Starting phenix.real_space_refine on Mon Mar 18 20:54:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mwq_9277/03_2024/6mwq_9277.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mwq_9277/03_2024/6mwq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mwq_9277/03_2024/6mwq_9277.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mwq_9277/03_2024/6mwq_9277.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mwq_9277/03_2024/6mwq_9277.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mwq_9277/03_2024/6mwq_9277.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 Residue "G ARG 92": "NH1" <-> "NH2" Residue "G PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 92": "NH1" <-> "NH2" Residue "J PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 92": "NH1" <-> "NH2" Residue "I PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 10.68, per 1000 atoms: 0.48 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 - 3.50 Amino acid : False - 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: 7.21 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 2.11 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: 5.87 Time building geometry restraints manager: 7.97 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: 100.81 - 107.44: 766 107.44 - 114.08: 12935 114.08 - 120.72: 8905 120.72 - 127.35: 7612 127.35 - 133.99: 228 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 2.440 nonbonded pdb=" O HIS C 99 " pdb=" OG1 THR C 103 " model vdw 2.323 2.440 nonbonded pdb=" O ALA C 448 " pdb=" OH TYR C 470 " model vdw 2.339 2.440 nonbonded pdb=" O HIS B 99 " pdb=" OG1 THR B 103 " model vdw 2.344 2.440 nonbonded pdb=" O ALA D 448 " pdb=" OH TYR D 470 " model vdw 2.348 2.440 ... (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 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.620 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 51.360 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.100 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:10.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.550 ------------------------------------------------------------------------------- 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= 0.076 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.003 0.000 TRP A 482 HIS 0.001 0.000 HIS A 189 PHE 0.003 0.000 PHE D 248 TYR 0.004 0.000 TYR A 391 ARG 0.001 0.000 ARG D 426 *********************** 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 fitting. rotamer outliers: 3 poor density : 522 time to evaluate : 2.344 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: -0.2689 (mmm) REVERT: I 81 LYS cc_start: -0.0094 (mttp) cc_final: -0.0448 (mttt) REVERT: I 209 GLU cc_start: 0.1730 (tp30) cc_final: -0.0246 (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: 1.3100 time to fit residues: 778.2621 Evaluate side-chains 232 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 119 optimal weight: 0.5980 chunk 73 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 chunk 115 optimal weight: 0.5980 chunk 222 optimal weight: 0.0870 chunk 86 optimal weight: 0.0570 chunk 135 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 overall best weight: 0.8678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 99 HIS A 106 HIS ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 ASN A 223 ASN A 294 GLN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 HIS ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN G 160 ASN ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 70 GLN B 73 HIS B 95 GLN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN B 325 HIS B 388 HIS B 503 ASN J 24 HIS J 144 HIS J 160 ASN ** J 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 70 GLN C 99 HIS C 106 HIS C 229 GLN ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 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 66 HIS D 70 GLN D 73 HIS D 95 GLN D 99 HIS D 139 HIS D 170 ASN D 223 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN D 388 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 H 195 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4404 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22481 Z= 0.226 Angle : 0.644 9.763 30446 Z= 0.323 Chirality : 0.044 0.169 3454 Planarity : 0.004 0.058 3978 Dihedral : 3.217 24.726 3046 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.67 % Favored : 95.05 % Rotamer: Outliers : 2.76 % Allowed : 11.54 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.14), residues: 2851 helix: -3.77 (0.11), residues: 860 sheet: -1.45 (0.20), residues: 672 loop : -2.41 (0.16), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 56 HIS 0.009 0.001 HIS C 414 PHE 0.013 0.001 PHE H 110 TYR 0.018 0.002 TYR J 141 ARG 0.008 0.001 ARG B 211 *********************** 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 312 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 247 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 167 ILE cc_start: 0.3952 (OUTLIER) cc_final: 0.3681 (pp) REVERT: B 337 ASN cc_start: 0.6133 (p0) cc_final: 0.5869 (p0) REVERT: J 84 MET cc_start: 0.0636 (mmt) cc_final: -0.0456 (mmm) REVERT: C 175 LEU cc_start: 0.5604 (OUTLIER) cc_final: 0.5098 (tm) REVERT: D 447 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5676 (tp30) REVERT: H 51 LYS cc_start: 0.3836 (OUTLIER) cc_final: 0.3495 (tptt) REVERT: H 205 LYS cc_start: 0.1775 (mmtt) cc_final: 0.1337 (pptt) outliers start: 65 outliers final: 24 residues processed: 297 average time/residue: 1.2879 time to fit residues: 437.3442 Evaluate side-chains 213 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 167 ILE 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 428 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 226 THR Chi-restraints excluded: chain C residue 175 LEU 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 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 320 LEU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 72 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 258 optimal weight: 0.9990 chunk 279 optimal weight: 6.9990 chunk 230 optimal weight: 1.9990 chunk 256 optimal weight: 0.0470 chunk 88 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 overall best weight: 1.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 73 HIS A 95 GLN A 139 HIS A 294 GLN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 HIS ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS G 166 ASN ** G 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS B 106 HIS B 229 GLN B 294 GLN B 325 HIS ** J 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 177 HIS C 73 HIS C 95 GLN C 325 HIS C 337 ASN C 451 ASN ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 GLN I 194 ASN D 121 ASN D 189 HIS D 294 GLN D 389 HIS D 400 ASN H 131 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4914 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22481 Z= 0.260 Angle : 0.608 8.933 30446 Z= 0.307 Chirality : 0.043 0.287 3454 Planarity : 0.004 0.056 3978 Dihedral : 3.351 16.379 3046 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.00 % Favored : 93.79 % Rotamer: Outliers : 3.65 % Allowed : 12.69 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.14), residues: 2851 helix: -2.89 (0.13), residues: 949 sheet: -1.24 (0.21), residues: 647 loop : -2.24 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 316 HIS 0.009 0.001 HIS A 388 PHE 0.019 0.001 PHE A 262 TYR 0.032 0.002 TYR G 102 ARG 0.011 0.001 ARG B 369 *********************** 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 294 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 208 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 74 MET cc_start: 0.0045 (mtp) cc_final: -0.2276 (mmm) REVERT: G 84 MET cc_start: 0.1816 (mmt) cc_final: 0.0862 (mmt) REVERT: B 472 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.6011 (ttp-170) REVERT: J 168 GLU cc_start: 0.2760 (mt-10) cc_final: 0.1778 (mm-30) REVERT: C 175 LEU cc_start: 0.5708 (OUTLIER) cc_final: 0.5176 (tm) REVERT: C 260 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6465 (ttp-110) REVERT: I 205 LYS cc_start: 0.2680 (OUTLIER) cc_final: 0.0351 (mmpt) REVERT: D 447 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.5889 (tp30) REVERT: H 51 LYS cc_start: 0.3351 (OUTLIER) cc_final: 0.3100 (tptt) REVERT: H 84 MET cc_start: -0.0281 (mpm) cc_final: -0.0568 (mpt) REVERT: H 109 LYS cc_start: 0.0379 (OUTLIER) cc_final: -0.0047 (tppt) REVERT: H 149 MET cc_start: -0.0706 (mpt) cc_final: -0.2208 (mmp) outliers start: 86 outliers final: 30 residues processed: 272 average time/residue: 1.4220 time to fit residues: 442.7222 Evaluate side-chains 187 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain B residue 497 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 175 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 220 VAL 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 282 VAL Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 220 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 0.6980 chunk 194 optimal weight: 30.0000 chunk 134 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 30.0000 chunk 173 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 chunk 274 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 245 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN A 294 GLN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN G 140 ASN ** G 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 HIS B 406 HIS B 443 GLN ** J 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 189 HIS C 229 GLN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN I 140 ASN ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS D 223 ASN D 294 GLN ** D 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN H 65 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5234 moved from start: 0.6752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 22481 Z= 0.449 Angle : 0.700 9.847 30446 Z= 0.356 Chirality : 0.048 0.280 3454 Planarity : 0.005 0.063 3978 Dihedral : 4.185 20.596 3046 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.44 % Favored : 94.35 % Rotamer: Outliers : 4.16 % Allowed : 13.75 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.15), residues: 2851 helix: -2.35 (0.14), residues: 949 sheet: -1.17 (0.21), residues: 630 loop : -2.13 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP D 316 HIS 0.012 0.002 HIS C 414 PHE 0.018 0.002 PHE A 248 TYR 0.023 0.002 TYR A 382 ARG 0.010 0.001 ARG B 369 *********************** 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 260 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 162 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8497 (tt) REVERT: G 84 MET cc_start: 0.2295 (mmt) cc_final: 0.1521 (mmt) REVERT: J 84 MET cc_start: 0.0054 (mtt) cc_final: -0.0359 (mmp) REVERT: C 228 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7015 (mmt180) REVERT: C 464 TRP cc_start: 0.8029 (OUTLIER) cc_final: 0.7785 (m-90) REVERT: I 149 MET cc_start: 0.0784 (mtm) cc_final: 0.0204 (mtm) REVERT: D 447 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5984 (tp30) REVERT: D 464 TRP cc_start: 0.8649 (OUTLIER) cc_final: 0.8251 (m-90) REVERT: H 16 GLU cc_start: 0.2798 (OUTLIER) cc_final: 0.2328 (mm-30) REVERT: H 84 MET cc_start: -0.0124 (mpm) cc_final: -0.0327 (mpt) outliers start: 98 outliers final: 33 residues processed: 241 average time/residue: 1.3357 time to fit residues: 366.4376 Evaluate side-chains 163 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 124 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 230 LEU 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 499 ARG Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 220 VAL 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 207 SER Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 464 TRP 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 299 LEU Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 464 TRP Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 74 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 3.9990 chunk 155 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 140 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 189 HIS A 294 GLN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN ** J 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 GLN ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN ** D 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5242 moved from start: 0.7049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22481 Z= 0.325 Angle : 0.591 8.693 30446 Z= 0.299 Chirality : 0.044 0.240 3454 Planarity : 0.004 0.045 3978 Dihedral : 3.870 19.769 3046 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.59 % Favored : 95.23 % Rotamer: Outliers : 3.90 % Allowed : 15.27 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.15), residues: 2851 helix: -1.73 (0.15), residues: 964 sheet: -1.05 (0.21), residues: 637 loop : -1.98 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 316 HIS 0.011 0.001 HIS C 414 PHE 0.019 0.001 PHE D 313 TYR 0.021 0.002 TYR J 38 ARG 0.009 0.001 ARG G 105 *********************** 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 242 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 150 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8532 (t80) REVERT: A 464 TRP cc_start: 0.8348 (OUTLIER) cc_final: 0.7318 (m-90) REVERT: G 84 MET cc_start: 0.2497 (mmt) cc_final: 0.1681 (mmt) REVERT: B 339 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8400 (mt) REVERT: B 464 TRP cc_start: 0.8403 (OUTLIER) cc_final: 0.8090 (m-90) REVERT: C 294 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7420 (mt0) REVERT: I 205 LYS cc_start: 0.3254 (OUTLIER) cc_final: 0.1725 (tptt) REVERT: D 339 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8304 (mm) REVERT: D 464 TRP cc_start: 0.8662 (OUTLIER) cc_final: 0.7775 (m-90) REVERT: H 16 GLU cc_start: 0.2842 (OUTLIER) cc_final: 0.2316 (mm-30) REVERT: H 149 MET cc_start: -0.0335 (mpt) cc_final: -0.2498 (mmp) outliers start: 92 outliers final: 40 residues processed: 221 average time/residue: 1.2990 time to fit residues: 328.1551 Evaluate side-chains 178 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 129 time to evaluate : 2.581 ------------------------------------------------------------------------------- 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 342 TYR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 205 THR 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 339 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 220 VAL 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 230 LEU Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 464 TRP Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 72 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 0.0030 chunk 247 optimal weight: 0.8980 chunk 54 optimal weight: 20.0000 chunk 161 optimal weight: 6.9990 chunk 67 optimal weight: 0.0370 chunk 274 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 127 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 0.0010 chunk 144 optimal weight: 30.0000 overall best weight: 0.2274 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 ASN G 73 HIS ** G 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN B 493 GLN C 154 ASN 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 D 503 ASN H 65 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5155 moved from start: 0.7043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22481 Z= 0.139 Angle : 0.520 14.175 30446 Z= 0.255 Chirality : 0.040 0.239 3454 Planarity : 0.003 0.038 3978 Dihedral : 3.487 17.755 3046 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.05 % Favored : 96.77 % Rotamer: Outliers : 2.63 % Allowed : 16.89 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.15), residues: 2851 helix: -1.17 (0.16), residues: 952 sheet: -0.90 (0.21), residues: 637 loop : -1.89 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 316 HIS 0.008 0.001 HIS C 325 PHE 0.012 0.001 PHE D 313 TYR 0.020 0.001 TYR J 38 ARG 0.006 0.000 ARG B 369 *********************** 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 211 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 149 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.7068 (m-90) REVERT: G 84 MET cc_start: 0.2451 (mmt) cc_final: 0.2174 (tpp) REVERT: B 339 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8494 (mt) REVERT: B 464 TRP cc_start: 0.8319 (OUTLIER) cc_final: 0.7713 (m-90) REVERT: J 84 MET cc_start: 0.0651 (OUTLIER) cc_final: -0.0526 (mmp) REVERT: J 168 GLU cc_start: 0.2846 (mt-10) cc_final: 0.1850 (mm-30) REVERT: I 205 LYS cc_start: 0.3025 (OUTLIER) cc_final: 0.1509 (tptt) REVERT: D 464 TRP cc_start: 0.8454 (OUTLIER) cc_final: 0.7334 (m-90) REVERT: H 149 MET cc_start: -0.0513 (mpt) cc_final: -0.2539 (mmp) REVERT: H 181 ASN cc_start: 0.1685 (m-40) cc_final: 0.1156 (m110) outliers start: 62 outliers final: 27 residues processed: 200 average time/residue: 1.2777 time to fit residues: 293.2741 Evaluate side-chains 161 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 128 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 339 LEU 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 84 MET Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 148 ILE 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 409 THR Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain D residue 180 GLN 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 464 TRP Chi-restraints excluded: chain D residue 503 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 200 optimal weight: 30.0000 chunk 155 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 273 optimal weight: 20.0000 chunk 171 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 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 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN C 325 HIS ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 HIS D 294 GLN ** D 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 503 ASN D 508 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5239 moved from start: 0.7297 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= 0.270 Angle : 0.563 13.490 30446 Z= 0.279 Chirality : 0.043 0.237 3454 Planarity : 0.003 0.036 3978 Dihedral : 3.575 18.859 3046 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.74 % Favored : 95.09 % Rotamer: Outliers : 3.22 % Allowed : 16.80 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.16), residues: 2851 helix: -0.88 (0.17), residues: 940 sheet: -0.85 (0.21), residues: 654 loop : -1.73 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 316 HIS 0.007 0.001 HIS C 414 PHE 0.015 0.001 PHE D 313 TYR 0.023 0.001 TYR J 38 ARG 0.005 0.000 ARG B 369 *********************** 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 211 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 135 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 HIS cc_start: 0.6241 (OUTLIER) cc_final: 0.5947 (m90) REVERT: A 464 TRP cc_start: 0.8321 (OUTLIER) cc_final: 0.7128 (m-90) REVERT: G 74 MET cc_start: -0.0201 (mtm) cc_final: -0.0939 (tmm) REVERT: G 84 MET cc_start: 0.2565 (mmt) cc_final: 0.1787 (mmt) REVERT: B 339 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8591 (mt) REVERT: B 464 TRP cc_start: 0.8395 (OUTLIER) cc_final: 0.8075 (m-90) REVERT: J 84 MET cc_start: 0.0809 (OUTLIER) cc_final: -0.0500 (mmp) REVERT: C 260 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6766 (ttp80) REVERT: C 464 TRP cc_start: 0.8030 (OUTLIER) cc_final: 0.7784 (m-90) REVERT: I 205 LYS cc_start: 0.3052 (OUTLIER) cc_final: 0.2237 (tptt) REVERT: D 339 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8219 (mm) REVERT: D 342 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.8119 (t80) REVERT: D 464 TRP cc_start: 0.8640 (OUTLIER) cc_final: 0.7738 (m-90) REVERT: H 181 ASN cc_start: 0.1809 (m-40) cc_final: 0.1369 (m-40) REVERT: H 206 ASP cc_start: 0.2276 (t0) cc_final: 0.1889 (t70) outliers start: 76 outliers final: 38 residues processed: 195 average time/residue: 1.2063 time to fit residues: 271.8154 Evaluate side-chains 173 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 124 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 230 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 445 GLU Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 444 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 13 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 148 ILE 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 260 ARG Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 464 TRP Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain I residue 205 LYS 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 342 TYR Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 464 TRP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 212 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 174 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 249 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS B 493 GLN J 194 ASN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN ** D 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5227 moved from start: 0.7404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22481 Z= 0.216 Angle : 0.549 13.067 30446 Z= 0.271 Chirality : 0.042 0.232 3454 Planarity : 0.003 0.034 3978 Dihedral : 3.531 17.735 3046 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.96 % Favored : 95.86 % Rotamer: Outliers : 2.63 % Allowed : 17.10 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2851 helix: -0.60 (0.17), residues: 940 sheet: -0.78 (0.21), residues: 655 loop : -1.67 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 316 HIS 0.021 0.001 HIS C 325 PHE 0.014 0.001 PHE D 313 TYR 0.022 0.001 TYR J 38 ARG 0.004 0.000 ARG B 369 *********************** 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 191 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 129 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 HIS cc_start: 0.6227 (OUTLIER) cc_final: 0.5912 (m90) REVERT: A 464 TRP cc_start: 0.8318 (OUTLIER) cc_final: 0.7129 (m-90) REVERT: G 74 MET cc_start: -0.0479 (mtm) cc_final: -0.1132 (tmm) REVERT: G 84 MET cc_start: 0.2602 (mmt) cc_final: 0.2364 (tpp) REVERT: B 275 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7801 (tt) REVERT: B 339 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8615 (mt) REVERT: C 260 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6781 (ttp80) REVERT: I 205 LYS cc_start: 0.2891 (OUTLIER) cc_final: 0.2066 (tptt) REVERT: D 339 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8199 (mm) REVERT: D 464 TRP cc_start: 0.8578 (OUTLIER) cc_final: 0.7566 (m-90) REVERT: H 181 ASN cc_start: 0.1767 (m-40) cc_final: 0.1345 (m-40) REVERT: H 206 ASP cc_start: 0.2315 (t0) cc_final: 0.1916 (t70) outliers start: 62 outliers final: 32 residues processed: 177 average time/residue: 1.2608 time to fit residues: 257.4074 Evaluate side-chains 165 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 125 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 230 LEU 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 445 GLU Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 134 THR 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 333 MET Chi-restraints excluded: chain B residue 339 LEU 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 133 LEU Chi-restraints excluded: chain J residue 148 ILE 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 260 ARG Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain I residue 205 LYS 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 464 TRP Chi-restraints excluded: chain H residue 72 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 0.9980 chunk 239 optimal weight: 0.7980 chunk 255 optimal weight: 0.3980 chunk 153 optimal weight: 0.4980 chunk 111 optimal weight: 0.2980 chunk 200 optimal weight: 30.0000 chunk 78 optimal weight: 9.9990 chunk 230 optimal weight: 4.9990 chunk 241 optimal weight: 0.9990 chunk 254 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 388 HIS ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 GLN ** 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** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN D 400 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5194 moved from start: 0.7434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22481 Z= 0.158 Angle : 0.524 12.925 30446 Z= 0.256 Chirality : 0.041 0.230 3454 Planarity : 0.003 0.032 3978 Dihedral : 3.372 16.684 3046 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.65 % Favored : 96.18 % Rotamer: Outliers : 2.46 % Allowed : 17.27 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.16), residues: 2851 helix: -0.28 (0.17), residues: 944 sheet: -0.64 (0.22), residues: 633 loop : -1.63 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 316 HIS 0.009 0.001 HIS C 325 PHE 0.015 0.001 PHE J 95 TYR 0.018 0.001 TYR C 470 ARG 0.005 0.000 ARG B 369 *********************** 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 194 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 136 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 HIS cc_start: 0.6168 (OUTLIER) cc_final: 0.5871 (m90) REVERT: A 464 TRP cc_start: 0.8285 (OUTLIER) cc_final: 0.7133 (m-90) REVERT: G 74 MET cc_start: -0.0545 (mtm) cc_final: -0.1254 (tmm) REVERT: G 84 MET cc_start: 0.2589 (mmt) cc_final: 0.1846 (mmt) REVERT: B 275 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7700 (tt) REVERT: B 464 TRP cc_start: 0.8325 (OUTLIER) cc_final: 0.7746 (m-90) REVERT: J 84 MET cc_start: 0.1141 (mtt) cc_final: -0.0210 (mmp) REVERT: C 260 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6748 (ttp80) REVERT: I 205 LYS cc_start: 0.2825 (OUTLIER) cc_final: 0.2086 (tptt) REVERT: D 48 MET cc_start: 0.2547 (tmt) cc_final: 0.2200 (tmt) REVERT: D 342 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.7993 (t80) REVERT: D 464 TRP cc_start: 0.8487 (OUTLIER) cc_final: 0.7333 (m-90) REVERT: H 181 ASN cc_start: 0.1560 (m-40) cc_final: 0.1075 (m-40) REVERT: H 206 ASP cc_start: 0.2352 (t0) cc_final: 0.1990 (t70) outliers start: 58 outliers final: 31 residues processed: 182 average time/residue: 1.2628 time to fit residues: 263.9234 Evaluate side-chains 163 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 124 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 230 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 445 GLU Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain I residue 205 LYS 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 342 TYR Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 464 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 20.0000 chunk 164 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 187 optimal weight: 0.0570 chunk 282 optimal weight: 7.9990 chunk 260 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 chunk 23 optimal weight: 0.2980 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS D 294 GLN ** D 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5225 moved from start: 0.7551 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= 0.205 Angle : 0.545 12.699 30446 Z= 0.267 Chirality : 0.042 0.230 3454 Planarity : 0.003 0.032 3978 Dihedral : 3.413 16.836 3046 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.17 % Favored : 95.65 % Rotamer: Outliers : 2.12 % Allowed : 17.86 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.16), residues: 2851 helix: -0.23 (0.17), residues: 971 sheet: -0.59 (0.22), residues: 633 loop : -1.57 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 316 HIS 0.006 0.001 HIS B 139 PHE 0.017 0.001 PHE J 95 TYR 0.019 0.001 TYR C 470 ARG 0.006 0.000 ARG C 224 ********************** 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 182 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 132 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 HIS cc_start: 0.6214 (OUTLIER) cc_final: 0.5897 (m90) REVERT: A 464 TRP cc_start: 0.8306 (OUTLIER) cc_final: 0.7185 (m-90) REVERT: G 74 MET cc_start: -0.0523 (mtm) cc_final: -0.1199 (tmm) REVERT: G 84 MET cc_start: 0.2528 (mmt) cc_final: 0.2285 (tpp) REVERT: B 275 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7748 (tt) REVERT: C 260 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6726 (ttp80) REVERT: I 205 LYS cc_start: 0.2862 (OUTLIER) cc_final: 0.2113 (tptt) REVERT: D 48 MET cc_start: 0.2559 (tmt) cc_final: 0.2209 (tmt) REVERT: D 342 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.8011 (t80) REVERT: D 464 TRP cc_start: 0.8566 (OUTLIER) cc_final: 0.7451 (m-90) REVERT: H 181 ASN cc_start: 0.1823 (m-40) cc_final: 0.1255 (m-40) REVERT: H 206 ASP cc_start: 0.2347 (t0) cc_final: 0.2018 (t70) outliers start: 50 outliers final: 34 residues processed: 171 average time/residue: 1.2449 time to fit residues: 247.6045 Evaluate side-chains 165 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 124 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 230 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 445 GLU Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 333 MET 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 133 LEU Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 342 TYR Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 464 TRP Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 212 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 198 optimal weight: 40.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 ASN ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN D 294 GLN ** D 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.213953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.122787 restraints weight = 35719.607| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.46 r_work: 0.3300 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.7716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22481 Z= 0.228 Angle : 0.564 12.485 30446 Z= 0.277 Chirality : 0.042 0.230 3454 Planarity : 0.003 0.032 3978 Dihedral : 3.512 16.770 3046 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.28 % Favored : 95.55 % Rotamer: Outliers : 2.21 % Allowed : 17.90 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.16), residues: 2851 helix: -0.12 (0.17), residues: 983 sheet: -0.59 (0.21), residues: 654 loop : -1.47 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 316 HIS 0.007 0.001 HIS B 139 PHE 0.016 0.001 PHE J 95 TYR 0.021 0.001 TYR C 470 ARG 0.006 0.000 ARG C 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8394.62 seconds wall clock time: 149 minutes 9.63 seconds (8949.63 seconds total)