residues: 1992 sheet: -0.51 (0.19), residues: 786 loop : -1.51 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 219 TYR 0.032 0.001 TYR L 222 PHE 0.043 0.002 PHE J 92 TRP 0.018 0.002 TRP D 397 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (41850) covalent geometry : angle 0.64657 / 0.32 (56850) hydrogen bonds : bond 0.03625 / 2.36 ( 1290) hydrogen bonds : angle 4.90921 / 3.38 ( 3798) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 90 MET cc_start: 0.9093 (ttp) cc_final: 0.8556 (tmm) REVERT: L 298 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7476 (t0) REVERT: L 300 MET cc_start: 0.7801 (mmt) cc_final: 0.6789 (mtt) outliers start: 2 outliers final: 0 residues processed: 72 average time/residue: 0.0761 time to fit residues: 6.5277 Evaluate side-chains 45 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.087 Evaluate side-chains 71 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 241 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7778 (mtm110) REVERT: N 262 ARG cc_start: 0.8425 (mtp85) cc_final: 0.7922 (ptm-80) REVERT: N 267 MET cc_start: 0.6913 (tmm) cc_final: 0.6642 (tmm) REVERT: N 299 MET cc_start: 0.6731 (mmm) cc_final: 0.6044 (mmm) REVERT: N 300 MET cc_start: 0.8370 (mtt) cc_final: 0.7506 (mtp) REVERT: N 306 ARG cc_start: 0.7051 (mtt90) cc_final: 0.6513 (mtm-85) REVERT: N 323 MET cc_start: 0.7911 (pmm) cc_final: 0.7345 (pmm) REVERT: N 326 VAL cc_start: 0.9127 (t) cc_final: 0.8719 (t) REVERT: N 363 MET cc_start: 0.6948 (mpp) cc_final: 0.6576 (ttp) REVERT: N 426 GLN cc_start: 0.5280 (tt0) cc_final: 0.4143 (tm-30) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0632 time to fit residues: 5.4447 Evaluate side-chains 52 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: [311, 36, 220, 268, 0, 372, 407, 400, 170, 1, 273] chunk 311 optimal weight: 0.0020 chunk 36 optimal weight: 0.9980 chunk 220 optimal weight: 0.0970 chunk 268 optimal weight: 0.0020 chunk 0 optimal weight: 30.0000 chunk 372 optimal weight: 0.0970 chunk 407 optimal weight: 8.9990 chunk 400 optimal weight: 0.1980 chunk 170 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 273 optimal weight: 4.9990 overall best weight: 0.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 195 HIS L 298 ASN L 404 HIS ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.089876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.079413 restraints weight = 13077.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.081514 restraints weight = 8624.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.083013 restraints weight = 6155.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.084112 restraints weight = 4672.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.085005 restraints weight = 3717.881| |-----------------------------------------------------------------------------| r_work (final): 0.3576 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.084199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.075047 restraints weight = 14434.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.076964 restraints weight = 9271.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.078299 restraints weight = 6434.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.079333 restraints weight = 4790.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.080090 restraints weight = 3725.322| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.6368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 41850 Z= 0.116 Angle : 0.632 13.942 56850 Z= 0.313 Chirality : 0.044 0.146 6198 Planarity : 0.004 0.041 7410 Dihedral : 10.788 175.565 5790 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.11), residues: 5136 helix: -0.94 (0.11), residues: 1980 sheet: -0.32 (0.19), residues: 786 loop : -1.49 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 2 TYR 0.041 0.002 TYR D 212 PHE 0.021 0.001 PHE J 92 TRP 0.014 0.002 TRP B 397 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (41850) covalent geometry : angle 0.63246 / 0.31 (56850) hydrogen bonds : bond 0.03468 / 2.26 ( 1290) hydrogen bonds : angle 4.74067 / 3.26 ( 3798) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 84 LEU cc_start: 0.9269 (tp) cc_final: 0.9067 (tp) REVERT: L 200 PHE cc_start: 0.9184 (m-80) cc_final: 0.8728 (m-10) REVERT: L 201 MET cc_start: 0.8536 (mpp) cc_final: 0.8261 (mpp) REVERT: L 300 MET cc_start: 0.7720 (mmt) cc_final: 0.7224 (mmp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0733 time to fit residues: 5.9823 Evaluate side-chains 48 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.134 Evaluate side-chains 70 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 262 ARG cc_start: 0.8289 (mtp85) cc_final: 0.7727 (ttm-80) REVERT: N 323 MET cc_start: 0.7917 (pmm) cc_final: 0.7250 (pmm) REVERT: N 363 MET cc_start: 0.7155 (mpp) cc_final: 0.6320 (ttp) REVERT: N 378 PHE cc_start: 0.7566 (m-80) cc_final: 0.7330 (m-80) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0620 time to fit residues: 5.3739 Evaluate side-chains 48 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: [62, 234, 208, 7, 160, 128, 72, 233, 189, 335, 296] chunk 62 optimal weight: 20.0000 chunk 234 optimal weight: 8.9990 chunk 208 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 160 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 233 optimal weight: 10.0000 chunk 189 optimal weight: 30.0000 chunk 335 optimal weight: 30.0000 chunk 296 optimal weight: 8.9990 overall best weight: 10.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 224 ASN L 298 ASN N 28 HIS ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 115 ASN N 414 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.082913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.072579 restraints weight = 13983.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.074415 restraints weight = 9465.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.075766 restraints weight = 6927.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.076870 restraints weight = 5384.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.077651 restraints weight = 4323.858| |-----------------------------------------------------------------------------| r_work (final): 0.3434 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.076788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.068363 restraints weight = 16125.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.070099 restraints weight = 10626.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.071302 restraints weight = 7509.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.072225 restraints weight = 5642.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072911 restraints weight = 4417.997| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.6509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 41850 Z= 0.227 Angle : 0.717 8.248 56850 Z= 0.369 Chirality : 0.047 0.147 6198 Planarity : 0.005 0.037 7410 Dihedral : 11.397 177.568 5790 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.12), residues: 5136 helix: -0.54 (0.11), residues: 2082 sheet: -0.33 (0.19), residues: 804 loop : -1.24 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 2 TYR 0.024 0.002 TYR M 81 PHE 0.022 0.003 PHE B 92 TRP 0.012 0.002 TRP L 405 HIS 0.009 0.002 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.23 (41850) covalent geometry : angle 0.71664 / 0.37 (56850) hydrogen bonds : bond 0.03931 / 2.53 ( 1290) hydrogen bonds : angle 5.02049 / 3.45 ( 3798) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 137 HIS cc_start: 0.7047 (p90) cc_final: 0.6632 (p90) REVERT: L 200 PHE cc_start: 0.9190 (m-80) cc_final: 0.8342 (m-10) REVERT: L 300 MET cc_start: 0.7936 (mmt) cc_final: 0.6703 (mmt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0719 time to fit residues: 4.9187 Evaluate side-chains 46 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.096 Evaluate side-chains 55 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 1 MET cc_start: 0.4344 (mmp) cc_final: 0.3996 (mmm) REVERT: N 262 ARG cc_start: 0.8287 (mtp85) cc_final: 0.7781 (ttm-80) REVERT: N 300 MET cc_start: 0.8427 (mtt) cc_final: 0.7727 (mtp) REVERT: N 323 MET cc_start: 0.7997 (pmm) cc_final: 0.7602 (pmm) REVERT: N 363 MET cc_start: 0.7038 (mpp) cc_final: 0.6418 (ttp) REVERT: N 388 MET cc_start: 0.7186 (ptm) cc_final: 0.6882 (mmt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0509 time to fit residues: 3.6521 Evaluate side-chains 48 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: [439, 502, 183, 265, 338, 207, 385, 226, 157, 445, 152] chunk 439 optimal weight: 20.0000 chunk 502 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 265 optimal weight: 30.0000 chunk 338 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 385 optimal weight: 8.9990 chunk 226 optimal weight: 0.0040 chunk 157 optimal weight: 30.0000 chunk 445 optimal weight: 0.0170 chunk 152 optimal weight: 0.0270 overall best weight: 2.0092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 131 GLN L 298 ASN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.086201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.075715 restraints weight = 13195.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.077634 restraints weight = 8932.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.079080 restraints weight = 6525.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.080165 restraints weight = 5031.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.080983 restraints weight = 4050.191| |-----------------------------------------------------------------------------| r_work (final): 0.3490 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.079716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.070779 restraints weight = 15820.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.072502 restraints weight = 10514.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.073798 restraints weight = 7563.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074692 restraints weight = 5677.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.075474 restraints weight = 4491.137| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.6680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41850 Z= 0.119 Angle : 0.646 10.567 56850 Z= 0.323 Chirality : 0.044 0.153 6198 Planarity : 0.004 0.043 7410 Dihedral : 10.972 166.618 5790 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.14 % Allowed : 1.63 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.12), residues: 5136 helix: -0.26 (0.11), residues: 2016 sheet: -0.14 (0.20), residues: 762 loop : -1.43 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 324 TYR 0.015 0.001 TYR A 81 PHE 0.033 0.002 PHE I 253 TRP 0.011 0.002 TRP C 21 HIS 0.005 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (41850) covalent geometry : angle 0.64565 / 0.32 (56850) hydrogen bonds : bond 0.03362 / 2.17 ( 1290) hydrogen bonds : angle 4.68744 / 3.20 ( 3798) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 200 PHE cc_start: 0.9091 (m-80) cc_final: 0.8698 (m-10) REVERT: L 201 MET cc_start: 0.8702 (mpp) cc_final: 0.8456 (mpp) REVERT: L 242 PHE cc_start: 0.7928 (m-80) cc_final: 0.7630 (m-80) REVERT: L 253 PHE cc_start: 0.8196 (m-80) cc_final: 0.7899 (m-80) REVERT: L 300 MET cc_start: 0.7529 (mmt) cc_final: 0.6973 (mmp) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 0.0672 time to fit residues: 4.9367 Evaluate side-chains 44 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.127 Evaluate side-chains 61 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: N 1 MET cc_start: 0.3840 (mmp) cc_final: 0.3499 (mmm) REVERT: N 262 ARG cc_start: 0.8447 (mtp85) cc_final: 0.7864 (ttm-80) REVERT: N 279 GLN cc_start: 0.6983 (mp10) cc_final: 0.6717 (mp10) REVERT: N 323 MET cc_start: 0.8069 (pmm) cc_final: 0.7354 (pmm) REVERT: N 363 MET cc_start: 0.7171 (mpp) cc_final: 0.6449 (ttp) REVERT: N 378 PHE cc_start: 0.8094 (m-80) cc_final: 0.7886 (m-80) REVERT: N 388 MET cc_start: 0.7327 (ptm) cc_final: 0.7059 (mmt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0548 time to fit residues: 4.2724 Evaluate side-chains 45 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: [407, 18, 465, 218, 72, 110, 401, 453, 362, 439, 127] chunk 407 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 465 optimal weight: 0.0030 chunk 218 optimal weight: 0.0570 chunk 72 optimal weight: 0.0270 chunk 110 optimal weight: 9.9990 chunk 401 optimal weight: 7.9990 chunk 453 optimal weight: 6.9990 chunk 362 optimal weight: 6.9990 chunk 439 optimal weight: 20.0000 chunk 127 optimal weight: 4.9990 overall best weight: 1.4170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 131 GLN ** L 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 298 ASN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 334 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.087552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.076673 restraints weight = 13493.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.078615 restraints weight = 9122.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.080059 restraints weight = 6700.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.081172 restraints weight = 5220.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.082025 restraints weight = 4220.637| |-----------------------------------------------------------------------------| r_work (final): 0.3530 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.080261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.071304 restraints weight = 15316.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.073052 restraints weight = 10157.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.074385 restraints weight = 7289.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.075374 restraints weight = 5497.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.076095 restraints weight = 4315.562| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.6999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 41850 Z= 0.114 Angle : 0.656 13.031 56850 Z= 0.323 Chirality : 0.044 0.161 6198 Planarity : 0.004 0.042 7410 Dihedral : 10.717 162.324 5790 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.14 % Allowed : 0.95 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.12), residues: 5136 helix: -0.13 (0.11), residues: 2010 sheet: -0.04 (0.20), residues: 762 loop : -1.35 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 324 TYR 0.034 0.002 TYR K 212 PHE 0.031 0.001 PHE C 253 TRP 0.012 0.001 TRP C 21 HIS 0.008 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (41850) covalent geometry : angle 0.65635 / 0.32 (56850) hydrogen bonds : bond 0.03130 / 2.04 ( 1290) hydrogen bonds : angle 4.57263 / 3.12 ( 3798) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 84 LEU cc_start: 0.9116 (tp) cc_final: 0.8745 (tp) REVERT: L 130 LEU cc_start: 0.8059 (mm) cc_final: 0.7635 (tt) REVERT: L 200 PHE cc_start: 0.9076 (m-80) cc_final: 0.8693 (m-10) REVERT: L 201 MET cc_start: 0.8724 (mpp) cc_final: 0.8476 (mpp) REVERT: L 242 PHE cc_start: 0.7948 (m-80) cc_final: 0.7682 (m-80) REVERT: L 253 PHE cc_start: 0.8135 (m-80) cc_final: 0.7800 (m-80) REVERT: L 300 MET cc_start: 0.7361 (mmt) cc_final: 0.6821 (mmt) outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.0629 time to fit residues: 4.8197 Evaluate side-chains 45 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.091 Evaluate side-chains 64 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: N 187 LEU cc_start: 0.8342 (mp) cc_final: 0.6880 (mp) REVERT: N 198 GLU cc_start: 0.7925 (mp0) cc_final: 0.7653 (mp0) REVERT: N 262 ARG cc_start: 0.8306 (mtp85) cc_final: 0.7750 (ttm-80) REVERT: N 279 GLN cc_start: 0.6928 (mp10) cc_final: 0.6684 (mp10) REVERT: N 293 MET cc_start: 0.7330 (mpp) cc_final: 0.7108 (mpp) REVERT: N 323 MET cc_start: 0.8061 (pmm) cc_final: 0.7523 (pmm) REVERT: N 363 MET cc_start: 0.7159 (mpp) cc_final: 0.6451 (ttp) REVERT: N 378 PHE cc_start: 0.8086 (m-80) cc_final: 0.7864 (m-80) REVERT: N 385 PHE cc_start: 0.6521 (t80) cc_final: 0.5903 (t80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0520 time to fit residues: 4.2250 Evaluate side-chains 46 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: [107, 348, 102, 196, 21, 295, 471, 485, 88, 62, 500] chunk 107 optimal weight: 2.9990 chunk 348 optimal weight: 1.9990 chunk 102 optimal weight: 0.0070 chunk 196 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 295 optimal weight: 7.9990 chunk 471 optimal weight: 20.0000 chunk 485 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 500 optimal weight: 0.0030 overall best weight: 1.8014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 298 ASN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.086042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.074979 restraints weight = 13966.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.077010 restraints weight = 9389.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.078554 restraints weight = 6850.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.079666 restraints weight = 5286.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.080535 restraints weight = 4266.157| |-----------------------------------------------------------------------------| r_work (final): 0.3486 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.080935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.071660 restraints weight = 14978.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.073573 restraints weight = 9609.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074950 restraints weight = 6677.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.075992 restraints weight = 4952.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.076738 restraints weight = 3830.289| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.7163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 41850 Z= 0.112 Angle : 0.645 12.482 56850 Z= 0.317 Chirality : 0.044 0.152 6198 Planarity : 0.004 0.042 7410 Dihedral : 10.481 157.019 5790 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.12), residues: 5136 helix: -0.11 (0.11), residues: 2052 sheet: 0.13 (0.21), residues: 762 loop : -1.21 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 324 TYR 0.018 0.001 TYR J 183 PHE 0.029 0.001 PHE M 253 TRP 0.012 0.001 TRP C 21 HIS 0.013 0.001 HIS M 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (41850) covalent geometry : angle 0.64520 / 0.32 (56850) hydrogen bonds : bond 0.03146 / 2.07 ( 1290) hydrogen bonds : angle 4.51315 / 3.08 ( 3798) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 200 PHE cc_start: 0.9076 (m-80) cc_final: 0.8765 (m-10) REVERT: L 201 MET cc_start: 0.8645 (mpp) cc_final: 0.8420 (mpp) REVERT: L 242 PHE cc_start: 0.8030 (m-80) cc_final: 0.7705 (m-80) REVERT: L 300 MET cc_start: 0.7552 (mmt) cc_final: 0.6554 (mmt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0627 time to fit residues: 4.7249 Evaluate side-chains 45 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.118 Evaluate side-chains 64 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: N 20 PHE cc_start: 0.7789 (t80) cc_final: 0.7566 (t80) REVERT: N 187 LEU cc_start: 0.8397 (mp) cc_final: 0.6714 (mp) REVERT: N 262 ARG cc_start: 0.8311 (mtp85) cc_final: 0.7759 (ttm-80) REVERT: N 293 MET cc_start: 0.7292 (mpp) cc_final: 0.7058 (mpp) REVERT: N 323 MET cc_start: 0.7942 (pmm) cc_final: 0.7481 (pmm) REVERT: N 363 MET cc_start: 0.6972 (mpp) cc_final: 0.6386 (ttp) REVERT: N 378 PHE cc_start: 0.7868 (m-80) cc_final: 0.7578 (m-80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0599 time to fit residues: 4.7637 Evaluate side-chains 48 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: [371, 383, 209, 45, 192, 73, 472, 291, 177, 362, 178] chunk 371 optimal weight: 0.0060 chunk 383 optimal weight: 9.9990 chunk 209 optimal weight: 30.0000 chunk 45 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 472 optimal weight: 5.9990 chunk 291 optimal weight: 0.0770 chunk 177 optimal weight: 7.9990 chunk 362 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 overall best weight: 1.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 8 HIS ** L 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 224 ASN L 298 ASN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.086562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.075999 restraints weight = 13571.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.078052 restraints weight = 9135.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.079536 restraints weight = 6618.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.080584 restraints weight = 5085.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.081361 restraints weight = 4082.714| |-----------------------------------------------------------------------------| r_work (final): 0.3499 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.081264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.072121 restraints weight = 15001.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.073964 restraints weight = 9807.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.075342 restraints weight = 6926.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.076378 restraints weight = 5152.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.077116 restraints weight = 4000.493| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.7394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 41850 Z= 0.110 Angle : 0.639 14.037 56850 Z= 0.309 Chirality : 0.044 0.156 6198 Planarity : 0.004 0.041 7410 Dihedral : 10.104 145.997 5790 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.14 % Allowed : 0.54 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.12), residues: 5136 helix: 0.09 (0.11), residues: 2028 sheet: 0.35 (0.21), residues: 744 loop : -1.19 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 324 TYR 0.025 0.001 TYR K 281 PHE 0.018 0.001 PHE B 167 TRP 0.010 0.001 TRP M 21 HIS 0.007 0.001 HIS H 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (41850) covalent geometry : angle 0.63929 / 0.31 (56850) hydrogen bonds : bond 0.03111 / 2.04 ( 1290) hydrogen bonds : angle 4.46656 / 3.06 ( 3798) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 200 PHE cc_start: 0.9030 (m-80) cc_final: 0.8813 (m-10) REVERT: L 242 PHE cc_start: 0.7911 (m-80) cc_final: 0.7450 (m-80) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0616 time to fit residues: 4.3243 Evaluate side-chains 41 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.125 Evaluate side-chains 63 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 20 PHE cc_start: 0.7825 (t80) cc_final: 0.7573 (t80) REVERT: N 163 ILE cc_start: 0.8088 (pt) cc_final: 0.7750 (pt) REVERT: N 187 LEU cc_start: 0.8345 (mp) cc_final: 0.6882 (mp) REVERT: N 198 GLU cc_start: 0.7759 (mp0) cc_final: 0.7536 (mp0) REVERT: N 201 CYS cc_start: 0.7968 (m) cc_final: 0.6402 (p) REVERT: N 262 ARG cc_start: 0.8348 (mtp85) cc_final: 0.7776 (ttm-80) REVERT: N 279 GLN cc_start: 0.7093 (mp10) cc_final: 0.6792 (mp10) REVERT: N 323 MET cc_start: 0.7966 (pmm) cc_final: 0.7505 (pmm) REVERT: N 363 MET cc_start: 0.6918 (mpp) cc_final: 0.6421 (ttp) REVERT: N 378 PHE cc_start: 0.7973 (m-80) cc_final: 0.7706 (m-80) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.0631 time to fit residues: 4.9138 Evaluate side-chains 47 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: [164, 333, 134, 452, 429, 172, 307, 408, 2, 361, 285] chunk 164 optimal weight: 1.9990 chunk 333 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 452 optimal weight: 0.0870 chunk 429 optimal weight: 0.7980 chunk 172 optimal weight: 10.0000 chunk 307 optimal weight: 0.6980 chunk 408 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 361 optimal weight: 9.9990 chunk 285 optimal weight: 5.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 298 ASN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 298 ASN ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.087076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.076466 restraints weight = 14118.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.078404 restraints weight = 9557.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.079916 restraints weight = 7018.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.080943 restraints weight = 5439.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.081811 restraints weight = 4432.013| |-----------------------------------------------------------------------------| r_work (final): 0.3499 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.082061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.072471 restraints weight = 14895.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.074317 restraints weight = 9744.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.075701 restraints weight = 6900.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076730 restraints weight = 5189.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.077520 restraints weight = 4069.549| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.7599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 41850 Z= 0.109 Angle : 0.633 14.501 56850 Z= 0.307 Chirality : 0.044 0.155 6198 Planarity : 0.004 0.042 7410 Dihedral : 9.551 129.089 5790 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.12), residues: 5136 helix: 0.12 (0.11), residues: 2028 sheet: 0.54 (0.21), residues: 732 loop : -1.20 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 324 TYR 0.023 0.001 TYR K 281 PHE 0.016 0.001 PHE N 167 TRP 0.010 0.001 TRP M 21 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (41850) covalent geometry : angle 0.63267 / 0.31 (56850) hydrogen bonds : bond 0.02981 / 1.97 ( 1290) hydrogen bonds : angle 4.42062 / 3.03 ( 3798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2667.61 seconds wall clock time: 48 minutes 27.56 seconds (2907.56 seconds total)