Starting phenix.real_space_refine on Sun Aug 24 17:37:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mwq_9277/08_2025/6mwq_9277.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mwq_9277/08_2025/6mwq_9277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mwq_9277/08_2025/6mwq_9277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mwq_9277/08_2025/6mwq_9277.map" model { file = "/net/cci-nas-00/data/ceres_data/6mwq_9277/08_2025/6mwq_9277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mwq_9277/08_2025/6mwq_9277.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 76 5.16 5 C 13926 2.51 5 N 3841 2.21 5 O 4229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22072 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3730 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain: "G" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1794 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 215} Chain: "B" Number of atoms: 3730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3730 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain: "J" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1786 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 214} Chain breaks: 1 Chain: "C" Number of atoms: 3730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3730 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain: "I" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1786 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 214} Chain breaks: 1 Chain: "D" Number of atoms: 3730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3730 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain: "H" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1786 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 214} Chain breaks: 1 Time building chain proxies: 4.53, per 1000 atoms: 0.21 Number of scatterers: 22072 At special positions: 0 Unit cell: (168.794, 156.322, 165.468, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 76 16.00 O 4229 8.00 N 3841 7.00 C 13926 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: 1.62 Conformation dependent library (CDL) restraints added in 703.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5234 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 29 sheets defined 35.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 27 through 39 removed outlier: 3.510A pdb=" N LYS A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.676A pdb=" N VAL A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG A 45 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE A 46 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 71 removed outlier: 4.185A pdb=" N LEU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 81 removed outlier: 3.625A pdb=" N VAL A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 102 removed outlier: 4.004A pdb=" N LEU A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 removed outlier: 3.521A pdb=" N LEU A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 removed outlier: 4.041A pdb=" N LEU A 133 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 134 " --> pdb=" O PRO A 130 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 150 removed outlier: 4.108A pdb=" N GLU A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N HIS A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 179 through 190 removed outlier: 3.632A pdb=" N ASN A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.210A pdb=" N ARG A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.856A pdb=" N ARG A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 230 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 231 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.879A pdb=" N VAL A 238 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN A 239 " --> pdb=" O ASP A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 239' Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.568A pdb=" N LYS A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 removed outlier: 4.351A pdb=" N ALA A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLN A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 307 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 342 removed outlier: 3.820A pdb=" N ASN A 337 " --> pdb=" O MET A 333 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 366 through 378 removed outlier: 4.021A pdb=" N TYR A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 386 removed outlier: 4.024A pdb=" N ALA A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 380 through 386' Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.674A pdb=" N THR A 395 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.684A pdb=" N ILE A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 423 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 457 removed outlier: 3.885A pdb=" N SER A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.735A pdb=" N LYS A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 476 through 481' Processing helix chain 'A' and resid 488 through 507 removed outlier: 3.711A pdb=" N GLU A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR A 496 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 497 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N CYS A 507 " --> pdb=" O ASN A 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 8 removed outlier: 3.773A pdb=" N GLU G 5 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU G 6 " --> pdb=" O GLY G 3 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE G 7 " --> pdb=" O GLU G 4 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR G 8 " --> pdb=" O GLU G 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 8' Processing helix chain 'B' and resid 27 through 39 removed outlier: 3.516A pdb=" N LYS B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.663A pdb=" N VAL B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE B 46 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 71 removed outlier: 4.208A pdb=" N LEU B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 81 removed outlier: 3.625A pdb=" N VAL B 77 " --> pdb=" O HIS B 73 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 102 removed outlier: 4.080A pdb=" N LEU B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 removed outlier: 4.152A pdb=" N VAL B 110 " --> pdb=" O HIS B 106 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 137 removed outlier: 3.997A pdb=" N LEU B 133 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 134 " --> pdb=" O PRO B 130 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 150 removed outlier: 3.789A pdb=" N LYS B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS B 149 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 178 through 187 removed outlier: 3.655A pdb=" N LEU B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 207 through 212 removed outlier: 4.212A pdb=" N ARG B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 233 removed outlier: 3.858A pdb=" N ARG B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 230 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU B 231 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.865A pdb=" N VAL B 238 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN B 239 " --> pdb=" O ASP B 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 235 through 239' Processing helix chain 'B' and resid 262 through 270 removed outlier: 3.546A pdb=" N LYS B 267 " --> pdb=" O PRO B 263 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 310 removed outlier: 4.385A pdb=" N ALA B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 307 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LYS B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 342 removed outlier: 3.779A pdb=" N ASN B 337 " --> pdb=" O MET B 333 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 366 through 378 removed outlier: 4.032A pdb=" N TYR B 372 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 376 " --> pdb=" O TYR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 386 removed outlier: 4.045A pdb=" N ALA B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER B 386 " --> pdb=" O TYR B 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 380 through 386' Processing helix chain 'B' and resid 391 through 395 removed outlier: 3.639A pdb=" N THR B 395 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.690A pdb=" N ILE B 417 " --> pdb=" O SER B 413 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA B 418 " --> pdb=" O HIS B 414 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 423 " --> pdb=" O MET B 419 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG B 427 " --> pdb=" O THR B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 457 removed outlier: 3.887A pdb=" N SER B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN B 453 " --> pdb=" O SER B 449 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 455 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 481 removed outlier: 3.734A pdb=" N LYS B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 476 through 481' Processing helix chain 'B' and resid 488 through 507 removed outlier: 3.695A pdb=" N GLU B 494 " --> pdb=" O LYS B 490 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU B 495 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR B 496 " --> pdb=" O ALA B 492 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 497 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS B 507 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 8 removed outlier: 3.811A pdb=" N GLU J 5 " --> pdb=" O LYS J 2 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU J 6 " --> pdb=" O GLY J 3 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE J 7 " --> pdb=" O GLU J 4 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR J 8 " --> pdb=" O GLU J 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 2 through 8' Processing helix chain 'J' and resid 56 through 60 removed outlier: 3.801A pdb=" N VAL J 60 " --> pdb=" O PRO J 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 39 removed outlier: 3.522A pdb=" N LYS C 31 " --> pdb=" O ASP C 27 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.658A pdb=" N VAL C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG C 45 " --> pdb=" O ASP C 41 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE C 46 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 50 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 71 removed outlier: 4.191A pdb=" N LEU C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 81 removed outlier: 3.615A pdb=" N VAL C 77 " --> pdb=" O HIS C 73 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 102 removed outlier: 4.062A pdb=" N LEU C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 129 through 138 removed outlier: 4.001A pdb=" N LEU C 133 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 134 " --> pdb=" O PRO C 130 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 150 removed outlier: 4.029A pdb=" N GLU C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS C 149 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.562A pdb=" N ASN C 170 " --> pdb=" O ILE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.570A pdb=" N ILE C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 190 removed outlier: 3.843A pdb=" N LEU C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER C 185 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 187 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS C 189 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.199A pdb=" N ARG C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 233 removed outlier: 3.876A pdb=" N ARG C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 230 " --> pdb=" O PHE C 226 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU C 231 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 239 removed outlier: 3.883A pdb=" N VAL C 238 " --> pdb=" O ASP C 235 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN C 239 " --> pdb=" O ASP C 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 235 through 239' Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.945A pdb=" N TYR C 253 " --> pdb=" O HIS C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 270 removed outlier: 3.501A pdb=" N ILE C 266 " --> pdb=" O PHE C 262 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 267 " --> pdb=" O PRO C 263 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 310 removed outlier: 4.383A pdb=" N ALA C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLN C 305 " --> pdb=" O GLU C 301 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS C 307 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYS C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 342 removed outlier: 3.887A pdb=" N ASN C 337 " --> pdb=" O MET C 333 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 338 " --> pdb=" O GLU C 334 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 345 No H-bonds generated for 'chain 'C' and resid 343 through 345' Processing helix chain 'C' and resid 366 through 379 removed outlier: 4.028A pdb=" N TYR C 372 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C 376 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 386 removed outlier: 4.007A pdb=" N ALA C 384 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 385 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER C 386 " --> pdb=" O TYR C 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 380 through 386' Processing helix chain 'C' and resid 391 through 395 removed outlier: 3.679A pdb=" N THR C 395 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 427 removed outlier: 3.718A pdb=" N ILE C 417 " --> pdb=" O SER C 413 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C 418 " --> pdb=" O HIS C 414 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 423 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG C 427 " --> pdb=" O THR C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 457 removed outlier: 3.879A pdb=" N SER C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 452 " --> pdb=" O ALA C 448 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN C 453 " --> pdb=" O SER C 449 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 454 " --> pdb=" O ILE C 450 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 455 " --> pdb=" O ASN C 451 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN C 456 " --> pdb=" O LEU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.724A pdb=" N LYS C 480 " --> pdb=" O ALA C 476 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA C 481 " --> pdb=" O SER C 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 476 through 481' Processing helix chain 'C' and resid 488 through 507 removed outlier: 3.670A pdb=" N GLU C 494 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU C 495 " --> pdb=" O ALA C 491 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR C 496 " --> pdb=" O ALA C 492 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 497 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 506 " --> pdb=" O ALA C 502 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS C 507 " --> pdb=" O ASN C 503 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 8 removed outlier: 3.813A pdb=" N GLU I 5 " --> pdb=" O LYS I 2 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU I 6 " --> pdb=" O GLY I 3 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE I 7 " --> pdb=" O GLU I 4 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR I 8 " --> pdb=" O GLU I 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2 through 8' Processing helix chain 'I' and resid 56 through 60 removed outlier: 3.802A pdb=" N VAL I 60 " --> pdb=" O PRO I 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 39 removed outlier: 3.517A pdb=" N LYS D 31 " --> pdb=" O ASP D 27 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 32 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 51 removed outlier: 3.662A pdb=" N VAL D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG D 45 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN D 50 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 71 removed outlier: 4.204A pdb=" N LEU D 67 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 removed outlier: 3.626A pdb=" N VAL D 77 " --> pdb=" O HIS D 73 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 102 removed outlier: 4.131A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 114 removed outlier: 4.029A pdb=" N VAL D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 138 removed outlier: 3.969A pdb=" N LEU D 133 " --> pdb=" O THR D 129 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 134 " --> pdb=" O PRO D 130 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 150 removed outlier: 3.851A pdb=" N GLU D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS D 149 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 Processing helix chain 'D' and resid 178 through 187 removed outlier: 3.830A pdb=" N LEU D 182 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 184 " --> pdb=" O GLN D 180 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE D 187 " --> pdb=" O ASN D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 191 Processing helix chain 'D' and resid 207 through 212 removed outlier: 4.208A pdb=" N ARG D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 233 removed outlier: 3.855A pdb=" N ARG D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 230 " --> pdb=" O PHE D 226 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 239 removed outlier: 3.884A pdb=" N VAL D 238 " --> pdb=" O ASP D 235 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN D 239 " --> pdb=" O ASP D 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 235 through 239' Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.956A pdb=" N TYR D 253 " --> pdb=" O HIS D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 270 removed outlier: 3.520A pdb=" N ILE D 266 " --> pdb=" O PHE D 262 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS D 267 " --> pdb=" O PRO D 263 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER D 268 " --> pdb=" O GLN D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.678A pdb=" N LYS D 307 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LYS D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP D 309 " --> pdb=" O GLN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 342 removed outlier: 3.885A pdb=" N ASN D 337 " --> pdb=" O MET D 333 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 366 through 378 removed outlier: 4.038A pdb=" N TYR D 372 " --> pdb=" O LYS D 368 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 376 " --> pdb=" O TYR D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 386 removed outlier: 4.007A pdb=" N ALA D 384 " --> pdb=" O ALA D 380 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 385 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER D 386 " --> pdb=" O TYR D 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 380 through 386' Processing helix chain 'D' and resid 391 through 395 removed outlier: 3.660A pdb=" N THR D 395 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 427 removed outlier: 3.687A pdb=" N ILE D 417 " --> pdb=" O SER D 413 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA D 418 " --> pdb=" O HIS D 414 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR D 423 " --> pdb=" O MET D 419 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG D 427 " --> pdb=" O THR D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 457 removed outlier: 3.892A pdb=" N SER D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 452 " --> pdb=" O ALA D 448 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN D 453 " --> pdb=" O SER D 449 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 454 " --> pdb=" O ILE D 450 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 455 " --> pdb=" O ASN D 451 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 481 removed outlier: 3.737A pdb=" N LYS D 480 " --> pdb=" O ALA D 476 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA D 481 " --> pdb=" O SER D 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 476 through 481' Processing helix chain 'D' and resid 488 through 507 removed outlier: 3.689A pdb=" N GLU D 494 " --> pdb=" O LYS D 490 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU D 495 " --> pdb=" O ALA D 491 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR D 496 " --> pdb=" O ALA D 492 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL D 497 " --> pdb=" O GLN D 493 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 506 " --> pdb=" O ALA D 502 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS D 507 " --> pdb=" O ASN D 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 8 removed outlier: 3.801A pdb=" N GLU H 5 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU H 6 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE H 7 " --> pdb=" O GLU H 4 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR H 8 " --> pdb=" O GLU H 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 2 through 8' Processing helix chain 'H' and resid 56 through 60 removed outlier: 3.830A pdb=" N VAL H 60 " --> pdb=" O PRO H 57 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 7.939A pdb=" N VAL A 273 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 316 through 317 removed outlier: 3.699A pdb=" N TRP A 316 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 356 " --> pdb=" O TRP A 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 321 removed outlier: 6.566A pdb=" N LEU A 320 " --> pdb=" O LEU A 360 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA5, first strand: chain 'G' and resid 157 through 161 removed outlier: 3.837A pdb=" N PHE G 161 " --> pdb=" O HIS G 177 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG G 105 " --> pdb=" O GLU G 120 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU G 120 " --> pdb=" O ARG G 105 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU G 107 " --> pdb=" O ARG G 118 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG G 118 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS G 109 " --> pdb=" O VAL G 116 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN G 117 " --> pdb=" O LEU G 14 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU G 121 " --> pdb=" O ASP G 18 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU G 43 " --> pdb=" O LEU G 216 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU G 216 " --> pdb=" O LEU G 43 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE G 45 " --> pdb=" O MET G 214 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL G 215 " --> pdb=" O SER G 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 146 through 148 removed outlier: 3.964A pdb=" N VAL G 146 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR G 196 " --> pdb=" O GLY G 224 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY G 224 " --> pdb=" O TYR G 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 164 through 165 removed outlier: 3.929A pdb=" N GLN G 173 " --> pdb=" O HIS G 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 198 through 199 removed outlier: 7.939A pdb=" N VAL B 273 " --> pdb=" O ASP B 312 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 316 through 317 removed outlier: 3.692A pdb=" N TRP B 316 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 320 through 321 removed outlier: 6.554A pdb=" N LEU B 320 " --> pdb=" O LEU B 360 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 435 through 436 Processing sheet with id=AB3, first strand: chain 'J' and resid 157 through 161 removed outlier: 3.862A pdb=" N PHE J 161 " --> pdb=" O HIS J 177 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU J 107 " --> pdb=" O ARG J 118 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG J 118 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS J 109 " --> pdb=" O VAL J 116 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU J 14 " --> pdb=" O ASN J 117 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE J 119 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU J 16 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE J 13 " --> pdb=" O GLY J 32 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR J 42 " --> pdb=" O GLU J 33 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU J 43 " --> pdb=" O LEU J 216 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU J 216 " --> pdb=" O LEU J 43 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE J 45 " --> pdb=" O MET J 214 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL J 215 " --> pdb=" O SER J 204 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER J 204 " --> pdb=" O VAL J 215 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 20 through 21 Processing sheet with id=AB5, first strand: chain 'J' and resid 146 through 148 removed outlier: 3.983A pdb=" N VAL J 146 " --> pdb=" O LEU J 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 164 through 166 Processing sheet with id=AB7, first strand: chain 'C' and resid 198 through 199 removed outlier: 7.926A pdb=" N VAL C 273 " --> pdb=" O ASP C 312 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 316 through 317 removed outlier: 3.713A pdb=" N TRP C 316 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 435 through 436 Processing sheet with id=AC1, first strand: chain 'I' and resid 157 through 161 removed outlier: 3.863A pdb=" N PHE I 161 " --> pdb=" O HIS I 177 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU I 107 " --> pdb=" O ARG I 118 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG I 118 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS I 109 " --> pdb=" O VAL I 116 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU I 14 " --> pdb=" O ASN I 117 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE I 119 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU I 16 " --> pdb=" O ILE I 119 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE I 13 " --> pdb=" O GLY I 32 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR I 42 " --> pdb=" O GLU I 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU I 43 " --> pdb=" O LEU I 216 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU I 216 " --> pdb=" O LEU I 43 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE I 45 " --> pdb=" O MET I 214 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL I 215 " --> pdb=" O SER I 204 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER I 204 " --> pdb=" O VAL I 215 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 20 through 21 Processing sheet with id=AC3, first strand: chain 'I' and resid 146 through 148 removed outlier: 3.956A pdb=" N VAL I 146 " --> pdb=" O LEU I 197 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR I 196 " --> pdb=" O ALA I 223 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA I 223 " --> pdb=" O TYR I 196 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 164 through 166 Processing sheet with id=AC5, first strand: chain 'D' and resid 198 through 200 removed outlier: 7.939A pdb=" N VAL D 273 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 316 through 317 removed outlier: 3.700A pdb=" N TRP D 316 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 356 " --> pdb=" O TRP D 316 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 435 through 436 Processing sheet with id=AC8, first strand: chain 'H' and resid 157 through 161 removed outlier: 3.856A pdb=" N PHE H 161 " --> pdb=" O HIS H 177 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU H 107 " --> pdb=" O ARG H 118 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG H 118 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS H 109 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU H 14 " --> pdb=" O ASN H 117 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE H 119 " --> pdb=" O LEU H 14 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU H 16 " --> pdb=" O ILE H 119 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE H 13 " --> pdb=" O GLY H 32 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR H 42 " --> pdb=" O GLU H 33 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU H 43 " --> pdb=" O LEU H 216 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU H 216 " --> pdb=" O LEU H 43 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE H 45 " --> pdb=" O MET H 214 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL H 215 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER H 204 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 20 through 21 Processing sheet with id=AD1, first strand: chain 'H' and resid 147 through 148 Processing sheet with id=AD2, first strand: chain 'H' and resid 164 through 166 456 hydrogen bonds defined for protein. 1245 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: 3.05 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7459 1.34 - 1.46: 4455 1.46 - 1.58: 10459 1.58 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 22481 Sorted by residual: bond pdb=" N GLY G 123 " pdb=" CA GLY G 123 " ideal model delta sigma weight residual 1.449 1.463 -0.014 1.45e-02 4.76e+03 9.42e-01 bond pdb=" N GLN G 153 " pdb=" CA GLN G 153 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.94e-01 bond pdb=" CA ASP C 27 " pdb=" C ASP C 27 " ideal model delta sigma weight residual 1.532 1.524 0.008 9.60e-03 1.09e+04 7.59e-01 bond pdb=" CA ASP D 27 " pdb=" C ASP D 27 " ideal model delta sigma weight residual 1.532 1.524 0.008 9.60e-03 1.09e+04 7.44e-01 bond pdb=" CA ASP A 27 " pdb=" C ASP A 27 " ideal model delta sigma weight residual 1.532 1.524 0.008 9.60e-03 1.09e+04 7.25e-01 ... (remaining 22476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 29839 0.98 - 1.96: 371 1.96 - 2.94: 199 2.94 - 3.92: 23 3.92 - 4.90: 14 Bond angle restraints: 30446 Sorted by residual: angle pdb=" C LEU G 63 " pdb=" N VAL G 64 " pdb=" CA VAL G 64 " ideal model delta sigma weight residual 121.97 126.44 -4.47 1.80e+00 3.09e-01 6.17e+00 angle pdb=" C ALA G 223 " pdb=" CA ALA G 223 " pdb=" CB ALA G 223 " ideal model delta sigma weight residual 115.27 110.37 4.90 2.00e+00 2.50e-01 6.01e+00 angle pdb=" O ALA G 223 " pdb=" C ALA G 223 " pdb=" N GLY G 224 " ideal model delta sigma weight residual 120.83 122.62 -1.79 7.40e-01 1.83e+00 5.84e+00 angle pdb=" CA GLY A 25 " pdb=" C GLY A 25 " pdb=" N SER A 26 " ideal model delta sigma weight residual 118.95 116.72 2.23 1.06e+00 8.90e-01 4.44e+00 angle pdb=" CA GLY D 25 " pdb=" C GLY D 25 " pdb=" N SER D 26 " ideal model delta sigma weight residual 118.95 116.76 2.19 1.06e+00 8.90e-01 4.28e+00 ... (remaining 30441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.92: 13067 8.92 - 17.85: 308 17.85 - 26.77: 112 26.77 - 35.69: 23 35.69 - 44.61: 12 Dihedral angle restraints: 13522 sinusoidal: 5342 harmonic: 8180 Sorted by residual: dihedral pdb=" CB MET H 84 " pdb=" CG MET H 84 " pdb=" SD MET H 84 " pdb=" CE MET H 84 " ideal model delta sinusoidal sigma weight residual 60.00 104.61 -44.61 3 1.50e+01 4.44e-03 8.02e+00 dihedral pdb=" CB MET J 84 " pdb=" CG MET J 84 " pdb=" SD MET J 84 " pdb=" CE MET J 84 " ideal model delta sinusoidal sigma weight residual 60.00 104.33 -44.33 3 1.50e+01 4.44e-03 7.97e+00 dihedral pdb=" CB MET I 84 " pdb=" CG MET I 84 " pdb=" SD MET I 84 " pdb=" CE MET I 84 " ideal model delta sinusoidal sigma weight residual 60.00 104.33 -44.33 3 1.50e+01 4.44e-03 7.97e+00 ... (remaining 13519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1908 0.025 - 0.050: 1072 0.050 - 0.074: 237 0.074 - 0.099: 110 0.099 - 0.124: 127 Chirality restraints: 3454 Sorted by residual: chirality pdb=" CA VAL D 352 " pdb=" N VAL D 352 " pdb=" C VAL D 352 " pdb=" CB VAL D 352 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA VAL A 352 " pdb=" N VAL A 352 " pdb=" C VAL A 352 " pdb=" CB VAL A 352 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 chirality pdb=" CA VAL C 352 " pdb=" N VAL C 352 " pdb=" C VAL C 352 " pdb=" CB VAL C 352 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 3451 not shown) Planarity restraints: 3978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 129 " 0.017 5.00e-02 4.00e+02 2.51e-02 1.00e+00 pdb=" N PRO D 130 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO D 130 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 130 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 96 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.17e-01 pdb=" N PRO C 97 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO C 97 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 97 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 96 " -0.016 5.00e-02 4.00e+02 2.38e-02 9.06e-01 pdb=" N PRO A 97 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 97 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 97 " -0.013 5.00e-02 4.00e+02 ... (remaining 3975 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6911 2.84 - 3.35: 17696 3.35 - 3.87: 33641 3.87 - 4.38: 38806 4.38 - 4.90: 66684 Nonbonded interactions: 163738 Sorted by model distance: nonbonded pdb=" O HIS A 99 " pdb=" OG1 THR A 103 " model vdw 2.321 3.040 nonbonded pdb=" O HIS C 99 " pdb=" OG1 THR C 103 " model vdw 2.323 3.040 nonbonded pdb=" O ALA C 448 " pdb=" OH TYR C 470 " model vdw 2.339 3.040 nonbonded pdb=" O HIS B 99 " pdb=" OG1 THR B 103 " model vdw 2.344 3.040 nonbonded pdb=" O ALA D 448 " pdb=" OH TYR D 470 " model vdw 2.348 3.040 ... (remaining 163733 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'G' and (resid 1 through 62 or resid 64 through 226)) selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.740 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3689 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 : 0.001 0.017 22481 Z= 0.070 Angle : 0.362 4.905 30446 Z= 0.207 Chirality : 0.037 0.124 3454 Planarity : 0.002 0.025 3978 Dihedral : 4.660 44.613 8288 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 1.47 % Allowed : 11.05 % Favored : 87.48 % Rotamer: Outliers : 0.13 % Allowed : 0.72 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: -4.81 (0.13), residues: 2851 helix: -4.87 (0.05), residues: 756 sheet: -2.01 (0.19), residues: 685 loop : -2.76 (0.14), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 426 TYR 0.004 0.000 TYR A 391 PHE 0.003 0.000 PHE D 248 TRP 0.003 0.000 TRP A 482 HIS 0.001 0.000 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00115 (22481) covalent geometry : angle 0.36222 (30446) hydrogen bonds : bond 0.38393 ( 456) hydrogen bonds : angle 9.86463 ( 1245) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 522 time to evaluate : 0.512 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: G 74 MET cc_start: -0.0622 (mtp) cc_final: -0.2696 (mmm) REVERT: I 81 LYS cc_start: -0.0094 (mttp) cc_final: -0.0452 (mttt) REVERT: I 209 GLU cc_start: 0.1730 (tp30) cc_final: -0.0244 (mt-10) REVERT: H 205 LYS cc_start: 0.1837 (mmtt) cc_final: 0.1411 (pptt) outliers start: 3 outliers final: 0 residues processed: 524 average time/residue: 0.5788 time to fit residues: 343.6238 Evaluate side-chains 231 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0670 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 70 GLN A 73 HIS A 99 HIS A 106 HIS ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 ASN A 294 GLN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 HIS G 140 ASN G 160 ASN G 166 ASN ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN B 73 HIS B 95 GLN B 99 HIS B 106 HIS ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 HIS B 389 HIS B 503 ASN J 24 HIS J 144 HIS J 160 ASN ** J 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN C 73 HIS C 95 GLN C 99 HIS C 106 HIS ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN C 388 HIS C 389 HIS C 503 ASN I 24 HIS I 90 GLN I 140 ASN I 144 HIS I 145 ASN ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 HIS I 179 GLN D 70 GLN D 73 HIS D 95 GLN D 99 HIS D 121 ASN D 139 HIS ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN D 388 HIS D 389 HIS ** D 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 HIS H 65 GLN H 144 HIS H 177 HIS H 179 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.231357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.154080 restraints weight = 37618.022| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 3.92 r_work: 0.3729 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 22481 Z= 0.238 Angle : 0.728 8.900 30446 Z= 0.373 Chirality : 0.046 0.175 3454 Planarity : 0.005 0.060 3978 Dihedral : 3.539 25.693 3046 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.09 % Favored : 94.70 % Rotamer: Outliers : 2.84 % Allowed : 11.16 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: -4.12 (0.14), residues: 2851 helix: -3.79 (0.10), residues: 900 sheet: -1.42 (0.20), residues: 651 loop : -2.53 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 499 TYR 0.023 0.002 TYR B 382 PHE 0.013 0.002 PHE D 248 TRP 0.024 0.003 TRP J 56 HIS 0.009 0.002 HIS C 414 Details of bonding type rmsd covalent geometry : bond 0.00519 (22481) covalent geometry : angle 0.72768 (30446) hydrogen bonds : bond 0.03698 ( 456) hydrogen bonds : angle 6.20405 ( 1245) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 243 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8445 (tp30) REVERT: A 264 GLN cc_start: 0.7582 (tm-30) cc_final: 0.7378 (tp40) REVERT: A 390 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8971 (mm) REVERT: G 5 GLU cc_start: 0.4424 (mm-30) cc_final: 0.3818 (tp30) REVERT: G 27 SER cc_start: 0.4770 (m) cc_final: 0.4489 (p) REVERT: G 47 CYS cc_start: 0.2589 (t) cc_final: 0.2347 (p) REVERT: G 84 MET cc_start: 0.3376 (mmt) cc_final: 0.2873 (mmt) REVERT: G 107 GLU cc_start: 0.7669 (mp0) cc_final: 0.7382 (mp0) REVERT: B 133 LEU cc_start: 0.9169 (mt) cc_final: 0.8968 (mt) REVERT: B 334 GLU cc_start: 0.8440 (tp30) cc_final: 0.8199 (tp30) REVERT: B 368 LYS cc_start: 0.8245 (tmmt) cc_final: 0.8034 (ttpp) REVERT: B 444 SER cc_start: 0.8086 (t) cc_final: 0.7751 (p) REVERT: B 494 GLU cc_start: 0.8324 (tp30) cc_final: 0.8027 (tp30) REVERT: J 38 TYR cc_start: 0.4949 (m-10) cc_final: 0.4201 (m-10) REVERT: J 84 MET cc_start: 0.3665 (mmt) cc_final: 0.2509 (mmm) REVERT: J 168 GLU cc_start: 0.2996 (mt-10) cc_final: 0.2486 (mm-30) REVERT: C 175 LEU cc_start: 0.5589 (OUTLIER) cc_final: 0.5276 (tm) REVERT: C 186 ASP cc_start: 0.8078 (t70) cc_final: 0.7854 (t0) REVERT: C 264 GLN cc_start: 0.8730 (tp40) cc_final: 0.8191 (tp40) REVERT: C 334 GLU cc_start: 0.8371 (tp30) cc_final: 0.8123 (tp30) REVERT: C 406 HIS cc_start: 0.8039 (m-70) cc_final: 0.7822 (m90) REVERT: I 203 LEU cc_start: 0.3010 (mp) cc_final: 0.2752 (pt) REVERT: D 447 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7747 (tp30) outliers start: 67 outliers final: 24 residues processed: 297 average time/residue: 0.5710 time to fit residues: 192.3675 Evaluate side-chains 190 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 447 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 270 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 196 optimal weight: 0.5980 chunk 197 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 281 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 139 HIS A 294 GLN A 337 ASN ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN B 294 GLN J 173 GLN ** J 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 ASN I 140 ASN ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 GLN I 194 ASN D 189 HIS D 294 GLN D 400 ASN D 443 GLN D 503 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.218960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.131024 restraints weight = 35679.254| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.57 r_work: 0.3429 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 22481 Z= 0.216 Angle : 0.656 9.825 30446 Z= 0.337 Chirality : 0.046 0.275 3454 Planarity : 0.005 0.070 3978 Dihedral : 3.792 21.047 3046 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.03 % Favored : 93.76 % Rotamer: Outliers : 3.48 % Allowed : 12.56 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: -3.41 (0.14), residues: 2851 helix: -2.81 (0.13), residues: 952 sheet: -1.32 (0.21), residues: 644 loop : -2.18 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 105 TYR 0.030 0.002 TYR G 102 PHE 0.016 0.002 PHE A 248 TRP 0.030 0.003 TRP D 316 HIS 0.007 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00492 (22481) covalent geometry : angle 0.65551 (30446) hydrogen bonds : bond 0.03954 ( 456) hydrogen bonds : angle 5.40259 ( 1245) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 194 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ILE cc_start: 0.8420 (mt) cc_final: 0.8154 (pt) REVERT: A 396 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9133 (mp) REVERT: G 5 GLU cc_start: 0.4843 (mm-30) cc_final: 0.4259 (tp30) REVERT: G 84 MET cc_start: 0.3914 (mmt) cc_final: 0.3584 (mmt) REVERT: G 91 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7744 (tm-30) REVERT: G 167 ILE cc_start: 0.3438 (OUTLIER) cc_final: 0.3158 (pt) REVERT: B 315 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8736 (tmmm) REVERT: B 334 GLU cc_start: 0.8532 (tp30) cc_final: 0.8244 (tp30) REVERT: B 368 LYS cc_start: 0.8571 (tmmt) cc_final: 0.8307 (ttpp) REVERT: B 440 SER cc_start: 0.8630 (p) cc_final: 0.8344 (p) REVERT: B 443 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8349 (pm20) REVERT: B 444 SER cc_start: 0.9007 (t) cc_final: 0.8621 (p) REVERT: B 464 TRP cc_start: 0.8911 (OUTLIER) cc_final: 0.8427 (m-90) REVERT: B 494 GLU cc_start: 0.8731 (tp30) cc_final: 0.8458 (tp30) REVERT: J 84 MET cc_start: 0.3329 (mmt) cc_final: 0.3069 (mtt) REVERT: J 168 GLU cc_start: 0.3104 (mt-10) cc_final: 0.2574 (mm-30) REVERT: J 182 THR cc_start: 0.7479 (p) cc_final: 0.7247 (t) REVERT: C 175 LEU cc_start: 0.5851 (OUTLIER) cc_final: 0.5509 (tm) REVERT: C 228 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.6887 (mmt180) REVERT: C 264 GLN cc_start: 0.8952 (tp40) cc_final: 0.8550 (tp40) REVERT: C 406 HIS cc_start: 0.8407 (m-70) cc_final: 0.8098 (m-70) REVERT: C 461 LEU cc_start: 0.8631 (tm) cc_final: 0.8374 (tt) REVERT: I 209 GLU cc_start: 0.0584 (tp30) cc_final: -0.0840 (mt-10) REVERT: D 253 TYR cc_start: 0.7816 (m-10) cc_final: 0.7586 (m-10) REVERT: D 447 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7879 (tp30) REVERT: H 78 ASP cc_start: 0.2383 (t0) cc_final: 0.1684 (p0) REVERT: H 84 MET cc_start: 0.2815 (mpm) cc_final: 0.2230 (mpp) REVERT: H 109 LYS cc_start: 0.4262 (OUTLIER) cc_final: 0.3786 (tppt) REVERT: H 149 MET cc_start: 0.3298 (mpt) cc_final: 0.1722 (mmt) REVERT: H 218 GLU cc_start: 0.4429 (tt0) cc_final: 0.4033 (tm-30) outliers start: 82 outliers final: 25 residues processed: 261 average time/residue: 0.6345 time to fit residues: 185.8182 Evaluate side-chains 183 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 443 GLN Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain H residue 109 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 95 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 191 optimal weight: 0.8980 chunk 213 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 216 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 HIS J 177 HIS ** J 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN D 400 ASN H 65 GLN H 195 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.219473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.132159 restraints weight = 35616.805| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.44 r_work: 0.3447 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22481 Z= 0.116 Angle : 0.535 10.551 30446 Z= 0.267 Chirality : 0.041 0.254 3454 Planarity : 0.003 0.050 3978 Dihedral : 3.452 18.761 3046 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.61 % Favored : 96.18 % Rotamer: Outliers : 2.97 % Allowed : 13.96 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: -2.86 (0.15), residues: 2851 helix: -2.09 (0.15), residues: 939 sheet: -1.15 (0.21), residues: 642 loop : -2.01 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 237 TYR 0.014 0.001 TYR J 38 PHE 0.013 0.001 PHE D 313 TRP 0.018 0.002 TRP C 464 HIS 0.007 0.001 HIS C 414 Details of bonding type rmsd covalent geometry : bond 0.00268 (22481) covalent geometry : angle 0.53516 (30446) hydrogen bonds : bond 0.02596 ( 456) hydrogen bonds : angle 4.96768 ( 1245) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 160 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ILE cc_start: 0.8389 (mt) cc_final: 0.8100 (pt) REVERT: A 464 TRP cc_start: 0.9196 (OUTLIER) cc_final: 0.7648 (m-90) REVERT: G 5 GLU cc_start: 0.4771 (mm-30) cc_final: 0.4228 (tp30) REVERT: G 84 MET cc_start: 0.4181 (mmt) cc_final: 0.3888 (mmt) REVERT: G 103 LYS cc_start: 0.7778 (tptt) cc_final: 0.7544 (tptp) REVERT: B 334 GLU cc_start: 0.8497 (tp30) cc_final: 0.8213 (tp30) REVERT: B 368 LYS cc_start: 0.8527 (tmmt) cc_final: 0.8264 (ttpp) REVERT: B 464 TRP cc_start: 0.8977 (OUTLIER) cc_final: 0.8350 (m-90) REVERT: B 494 GLU cc_start: 0.8809 (tp30) cc_final: 0.8501 (tp30) REVERT: J 74 MET cc_start: 0.0747 (tpp) cc_final: 0.0320 (tmt) REVERT: J 84 MET cc_start: 0.2354 (mmt) cc_final: 0.1502 (mmm) REVERT: J 168 GLU cc_start: 0.3144 (mt-10) cc_final: 0.2628 (mm-30) REVERT: C 175 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5546 (tm) REVERT: C 264 GLN cc_start: 0.8995 (tp40) cc_final: 0.8601 (tp40) REVERT: C 406 HIS cc_start: 0.8419 (m-70) cc_final: 0.8136 (m-70) REVERT: C 461 LEU cc_start: 0.8612 (tm) cc_final: 0.8290 (tt) REVERT: C 477 SER cc_start: 0.9078 (m) cc_final: 0.8716 (t) REVERT: D 253 TYR cc_start: 0.7943 (m-10) cc_final: 0.7722 (m-10) REVERT: D 325 HIS cc_start: 0.8093 (p90) cc_final: 0.7858 (p90) REVERT: H 84 MET cc_start: 0.3282 (mpm) cc_final: 0.2651 (mpp) REVERT: H 149 MET cc_start: 0.3104 (mpt) cc_final: 0.1572 (mmp) REVERT: H 218 GLU cc_start: 0.4494 (tt0) cc_final: 0.4188 (tm-30) outliers start: 70 outliers final: 25 residues processed: 217 average time/residue: 0.6102 time to fit residues: 149.6434 Evaluate side-chains 169 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain H residue 65 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 176 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 277 optimal weight: 40.0000 chunk 88 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 213 optimal weight: 20.0000 chunk 111 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 147 optimal weight: 40.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 294 GLN ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 HIS ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN B 406 HIS ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS D 294 GLN D 400 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.214722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.122536 restraints weight = 35624.878| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.58 r_work: 0.3297 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.6762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 22481 Z= 0.226 Angle : 0.601 8.424 30446 Z= 0.306 Chirality : 0.044 0.240 3454 Planarity : 0.004 0.057 3978 Dihedral : 3.716 19.377 3046 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.02 % Favored : 94.77 % Rotamer: Outliers : 3.48 % Allowed : 13.66 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: -2.52 (0.15), residues: 2851 helix: -1.62 (0.16), residues: 949 sheet: -1.08 (0.22), residues: 627 loop : -1.91 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 369 TYR 0.020 0.002 TYR A 382 PHE 0.016 0.002 PHE D 313 TRP 0.020 0.002 TRP D 316 HIS 0.009 0.001 HIS C 414 Details of bonding type rmsd covalent geometry : bond 0.00514 (22481) covalent geometry : angle 0.60056 (30446) hydrogen bonds : bond 0.03135 ( 456) hydrogen bonds : angle 4.95477 ( 1245) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 163 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ILE cc_start: 0.8381 (mt) cc_final: 0.8153 (pt) REVERT: A 406 HIS cc_start: 0.8932 (OUTLIER) cc_final: 0.8669 (m-70) REVERT: A 464 TRP cc_start: 0.9294 (OUTLIER) cc_final: 0.7589 (m-90) REVERT: G 5 GLU cc_start: 0.5211 (mm-30) cc_final: 0.4745 (tp30) REVERT: G 84 MET cc_start: 0.4560 (mmt) cc_final: 0.4257 (mmt) REVERT: G 167 ILE cc_start: 0.3516 (OUTLIER) cc_final: 0.3258 (pt) REVERT: B 165 ASP cc_start: 0.8564 (m-30) cc_final: 0.8063 (p0) REVERT: B 299 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9186 (tt) REVERT: B 368 LYS cc_start: 0.8681 (tmmt) cc_final: 0.8414 (ttpp) REVERT: B 410 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7707 (tm-30) REVERT: B 464 TRP cc_start: 0.9081 (OUTLIER) cc_final: 0.8640 (m-90) REVERT: B 494 GLU cc_start: 0.8892 (tp30) cc_final: 0.8667 (tp30) REVERT: J 74 MET cc_start: 0.1222 (tpp) cc_final: 0.0628 (tmt) REVERT: J 84 MET cc_start: 0.2453 (mmt) cc_final: 0.1601 (mmm) REVERT: J 168 GLU cc_start: 0.3291 (mt-10) cc_final: 0.2775 (mm-30) REVERT: C 175 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5639 (tm) REVERT: C 228 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.6796 (mmt180) REVERT: C 236 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8060 (p0) REVERT: C 264 GLN cc_start: 0.9012 (tp40) cc_final: 0.8507 (tp-100) REVERT: C 477 SER cc_start: 0.9073 (m) cc_final: 0.8714 (t) REVERT: I 31 GLU cc_start: 0.4202 (pt0) cc_final: 0.3594 (tp30) REVERT: I 209 GLU cc_start: 0.0573 (tp30) cc_final: -0.0810 (mt-10) REVERT: D 210 LYS cc_start: 0.9079 (mppt) cc_final: 0.8817 (mppt) REVERT: D 447 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7946 (tp30) REVERT: H 78 ASP cc_start: 0.2293 (t0) cc_final: 0.1417 (p0) REVERT: H 84 MET cc_start: 0.3320 (mpm) cc_final: 0.2737 (mpp) REVERT: H 113 ASP cc_start: 0.4867 (t0) cc_final: 0.4528 (p0) REVERT: H 181 ASN cc_start: 0.3687 (m-40) cc_final: 0.3118 (m110) REVERT: H 218 GLU cc_start: 0.4531 (tt0) cc_final: 0.4245 (tm-30) outliers start: 82 outliers final: 33 residues processed: 231 average time/residue: 0.6345 time to fit residues: 165.3485 Evaluate side-chains 188 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 182 THR Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 447 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 6 optimal weight: 20.0000 chunk 156 optimal weight: 0.8980 chunk 66 optimal weight: 40.0000 chunk 279 optimal weight: 20.0000 chunk 172 optimal weight: 0.3980 chunk 74 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 269 optimal weight: 0.2980 chunk 176 optimal weight: 0.7980 chunk 267 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 400 ASN ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN C 254 GLN C 264 GLN C 400 ASN I 160 ASN D 294 GLN D 400 ASN H 65 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.216002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.126331 restraints weight = 35542.506| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.51 r_work: 0.3341 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.6922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22481 Z= 0.129 Angle : 0.528 8.461 30446 Z= 0.267 Chirality : 0.042 0.243 3454 Planarity : 0.003 0.043 3978 Dihedral : 3.528 17.911 3046 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.68 % Favored : 96.11 % Rotamer: Outliers : 2.72 % Allowed : 15.06 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: -2.20 (0.15), residues: 2851 helix: -1.16 (0.16), residues: 941 sheet: -0.95 (0.22), residues: 609 loop : -1.87 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 369 TYR 0.021 0.001 TYR C 470 PHE 0.015 0.001 PHE D 313 TRP 0.022 0.002 TRP C 464 HIS 0.009 0.001 HIS C 414 Details of bonding type rmsd covalent geometry : bond 0.00302 (22481) covalent geometry : angle 0.52832 (30446) hydrogen bonds : bond 0.02468 ( 456) hydrogen bonds : angle 4.66776 ( 1245) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 165 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ILE cc_start: 0.8394 (mt) cc_final: 0.8152 (pt) REVERT: A 406 HIS cc_start: 0.8889 (OUTLIER) cc_final: 0.8608 (m-70) REVERT: A 464 TRP cc_start: 0.9267 (OUTLIER) cc_final: 0.7540 (m-90) REVERT: G 5 GLU cc_start: 0.5335 (mm-30) cc_final: 0.4948 (tp30) REVERT: G 84 MET cc_start: 0.4806 (mmt) cc_final: 0.4524 (mmt) REVERT: G 103 LYS cc_start: 0.7621 (tptp) cc_final: 0.7068 (mptm) REVERT: G 167 ILE cc_start: 0.3563 (OUTLIER) cc_final: 0.3281 (pt) REVERT: G 209 GLU cc_start: 0.2129 (OUTLIER) cc_final: 0.1522 (tm-30) REVERT: B 165 ASP cc_start: 0.8625 (m-30) cc_final: 0.8122 (p0) REVERT: B 275 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9002 (tt) REVERT: B 368 LYS cc_start: 0.8585 (tmmt) cc_final: 0.8311 (ttpp) REVERT: B 411 LYS cc_start: 0.9172 (mppt) cc_final: 0.8931 (mppt) REVERT: B 494 GLU cc_start: 0.8889 (tp30) cc_final: 0.8571 (tp30) REVERT: B 498 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8275 (ptpp) REVERT: J 74 MET cc_start: 0.1742 (tpp) cc_final: 0.1258 (tmt) REVERT: J 168 GLU cc_start: 0.3336 (mt-10) cc_final: 0.2814 (mm-30) REVERT: C 236 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8031 (p0) REVERT: C 264 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8656 (tm-30) REVERT: C 290 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7276 (mm-30) REVERT: C 477 SER cc_start: 0.9054 (m) cc_final: 0.8740 (t) REVERT: I 31 GLU cc_start: 0.4245 (pt0) cc_final: 0.3655 (tp30) REVERT: I 203 LEU cc_start: 0.3876 (OUTLIER) cc_final: 0.3346 (pt) REVERT: I 209 GLU cc_start: 0.0392 (tp30) cc_final: -0.0867 (mt-10) REVERT: D 210 LYS cc_start: 0.9136 (mppt) cc_final: 0.8933 (mppt) REVERT: D 339 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8828 (mt) REVERT: D 447 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7979 (tp30) REVERT: H 78 ASP cc_start: 0.2362 (t0) cc_final: 0.1450 (p0) REVERT: H 84 MET cc_start: 0.3658 (mpm) cc_final: 0.3125 (mpp) REVERT: H 113 ASP cc_start: 0.4849 (t0) cc_final: 0.4507 (p0) REVERT: H 206 ASP cc_start: 0.3986 (t70) cc_final: 0.3776 (t0) REVERT: H 218 GLU cc_start: 0.4576 (tt0) cc_final: 0.4333 (tm-30) outliers start: 64 outliers final: 26 residues processed: 215 average time/residue: 0.5891 time to fit residues: 143.5666 Evaluate side-chains 189 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 182 THR Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 447 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 268 optimal weight: 30.0000 chunk 226 optimal weight: 10.0000 chunk 230 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 213 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 294 GLN A 400 ASN ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS B 410 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS C 400 ASN I 165 HIS D 294 GLN D 400 ASN H 65 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.214275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.121814 restraints weight = 35900.279| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.69 r_work: 0.3285 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.7209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22481 Z= 0.172 Angle : 0.572 14.582 30446 Z= 0.287 Chirality : 0.043 0.241 3454 Planarity : 0.004 0.049 3978 Dihedral : 3.631 18.322 3046 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.77 % Favored : 95.02 % Rotamer: Outliers : 3.27 % Allowed : 14.85 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: -1.96 (0.16), residues: 2851 helix: -0.85 (0.16), residues: 949 sheet: -0.97 (0.22), residues: 627 loop : -1.72 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 499 TYR 0.025 0.002 TYR C 470 PHE 0.018 0.001 PHE J 95 TRP 0.023 0.002 TRP C 464 HIS 0.009 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00401 (22481) covalent geometry : angle 0.57234 (30446) hydrogen bonds : bond 0.02720 ( 456) hydrogen bonds : angle 4.61135 ( 1245) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 155 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 HIS cc_start: 0.9042 (OUTLIER) cc_final: 0.8752 (m-70) REVERT: A 464 TRP cc_start: 0.9289 (OUTLIER) cc_final: 0.7602 (m-90) REVERT: G 5 GLU cc_start: 0.5266 (mm-30) cc_final: 0.4887 (tp30) REVERT: G 84 MET cc_start: 0.4970 (mmt) cc_final: 0.4700 (mmt) REVERT: G 167 ILE cc_start: 0.3603 (OUTLIER) cc_final: 0.3314 (pt) REVERT: B 165 ASP cc_start: 0.8663 (m-30) cc_final: 0.8223 (p0) REVERT: B 275 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9025 (tt) REVERT: B 368 LYS cc_start: 0.8644 (tmmt) cc_final: 0.8376 (ttpp) REVERT: B 464 TRP cc_start: 0.9074 (OUTLIER) cc_final: 0.8534 (m-90) REVERT: B 494 GLU cc_start: 0.8918 (tp30) cc_final: 0.8584 (tp30) REVERT: B 498 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8334 (ptpp) REVERT: J 74 MET cc_start: 0.1741 (tpp) cc_final: 0.1239 (tmt) REVERT: J 84 MET cc_start: 0.2057 (OUTLIER) cc_final: 0.1399 (mmp) REVERT: J 168 GLU cc_start: 0.3207 (mt-10) cc_final: 0.2729 (mm-30) REVERT: J 178 TYR cc_start: 0.8237 (m-80) cc_final: 0.7998 (m-80) REVERT: C 228 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.6834 (mmt180) REVERT: C 236 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8005 (p0) REVERT: C 264 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8692 (tm-30) REVERT: C 290 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7337 (mm-30) REVERT: C 477 SER cc_start: 0.9029 (m) cc_final: 0.8779 (t) REVERT: I 31 GLU cc_start: 0.4201 (pt0) cc_final: 0.3593 (tp30) REVERT: I 203 LEU cc_start: 0.3951 (OUTLIER) cc_final: 0.3427 (pt) REVERT: D 210 LYS cc_start: 0.9171 (mppt) cc_final: 0.8950 (mppt) REVERT: D 339 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8777 (mt) REVERT: D 447 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8108 (tp30) REVERT: H 51 LYS cc_start: 0.4620 (OUTLIER) cc_final: 0.4381 (tptp) REVERT: H 78 ASP cc_start: 0.2359 (t0) cc_final: 0.1500 (p0) REVERT: H 84 MET cc_start: 0.3758 (mpm) cc_final: 0.3119 (mpp) REVERT: H 113 ASP cc_start: 0.4975 (t0) cc_final: 0.4625 (p0) REVERT: H 181 ASN cc_start: 0.3893 (t0) cc_final: 0.3592 (m110) REVERT: H 218 GLU cc_start: 0.4708 (tt0) cc_final: 0.4476 (tm-30) outliers start: 77 outliers final: 35 residues processed: 217 average time/residue: 0.5700 time to fit residues: 140.6648 Evaluate side-chains 192 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 182 THR Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 65 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 204 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 249 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 142 optimal weight: 30.0000 chunk 197 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 400 ASN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN D 325 HIS D 400 ASN H 65 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.214521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.124151 restraints weight = 35374.514| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.55 r_work: 0.3306 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.7318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22481 Z= 0.143 Angle : 0.560 13.550 30446 Z= 0.279 Chirality : 0.042 0.234 3454 Planarity : 0.003 0.043 3978 Dihedral : 3.595 17.347 3046 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.10 % Favored : 95.69 % Rotamer: Outliers : 2.97 % Allowed : 15.32 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: -1.74 (0.16), residues: 2851 helix: -0.59 (0.17), residues: 944 sheet: -0.91 (0.22), residues: 627 loop : -1.63 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 369 TYR 0.025 0.001 TYR C 470 PHE 0.015 0.001 PHE J 95 TRP 0.027 0.002 TRP C 464 HIS 0.022 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00339 (22481) covalent geometry : angle 0.55975 (30446) hydrogen bonds : bond 0.02503 ( 456) hydrogen bonds : angle 4.52680 ( 1245) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 153 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 HIS cc_start: 0.8922 (OUTLIER) cc_final: 0.8585 (m-70) REVERT: A 464 TRP cc_start: 0.9265 (OUTLIER) cc_final: 0.7567 (m-90) REVERT: G 5 GLU cc_start: 0.5258 (mm-30) cc_final: 0.4918 (tp30) REVERT: G 84 MET cc_start: 0.4868 (mmt) cc_final: 0.4585 (mmt) REVERT: G 167 ILE cc_start: 0.3644 (OUTLIER) cc_final: 0.3364 (pt) REVERT: B 165 ASP cc_start: 0.8642 (m-30) cc_final: 0.8097 (p0) REVERT: B 275 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.8978 (tt) REVERT: B 368 LYS cc_start: 0.8638 (tmmt) cc_final: 0.8375 (ttpp) REVERT: B 464 TRP cc_start: 0.9048 (OUTLIER) cc_final: 0.8530 (m-90) REVERT: B 494 GLU cc_start: 0.8939 (tp30) cc_final: 0.8603 (tp30) REVERT: B 498 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8264 (ptpp) REVERT: J 74 MET cc_start: 0.1679 (tpp) cc_final: 0.1065 (tmt) REVERT: J 84 MET cc_start: 0.2044 (OUTLIER) cc_final: 0.1356 (mmp) REVERT: J 122 LYS cc_start: 0.8621 (tptp) cc_final: 0.8369 (mptt) REVERT: J 168 GLU cc_start: 0.3128 (mt-10) cc_final: 0.2633 (mm-30) REVERT: J 178 TYR cc_start: 0.8240 (m-80) cc_final: 0.7959 (m-80) REVERT: J 180 GLN cc_start: 0.8886 (tp-100) cc_final: 0.8472 (tm-30) REVERT: C 175 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.6003 (tm) REVERT: C 228 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.6795 (mmt180) REVERT: C 236 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.7954 (p0) REVERT: C 264 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8691 (tm-30) REVERT: C 290 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7201 (mm-30) REVERT: C 477 SER cc_start: 0.8988 (m) cc_final: 0.8726 (t) REVERT: I 31 GLU cc_start: 0.4147 (pt0) cc_final: 0.3473 (tp30) REVERT: I 203 LEU cc_start: 0.3915 (OUTLIER) cc_final: 0.3329 (pt) REVERT: D 210 LYS cc_start: 0.9184 (mppt) cc_final: 0.8849 (mppt) REVERT: D 339 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8745 (mt) REVERT: D 342 TYR cc_start: 0.9347 (OUTLIER) cc_final: 0.8750 (t80) REVERT: H 51 LYS cc_start: 0.4677 (OUTLIER) cc_final: 0.4435 (tptp) REVERT: H 78 ASP cc_start: 0.2271 (t0) cc_final: 0.1412 (p0) REVERT: H 84 MET cc_start: 0.3377 (mpm) cc_final: 0.2717 (mpp) REVERT: H 113 ASP cc_start: 0.5239 (t0) cc_final: 0.4830 (p0) REVERT: H 181 ASN cc_start: 0.3904 (t0) cc_final: 0.3318 (m110) REVERT: H 218 GLU cc_start: 0.4711 (tt0) cc_final: 0.4471 (tm-30) outliers start: 70 outliers final: 34 residues processed: 210 average time/residue: 0.5770 time to fit residues: 137.2722 Evaluate side-chains 191 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 182 THR Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 325 HIS Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 342 TYR Chi-restraints excluded: chain D residue 472 ARG Chi-restraints excluded: chain H residue 51 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 168 optimal weight: 0.6980 chunk 71 optimal weight: 20.0000 chunk 131 optimal weight: 0.2980 chunk 266 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 265 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 chunk 204 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 114 optimal weight: 0.9980 chunk 260 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 400 ASN B 493 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN D 325 HIS D 400 ASN H 65 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.215689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.125693 restraints weight = 35866.142| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.46 r_work: 0.3334 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22481 Z= 0.107 Angle : 0.543 13.509 30446 Z= 0.270 Chirality : 0.041 0.231 3454 Planarity : 0.003 0.045 3978 Dihedral : 3.494 19.406 3046 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.03 % Favored : 95.79 % Rotamer: Outliers : 2.25 % Allowed : 16.29 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: -1.59 (0.16), residues: 2851 helix: -0.43 (0.17), residues: 956 sheet: -0.83 (0.22), residues: 633 loop : -1.58 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 369 TYR 0.023 0.001 TYR C 470 PHE 0.016 0.001 PHE J 95 TRP 0.025 0.001 TRP C 464 HIS 0.010 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00258 (22481) covalent geometry : angle 0.54282 (30446) hydrogen bonds : bond 0.02299 ( 456) hydrogen bonds : angle 4.39790 ( 1245) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 147 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 HIS cc_start: 0.8922 (OUTLIER) cc_final: 0.8606 (m-70) REVERT: A 464 TRP cc_start: 0.9227 (OUTLIER) cc_final: 0.7478 (m-90) REVERT: G 5 GLU cc_start: 0.5261 (mm-30) cc_final: 0.4936 (tp30) REVERT: G 84 MET cc_start: 0.4864 (mmt) cc_final: 0.4592 (mmt) REVERT: G 167 ILE cc_start: 0.3636 (OUTLIER) cc_final: 0.3358 (pt) REVERT: B 165 ASP cc_start: 0.8523 (m-30) cc_final: 0.8180 (p0) REVERT: B 275 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8952 (tt) REVERT: B 368 LYS cc_start: 0.8613 (tmmt) cc_final: 0.8343 (ttpp) REVERT: B 464 TRP cc_start: 0.9015 (OUTLIER) cc_final: 0.8418 (m-90) REVERT: B 494 GLU cc_start: 0.8908 (tp30) cc_final: 0.8606 (tp30) REVERT: J 74 MET cc_start: 0.1882 (tpp) cc_final: 0.1333 (tmt) REVERT: J 84 MET cc_start: 0.2046 (OUTLIER) cc_final: 0.1373 (mmp) REVERT: J 122 LYS cc_start: 0.8638 (tptp) cc_final: 0.8388 (mptt) REVERT: J 139 TYR cc_start: 0.2844 (OUTLIER) cc_final: 0.2485 (t80) REVERT: J 168 GLU cc_start: 0.3143 (mt-10) cc_final: 0.2645 (mm-30) REVERT: J 178 TYR cc_start: 0.8191 (m-80) cc_final: 0.7924 (m-80) REVERT: J 180 GLN cc_start: 0.8883 (tp-100) cc_final: 0.8491 (tm-30) REVERT: C 236 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.7838 (p0) REVERT: C 237 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8009 (mtm110) REVERT: C 264 GLN cc_start: 0.8902 (tp-100) cc_final: 0.8644 (tm-30) REVERT: C 290 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7175 (mm-30) REVERT: C 477 SER cc_start: 0.9003 (m) cc_final: 0.8760 (t) REVERT: I 31 GLU cc_start: 0.4171 (pt0) cc_final: 0.3516 (tp30) REVERT: I 203 LEU cc_start: 0.4034 (OUTLIER) cc_final: 0.3527 (pt) REVERT: D 210 LYS cc_start: 0.9193 (mppt) cc_final: 0.8850 (mppt) REVERT: D 342 TYR cc_start: 0.9302 (OUTLIER) cc_final: 0.8635 (t80) REVERT: H 78 ASP cc_start: 0.2237 (t0) cc_final: 0.1432 (p0) REVERT: H 84 MET cc_start: 0.3500 (mpm) cc_final: 0.2783 (mpp) REVERT: H 113 ASP cc_start: 0.4959 (t0) cc_final: 0.4614 (p0) REVERT: H 181 ASN cc_start: 0.3861 (t0) cc_final: 0.3586 (m110) REVERT: H 218 GLU cc_start: 0.4821 (tt0) cc_final: 0.4592 (tm-30) outliers start: 53 outliers final: 27 residues processed: 191 average time/residue: 0.5561 time to fit residues: 121.3251 Evaluate side-chains 179 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 139 TYR Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 325 HIS Chi-restraints excluded: chain D residue 342 TYR Chi-restraints excluded: chain D residue 472 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 38 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 181 optimal weight: 0.0470 chunk 112 optimal weight: 0.0870 chunk 92 optimal weight: 0.6980 chunk 1 optimal weight: 0.0010 chunk 263 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 overall best weight: 0.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 400 ASN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN D 325 HIS D 400 ASN H 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.216594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.127388 restraints weight = 35780.282| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.56 r_work: 0.3362 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.7343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 22481 Z= 0.095 Angle : 0.537 13.384 30446 Z= 0.265 Chirality : 0.041 0.229 3454 Planarity : 0.003 0.043 3978 Dihedral : 3.353 15.545 3046 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.61 % Favored : 96.21 % Rotamer: Outliers : 1.70 % Allowed : 16.84 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: -1.40 (0.16), residues: 2851 helix: -0.16 (0.17), residues: 956 sheet: -0.76 (0.22), residues: 633 loop : -1.54 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 260 TYR 0.020 0.001 TYR C 470 PHE 0.016 0.001 PHE J 95 TRP 0.023 0.001 TRP C 464 HIS 0.011 0.001 HIS D 325 Details of bonding type rmsd covalent geometry : bond 0.00229 (22481) covalent geometry : angle 0.53658 (30446) hydrogen bonds : bond 0.02120 ( 456) hydrogen bonds : angle 4.25729 ( 1245) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 HIS cc_start: 0.8916 (OUTLIER) cc_final: 0.8597 (m-70) REVERT: A 464 TRP cc_start: 0.9188 (OUTLIER) cc_final: 0.7371 (m-90) REVERT: G 5 GLU cc_start: 0.5358 (mm-30) cc_final: 0.5117 (tp30) REVERT: G 84 MET cc_start: 0.4745 (mmt) cc_final: 0.4479 (mmt) REVERT: G 167 ILE cc_start: 0.3689 (OUTLIER) cc_final: 0.3392 (pt) REVERT: B 165 ASP cc_start: 0.8483 (m-30) cc_final: 0.8179 (p0) REVERT: B 275 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8925 (tt) REVERT: B 464 TRP cc_start: 0.8951 (OUTLIER) cc_final: 0.8134 (m-90) REVERT: B 494 GLU cc_start: 0.8875 (tp30) cc_final: 0.8576 (tp30) REVERT: J 74 MET cc_start: 0.1959 (tpp) cc_final: 0.1455 (tmt) REVERT: J 84 MET cc_start: 0.2009 (OUTLIER) cc_final: 0.1357 (mmp) REVERT: J 122 LYS cc_start: 0.8640 (tptp) cc_final: 0.8338 (pttm) REVERT: J 168 GLU cc_start: 0.3152 (mt-10) cc_final: 0.2658 (mm-30) REVERT: J 178 TYR cc_start: 0.8183 (m-80) cc_final: 0.7867 (m-80) REVERT: J 180 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8470 (tm-30) REVERT: C 236 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.7770 (p0) REVERT: C 237 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7985 (mtm110) REVERT: C 264 GLN cc_start: 0.8894 (tp-100) cc_final: 0.8621 (tm-30) REVERT: C 290 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7136 (mm-30) REVERT: C 477 SER cc_start: 0.8990 (m) cc_final: 0.8780 (t) REVERT: I 31 GLU cc_start: 0.4108 (pt0) cc_final: 0.3464 (tp30) REVERT: D 210 LYS cc_start: 0.9187 (mppt) cc_final: 0.8858 (mppt) REVERT: D 342 TYR cc_start: 0.9265 (OUTLIER) cc_final: 0.8523 (t80) REVERT: H 78 ASP cc_start: 0.2214 (t0) cc_final: 0.1504 (p0) REVERT: H 84 MET cc_start: 0.3436 (mpm) cc_final: 0.2800 (mpp) REVERT: H 91 GLU cc_start: 0.5941 (pp20) cc_final: 0.5498 (pm20) REVERT: H 113 ASP cc_start: 0.5067 (t0) cc_final: 0.4711 (p0) REVERT: H 181 ASN cc_start: 0.4178 (t0) cc_final: 0.3457 (m110) REVERT: H 218 GLU cc_start: 0.4814 (tt0) cc_final: 0.4603 (tm-30) outliers start: 40 outliers final: 19 residues processed: 180 average time/residue: 0.5890 time to fit residues: 120.6940 Evaluate side-chains 167 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 342 TYR Chi-restraints excluded: chain H residue 65 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 130 optimal weight: 4.9990 chunk 203 optimal weight: 0.0570 chunk 21 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 278 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 388 HIS A 400 ASN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN D 400 ASN H 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.215555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.125488 restraints weight = 35685.317| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.71 r_work: 0.3329 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.7415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22481 Z= 0.124 Angle : 0.552 13.156 30446 Z= 0.272 Chirality : 0.042 0.229 3454 Planarity : 0.003 0.045 3978 Dihedral : 3.367 17.498 3046 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.21 % Favored : 95.62 % Rotamer: Outliers : 1.91 % Allowed : 16.67 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: -1.33 (0.16), residues: 2851 helix: -0.04 (0.17), residues: 956 sheet: -0.74 (0.22), residues: 636 loop : -1.54 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 369 TYR 0.022 0.001 TYR J 38 PHE 0.014 0.001 PHE J 95 TRP 0.022 0.001 TRP C 464 HIS 0.008 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00300 (22481) covalent geometry : angle 0.55209 (30446) hydrogen bonds : bond 0.02297 ( 456) hydrogen bonds : angle 4.25330 ( 1245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13324.99 seconds wall clock time: 225 minutes 47.59 seconds (13547.59 seconds total)