Starting phenix.real_space_refine on Mon Mar 25 14:00:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iok_9695/03_2024/6iok_9695.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iok_9695/03_2024/6iok_9695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iok_9695/03_2024/6iok_9695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iok_9695/03_2024/6iok_9695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iok_9695/03_2024/6iok_9695.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iok_9695/03_2024/6iok_9695.pdb" } resolution = 3.64 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= 0.023 sd= 3.031 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 141 5.16 5 C 31071 2.51 5 N 8466 2.21 5 O 9336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I ARG 34": "NH1" <-> "NH2" Residue "I ARG 186": "NH1" <-> "NH2" Residue "I ARG 221": "NH1" <-> "NH2" Residue "I ARG 239": "NH1" <-> "NH2" Residue "J ARG 44": "NH1" <-> "NH2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J ARG 186": "NH1" <-> "NH2" Residue "J ARG 198": "NH1" <-> "NH2" Residue "J ARG 221": "NH1" <-> "NH2" Residue "K ARG 44": "NH1" <-> "NH2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 188": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 221": "NH1" <-> "NH2" Residue "L ARG 277": "NH1" <-> "NH2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "M ARG 147": "NH1" <-> "NH2" Residue "M ARG 297": "NH1" <-> "NH2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N ARG 188": "NH1" <-> "NH2" Residue "N ARG 277": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 341": "NH1" <-> "NH2" Residue "C ARG 432": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 418": "NH1" <-> "NH2" Residue "F PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 918": "NH1" <-> "NH2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G ARG 791": "NH1" <-> "NH2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "E ARG 620": "NH1" <-> "NH2" Residue "E PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 699": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49014 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2505 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 14, 'TRANS': 314} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2538 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 14, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2518 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 316} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2543 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 14, 'TRANS': 319} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2522 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 14, 'TRANS': 316} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2542 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 14, 'TRANS': 319} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "A" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3486 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 17, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3486 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 17, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3486 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 17, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 7764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7764 Classifications: {'peptide': 1024} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 972} Chain breaks: 1 Chain: "G" Number of atoms: 7812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 7812 Classifications: {'peptide': 1030} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 978} Chain: "E" Number of atoms: 7812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 7812 Classifications: {'peptide': 1030} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 978} Time building chain proxies: 25.33, per 1000 atoms: 0.52 Number of scatterers: 49014 At special positions: 0 Unit cell: (141.75, 130.375, 344.75, 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 141 16.00 O 9336 8.00 N 8466 7.00 C 31071 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: 17.25 Conformation dependent library (CDL) restraints added in 9.5 seconds 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11858 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 68 sheets defined 47.1% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.51 Creating SS restraints... Processing helix chain 'I' and resid 73 through 101 removed outlier: 3.614A pdb=" N ALA I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASP I 79 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN I 86 " --> pdb=" O SER I 82 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU I 92 " --> pdb=" O ALA I 88 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN I 93 " --> pdb=" O SER I 89 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA I 94 " --> pdb=" O THR I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 104 No H-bonds generated for 'chain 'I' and resid 102 through 104' Processing helix chain 'I' and resid 107 through 136 removed outlier: 3.695A pdb=" N ALA I 124 " --> pdb=" O GLN I 120 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN I 131 " --> pdb=" O GLN I 127 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU I 132 " --> pdb=" O ALA I 128 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS I 136 " --> pdb=" O LEU I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 193 removed outlier: 3.782A pdb=" N ALA I 192 " --> pdb=" O ARG I 188 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER I 193 " --> pdb=" O ARG I 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 102 removed outlier: 4.147A pdb=" N ALA J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 134 removed outlier: 3.847A pdb=" N ALA J 114 " --> pdb=" O GLN J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 193 Processing helix chain 'J' and resid 201 through 203 No H-bonds generated for 'chain 'J' and resid 201 through 203' Processing helix chain 'K' and resid 76 through 101 removed outlier: 3.607A pdb=" N GLN K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER K 82 " --> pdb=" O ALA K 78 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 134 removed outlier: 3.622A pdb=" N ALA K 112 " --> pdb=" O LYS K 108 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA K 114 " --> pdb=" O GLN K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 193 removed outlier: 3.772A pdb=" N LEU K 185 " --> pdb=" O SER K 181 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER K 193 " --> pdb=" O ARG K 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 102 removed outlier: 3.938A pdb=" N ASN L 86 " --> pdb=" O SER L 82 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA L 102 " --> pdb=" O LYS L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 134 Processing helix chain 'L' and resid 181 through 193 Processing helix chain 'M' and resid 73 through 103 removed outlier: 4.488A pdb=" N ASP M 79 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR M 80 " --> pdb=" O TYR M 76 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER M 82 " --> pdb=" O ALA M 78 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN M 86 " --> pdb=" O SER M 82 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU M 99 " --> pdb=" O GLN M 95 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA M 102 " --> pdb=" O LYS M 98 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP M 103 " --> pdb=" O LEU M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 136 removed outlier: 3.630A pdb=" N ALA M 114 " --> pdb=" O GLN M 110 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN M 131 " --> pdb=" O GLN M 127 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS M 136 " --> pdb=" O LEU M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 190 removed outlier: 3.777A pdb=" N ARG M 186 " --> pdb=" O THR M 182 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 102 removed outlier: 3.801A pdb=" N SER N 89 " --> pdb=" O ALA N 85 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA N 102 " --> pdb=" O LYS N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 135 removed outlier: 3.625A pdb=" N THR N 135 " --> pdb=" O ASN N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 193 Processing helix chain 'A' and resid 46 through 60 removed outlier: 4.352A pdb=" N GLU A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 84 removed outlier: 3.643A pdb=" N GLN A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 199 removed outlier: 4.148A pdb=" N ARG A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 239 removed outlier: 3.572A pdb=" N LEU A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.603A pdb=" N GLN A 270 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 294 removed outlier: 3.527A pdb=" N HIS A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A 290 " --> pdb=" O ASN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 406 removed outlier: 4.332A pdb=" N THR A 380 " --> pdb=" O ARG A 376 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR A 406 " --> pdb=" O LYS A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 447 removed outlier: 3.603A pdb=" N THR A 430 " --> pdb=" O GLN A 426 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 447 " --> pdb=" O TYR A 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 60 Processing helix chain 'B' and resid 61 through 82 Processing helix chain 'B' and resid 131 through 198 Processing helix chain 'B' and resid 202 through 239 removed outlier: 3.650A pdb=" N LEU B 206 " --> pdb=" O SER B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 272 through 295 Processing helix chain 'B' and resid 312 through 316 removed outlier: 3.823A pdb=" N GLY B 315 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU B 316 " --> pdb=" O LEU B 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 312 through 316' Processing helix chain 'B' and resid 339 through 407 removed outlier: 4.173A pdb=" N THR B 380 " --> pdb=" O ARG B 376 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 447 removed outlier: 3.905A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 57 Processing helix chain 'C' and resid 61 through 83 removed outlier: 3.994A pdb=" N GLU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 199 removed outlier: 3.932A pdb=" N ASP C 180 " --> pdb=" O GLN C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 239 Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 272 through 294 removed outlier: 3.520A pdb=" N LEU C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 407 removed outlier: 4.144A pdb=" N ALA C 356 " --> pdb=" O ASP C 352 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR C 380 " --> pdb=" O ARG C 376 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 447 removed outlier: 3.985A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY C 447 " --> pdb=" O TYR C 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 removed outlier: 3.527A pdb=" N ASP F 7 " --> pdb=" O LYS F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 28 removed outlier: 3.669A pdb=" N ALA F 12 " --> pdb=" O ARG F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 67 removed outlier: 5.682A pdb=" N GLN F 63 " --> pdb=" O ASP F 59 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL F 64 " --> pdb=" O THR F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 112 Processing helix chain 'F' and resid 114 through 118 Processing helix chain 'F' and resid 119 through 126 removed outlier: 3.873A pdb=" N GLY F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 162 removed outlier: 3.549A pdb=" N LEU F 154 " --> pdb=" O THR F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 Processing helix chain 'F' and resid 189 through 196 removed outlier: 3.780A pdb=" N TYR F 196 " --> pdb=" O LYS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 211 Processing helix chain 'F' and resid 242 through 247 Processing helix chain 'F' and resid 299 through 314 Processing helix chain 'F' and resid 315 through 317 No H-bonds generated for 'chain 'F' and resid 315 through 317' Processing helix chain 'F' and resid 330 through 360 Processing helix chain 'F' and resid 361 through 366 removed outlier: 3.799A pdb=" N THR F 365 " --> pdb=" O ASN F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 386 Proline residue: F 373 - end of helix removed outlier: 3.555A pdb=" N PHE F 386 " --> pdb=" O VAL F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 423 removed outlier: 3.597A pdb=" N MET F 395 " --> pdb=" O ASN F 391 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLY F 403 " --> pdb=" O VAL F 399 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU F 404 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASP F 408 " --> pdb=" O LEU F 404 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA F 409 " --> pdb=" O LEU F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 454 removed outlier: 4.006A pdb=" N ALA F 430 " --> pdb=" O SER F 426 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY F 440 " --> pdb=" O GLY F 436 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA F 441 " --> pdb=" O GLN F 437 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL F 443 " --> pdb=" O GLN F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 457 No H-bonds generated for 'chain 'F' and resid 455 through 457' Processing helix chain 'F' and resid 461 through 489 Processing helix chain 'F' and resid 489 through 494 Processing helix chain 'F' and resid 512 through 529 Processing helix chain 'F' and resid 531 through 537 Processing helix chain 'F' and resid 540 through 556 removed outlier: 4.122A pdb=" N ILE F 544 " --> pdb=" O PRO F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 601 removed outlier: 4.016A pdb=" N THR F 587 " --> pdb=" O SER F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 643 through 656 removed outlier: 3.627A pdb=" N MET F 653 " --> pdb=" O LYS F 649 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N HIS F 654 " --> pdb=" O ARG F 650 " (cutoff:3.500A) Processing helix chain 'F' and resid 691 through 708 Processing helix chain 'F' and resid 731 through 739 removed outlier: 3.583A pdb=" N GLY F 739 " --> pdb=" O ALA F 735 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 755 removed outlier: 4.075A pdb=" N SER F 755 " --> pdb=" O ILE F 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 781 through 786 removed outlier: 3.600A pdb=" N LEU F 785 " --> pdb=" O PRO F 782 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER F 786 " --> pdb=" O ASP F 783 " (cutoff:3.500A) Processing helix chain 'F' and resid 835 through 848 removed outlier: 3.715A pdb=" N ALA F 839 " --> pdb=" O SER F 835 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS F 848 " --> pdb=" O GLU F 844 " (cutoff:3.500A) Processing helix chain 'F' and resid 860 through 868 removed outlier: 3.836A pdb=" N GLU F 864 " --> pdb=" O GLY F 860 " (cutoff:3.500A) Processing helix chain 'F' and resid 871 through 892 Processing helix chain 'F' and resid 897 through 902 Processing helix chain 'F' and resid 903 through 918 removed outlier: 4.699A pdb=" N GLY F 910 " --> pdb=" O LEU F 906 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA F 911 " --> pdb=" O GLY F 907 " (cutoff:3.500A) Processing helix chain 'F' and resid 923 through 954 removed outlier: 3.555A pdb=" N GLN F 927 " --> pdb=" O ASP F 923 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU F 943 " --> pdb=" O LYS F 939 " (cutoff:3.500A) Processing helix chain 'F' and resid 957 through 989 removed outlier: 4.779A pdb=" N ARG F 971 " --> pdb=" O ARG F 967 " (cutoff:3.500A) Proline residue: F 972 - end of helix Proline residue: F 986 - end of helix Processing helix chain 'F' and resid 994 through 1029 removed outlier: 3.742A pdb=" N GLN F 998 " --> pdb=" O GLY F 994 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL F1005 " --> pdb=" O ILE F1001 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL F1014 " --> pdb=" O VAL F1010 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE F1018 " --> pdb=" O VAL F1014 " (cutoff:3.500A) Proline residue: F1021 - end of helix Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 8 through 30 removed outlier: 4.257A pdb=" N ALA G 12 " --> pdb=" O ARG G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 61 removed outlier: 3.795A pdb=" N VAL G 57 " --> pdb=" O SER G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 69 Processing helix chain 'G' and resid 99 through 115 Processing helix chain 'G' and resid 119 through 126 Processing helix chain 'G' and resid 150 through 162 removed outlier: 3.797A pdb=" N LEU G 154 " --> pdb=" O THR G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 195 Processing helix chain 'G' and resid 199 through 211 Processing helix chain 'G' and resid 242 through 247 removed outlier: 3.819A pdb=" N PHE G 246 " --> pdb=" O THR G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 314 Processing helix chain 'G' and resid 329 through 359 Processing helix chain 'G' and resid 365 through 387 removed outlier: 4.478A pdb=" N THR G 369 " --> pdb=" O THR G 365 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE G 370 " --> pdb=" O LEU G 366 " (cutoff:3.500A) Proline residue: G 373 - end of helix Processing helix chain 'G' and resid 391 through 423 removed outlier: 3.831A pdb=" N MET G 395 " --> pdb=" O ASN G 391 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU G 404 " --> pdb=" O LEU G 400 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE G 410 " --> pdb=" O VAL G 406 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL G 411 " --> pdb=" O ASP G 407 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL G 412 " --> pdb=" O ASP G 408 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL G 413 " --> pdb=" O ALA G 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 454 removed outlier: 6.395A pdb=" N GLY G 440 " --> pdb=" O GLY G 436 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA G 441 " --> pdb=" O GLN G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 455 through 458 removed outlier: 3.912A pdb=" N PHE G 458 " --> pdb=" O PRO G 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 455 through 458' Processing helix chain 'G' and resid 460 through 488 removed outlier: 4.024A pdb=" N VAL G 465 " --> pdb=" O GLY G 461 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE G 466 " --> pdb=" O SER G 462 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE G 470 " --> pdb=" O ILE G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 494 Processing helix chain 'G' and resid 512 through 537 removed outlier: 4.113A pdb=" N HIS G 537 " --> pdb=" O SER G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 559 removed outlier: 3.977A pdb=" N THR G 557 " --> pdb=" O ILE G 553 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE G 559 " --> pdb=" O MET G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 601 removed outlier: 4.003A pdb=" N THR G 587 " --> pdb=" O SER G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 633 through 637 removed outlier: 3.821A pdb=" N ARG G 637 " --> pdb=" O TRP G 634 " (cutoff:3.500A) Processing helix chain 'G' and resid 639 through 642 removed outlier: 3.589A pdb=" N ASN G 642 " --> pdb=" O GLY G 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 639 through 642' Processing helix chain 'G' and resid 643 through 655 Processing helix chain 'G' and resid 656 through 658 No H-bonds generated for 'chain 'G' and resid 656 through 658' Processing helix chain 'G' and resid 692 through 707 Processing helix chain 'G' and resid 731 through 738 Processing helix chain 'G' and resid 741 through 752 Processing helix chain 'G' and resid 782 through 787 removed outlier: 3.760A pdb=" N SER G 786 " --> pdb=" O ASP G 783 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS G 787 " --> pdb=" O ASP G 784 " (cutoff:3.500A) Processing helix chain 'G' and resid 835 through 847 removed outlier: 3.675A pdb=" N ALA G 839 " --> pdb=" O SER G 835 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL G 843 " --> pdb=" O ALA G 839 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU G 844 " --> pdb=" O MET G 840 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU G 845 " --> pdb=" O ALA G 841 " (cutoff:3.500A) Processing helix chain 'G' and resid 848 through 850 No H-bonds generated for 'chain 'G' and resid 848 through 850' Processing helix chain 'G' and resid 860 through 868 removed outlier: 4.315A pdb=" N GLU G 864 " --> pdb=" O GLY G 860 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG G 866 " --> pdb=" O SER G 862 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU G 867 " --> pdb=" O TYR G 863 " (cutoff:3.500A) Processing helix chain 'G' and resid 871 through 892 removed outlier: 3.893A pdb=" N ALA G 877 " --> pdb=" O PRO G 873 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU G 878 " --> pdb=" O ALA G 874 " (cutoff:3.500A) Processing helix chain 'G' and resid 897 through 902 Processing helix chain 'G' and resid 904 through 918 removed outlier: 3.869A pdb=" N VAL G 908 " --> pdb=" O VAL G 904 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLY G 910 " --> pdb=" O LEU G 906 " (cutoff:3.500A) Processing helix chain 'G' and resid 923 through 955 removed outlier: 3.973A pdb=" N GLY G 955 " --> pdb=" O LEU G 951 " (cutoff:3.500A) Processing helix chain 'G' and resid 957 through 969 Processing helix chain 'G' and resid 970 through 989 Proline residue: G 986 - end of helix removed outlier: 3.915A pdb=" N ILE G 989 " --> pdb=" O VAL G 985 " (cutoff:3.500A) Processing helix chain 'G' and resid 994 through 1029 removed outlier: 3.735A pdb=" N GLN G 998 " --> pdb=" O GLY G 994 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY G1004 " --> pdb=" O ALA G1000 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE G1018 " --> pdb=" O VAL G1014 " (cutoff:3.500A) Proline residue: G1021 - end of helix Processing helix chain 'E' and resid 2 through 7 removed outlier: 4.325A pdb=" N ASP E 7 " --> pdb=" O LYS E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 28 removed outlier: 3.976A pdb=" N ALA E 12 " --> pdb=" O ARG E 8 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU E 28 " --> pdb=" O GLY E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 61 removed outlier: 3.514A pdb=" N VAL E 57 " --> pdb=" O SER E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 69 Processing helix chain 'E' and resid 99 through 115 removed outlier: 3.911A pdb=" N GLN E 112 " --> pdb=" O GLN E 108 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU E 113 " --> pdb=" O ASN E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 126 Processing helix chain 'E' and resid 150 through 162 Processing helix chain 'E' and resid 162 through 168 removed outlier: 4.087A pdb=" N ARG E 168 " --> pdb=" O ASP E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 195 Processing helix chain 'E' and resid 199 through 211 removed outlier: 3.681A pdb=" N ASN E 211 " --> pdb=" O ILE E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 247 Processing helix chain 'E' and resid 298 through 313 removed outlier: 3.517A pdb=" N THR E 302 " --> pdb=" O ASN E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 359 Processing helix chain 'E' and resid 361 through 370 removed outlier: 4.539A pdb=" N ILE E 367 " --> pdb=" O ARG E 363 " (cutoff:3.500A) Proline residue: E 368 - end of helix Processing helix chain 'E' and resid 372 through 386 Processing helix chain 'E' and resid 391 through 423 removed outlier: 4.209A pdb=" N GLY E 403 " --> pdb=" O VAL E 399 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL E 406 " --> pdb=" O ILE E 402 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP E 408 " --> pdb=" O LEU E 404 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA E 409 " --> pdb=" O LEU E 405 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU E 423 " --> pdb=" O VAL E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 452 removed outlier: 4.068A pdb=" N GLY E 436 " --> pdb=" O ARG E 432 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN E 437 " --> pdb=" O LYS E 433 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLY E 440 " --> pdb=" O GLY E 436 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA E 441 " --> pdb=" O GLN E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 459 removed outlier: 3.759A pdb=" N ALA E 457 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE E 458 " --> pdb=" O PRO E 455 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE E 459 " --> pdb=" O MET E 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 454 through 459' Processing helix chain 'E' and resid 460 through 488 removed outlier: 3.777A pdb=" N GLY E 464 " --> pdb=" O GLY E 460 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN E 469 " --> pdb=" O VAL E 465 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE E 470 " --> pdb=" O ILE E 466 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU E 486 " --> pdb=" O VAL E 482 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU E 488 " --> pdb=" O VAL E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 496 Processing helix chain 'E' and resid 512 through 537 removed outlier: 3.756A pdb=" N HIS E 537 " --> pdb=" O SER E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 559 removed outlier: 3.607A pdb=" N VAL E 546 " --> pdb=" O LEU E 542 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE E 559 " --> pdb=" O MET E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 601 removed outlier: 3.803A pdb=" N THR E 587 " --> pdb=" O SER E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 643 through 656 Processing helix chain 'E' and resid 692 through 708 Processing helix chain 'E' and resid 731 through 739 removed outlier: 3.750A pdb=" N ALA E 735 " --> pdb=" O ASP E 731 " (cutoff:3.500A) Processing helix chain 'E' and resid 742 through 752 Processing helix chain 'E' and resid 781 through 786 removed outlier: 3.786A pdb=" N LEU E 785 " --> pdb=" O PRO E 782 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER E 786 " --> pdb=" O ASP E 783 " (cutoff:3.500A) Processing helix chain 'E' and resid 835 through 847 removed outlier: 3.721A pdb=" N ALA E 839 " --> pdb=" O SER E 835 " (cutoff:3.500A) Processing helix chain 'E' and resid 848 through 850 No H-bonds generated for 'chain 'E' and resid 848 through 850' Processing helix chain 'E' and resid 860 through 871 Processing helix chain 'E' and resid 871 through 892 removed outlier: 3.594A pdb=" N LEU E 875 " --> pdb=" O GLN E 871 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR E 891 " --> pdb=" O LEU E 887 " (cutoff:3.500A) Processing helix chain 'E' and resid 894 through 903 Processing helix chain 'E' and resid 903 through 919 removed outlier: 4.221A pdb=" N GLY E 907 " --> pdb=" O VAL E 903 " (cutoff:3.500A) Processing helix chain 'E' and resid 923 through 954 removed outlier: 4.423A pdb=" N ILE E 944 " --> pdb=" O ASN E 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 957 through 990 removed outlier: 4.790A pdb=" N ARG E 971 " --> pdb=" O ARG E 967 " (cutoff:3.500A) Proline residue: E 972 - end of helix Proline residue: E 986 - end of helix removed outlier: 3.523A pdb=" N SER E 990 " --> pdb=" O PRO E 986 " (cutoff:3.500A) Processing helix chain 'E' and resid 995 through 1028 removed outlier: 4.937A pdb=" N GLY E1004 " --> pdb=" O ALA E1000 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL E1005 " --> pdb=" O ILE E1001 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE E1017 " --> pdb=" O THR E1013 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N PHE E1018 " --> pdb=" O VAL E1014 " (cutoff:3.500A) Proline residue: E1021 - end of helix Processing sheet with id=AA1, first strand: chain 'I' and resid 320 through 324 removed outlier: 3.691A pdb=" N ILE I 321 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLY I 16 " --> pdb=" O THR I 323 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL I 15 " --> pdb=" O LYS I 336 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL I 338 " --> pdb=" O VAL I 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 28 through 36 removed outlier: 11.202A pdb=" N GLU I 30 " --> pdb=" O PRO I 180 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR I 237 " --> pdb=" O SER I 225 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N SER I 225 " --> pdb=" O THR I 237 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG I 239 " --> pdb=" O GLU I 223 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS I 205 " --> pdb=" O GLN I 260 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLN I 260 " --> pdb=" O LYS I 205 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER I 207 " --> pdb=" O GLN I 258 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 39 through 43 removed outlier: 3.861A pdb=" N ARG I 39 " --> pdb=" O GLN I 169 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN I 169 " --> pdb=" O ARG I 39 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA I 165 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 69 through 71 removed outlier: 6.764A pdb=" N GLN I 70 " --> pdb=" O LEU I 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 276 through 277 removed outlier: 3.842A pdb=" N ALA I 283 " --> pdb=" O ILE I 299 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA I 285 " --> pdb=" O ARG I 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 301 through 305 removed outlier: 4.573A pdb=" N ARG I 303 " --> pdb=" O LEU I 310 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 320 through 324 removed outlier: 5.978A pdb=" N ILE J 322 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL J 18 " --> pdb=" O ILE J 322 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 23 through 31 removed outlier: 6.709A pdb=" N VAL J 25 " --> pdb=" O GLN J 265 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLN J 265 " --> pdb=" O VAL J 25 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU J 27 " --> pdb=" O VAL J 263 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL J 263 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR J 29 " --> pdb=" O GLU J 261 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU J 261 " --> pdb=" O THR J 29 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU J 31 " --> pdb=" O LEU J 259 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU J 259 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 33 through 43 removed outlier: 7.860A pdb=" N GLY J 33 " --> pdb=" O VAL J 175 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N VAL J 175 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N THR J 35 " --> pdb=" O ILE J 173 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N ILE J 173 " --> pdb=" O THR J 35 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N ALA J 37 " --> pdb=" O ASP J 171 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ASP J 171 " --> pdb=" O ALA J 37 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG J 39 " --> pdb=" O GLN J 169 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN J 169 " --> pdb=" O ARG J 39 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA J 165 " --> pdb=" O VAL J 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 33 through 43 removed outlier: 7.860A pdb=" N GLY J 33 " --> pdb=" O VAL J 175 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N VAL J 175 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N THR J 35 " --> pdb=" O ILE J 173 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N ILE J 173 " --> pdb=" O THR J 35 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N ALA J 37 " --> pdb=" O ASP J 171 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ASP J 171 " --> pdb=" O ALA J 37 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG J 39 " --> pdb=" O GLN J 169 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN J 169 " --> pdb=" O ARG J 39 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA J 165 " --> pdb=" O VAL J 43 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR J 237 " --> pdb=" O SER J 225 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N SER J 225 " --> pdb=" O THR J 237 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ARG J 239 " --> pdb=" O GLU J 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 69 through 71 removed outlier: 6.817A pdb=" N GLN J 70 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 275 through 277 Processing sheet with id=AB4, first strand: chain 'K' and resid 320 through 324 removed outlier: 5.843A pdb=" N ILE K 322 " --> pdb=" O VAL K 18 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL K 18 " --> pdb=" O ILE K 322 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 22 through 23 removed outlier: 4.498A pdb=" N ILE K 268 " --> pdb=" O VAL K 311 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG K 303 " --> pdb=" O LEU K 310 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 61 through 62 removed outlier: 3.534A pdb=" N GLY K 143 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N GLN K 168 " --> pdb=" O GLU K 42 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N GLU K 42 " --> pdb=" O GLN K 168 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N LEU K 170 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 11.034A pdb=" N ILE K 40 " --> pdb=" O LEU K 170 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE K 38 " --> pdb=" O PRO K 172 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG K 34 " --> pdb=" O ASP K 176 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N GLU K 30 " --> pdb=" O PRO K 180 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER K 207 " --> pdb=" O GLN K 258 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 61 through 62 removed outlier: 3.534A pdb=" N GLY K 143 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N PHE K 224 " --> pdb=" O ARG K 239 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL K 241 " --> pdb=" O LEU K 222 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU K 222 " --> pdb=" O VAL K 241 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 51 through 54 removed outlier: 6.714A pdb=" N GLN K 70 " --> pdb=" O LEU K 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 275 through 277 removed outlier: 3.694A pdb=" N ALA K 285 " --> pdb=" O ARG K 297 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG K 297 " --> pdb=" O ALA K 285 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 14 through 16 Processing sheet with id=AC2, first strand: chain 'L' and resid 18 through 20 removed outlier: 4.867A pdb=" N LEU L 20 " --> pdb=" O ASP L 319 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP L 319 " --> pdb=" O LEU L 20 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 301 through 305 removed outlier: 4.783A pdb=" N ARG L 303 " --> pdb=" O LEU L 310 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL L 311 " --> pdb=" O ILE L 268 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE L 268 " --> pdb=" O VAL L 311 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLN L 260 " --> pdb=" O LYS L 205 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LYS L 205 " --> pdb=" O GLN L 260 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU L 208 " --> pdb=" O LEU L 218 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU L 218 " --> pdb=" O LEU L 208 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY L 220 " --> pdb=" O PRO L 243 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU L 222 " --> pdb=" O VAL L 241 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL L 241 " --> pdb=" O LEU L 222 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE L 224 " --> pdb=" O ARG L 239 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N GLN L 168 " --> pdb=" O GLU L 42 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N GLU L 42 " --> pdb=" O GLN L 168 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N LEU L 170 " --> pdb=" O ILE L 40 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N ILE L 40 " --> pdb=" O LEU L 170 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE L 38 " --> pdb=" O PRO L 172 " (cutoff:3.500A) removed outlier: 11.864A pdb=" N GLU L 30 " --> pdb=" O PRO L 180 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLN L 23 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLN L 265 " --> pdb=" O GLN L 23 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL L 25 " --> pdb=" O VAL L 263 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL L 263 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU L 27 " --> pdb=" O GLU L 261 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR L 29 " --> pdb=" O LEU L 259 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU L 259 " --> pdb=" O THR L 29 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 51 through 54 removed outlier: 6.504A pdb=" N GLN L 70 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 61 through 62 Processing sheet with id=AC6, first strand: chain 'L' and resid 275 through 277 removed outlier: 3.944A pdb=" N ALA L 283 " --> pdb=" O ILE L 299 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 287 through 288 Processing sheet with id=AC8, first strand: chain 'M' and resid 14 through 16 removed outlier: 6.736A pdb=" N VAL M 15 " --> pdb=" O VAL M 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'M' and resid 205 through 206 removed outlier: 3.526A pdb=" N ARG M 239 " --> pdb=" O GLU M 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 205 through 206 removed outlier: 3.526A pdb=" N ARG M 239 " --> pdb=" O GLU M 223 " (cutoff:3.500A) removed outlier: 11.697A pdb=" N GLU M 30 " --> pdb=" O PRO M 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 41 through 43 removed outlier: 4.312A pdb=" N ALA M 165 " --> pdb=" O VAL M 43 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 49 through 50 Processing sheet with id=AD4, first strand: chain 'M' and resid 268 through 270 removed outlier: 4.649A pdb=" N ILE M 268 " --> pdb=" O VAL M 311 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 276 through 277 Processing sheet with id=AD6, first strand: chain 'M' and resid 276 through 277 removed outlier: 4.629A pdb=" N LYS M 320 " --> pdb=" O VAL M 288 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 294 through 295 removed outlier: 3.517A pdb=" N VAL N 287 " --> pdb=" O GLU N 295 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LYS N 320 " --> pdb=" O VAL N 288 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLY N 16 " --> pdb=" O THR N 323 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 23 through 31 removed outlier: 6.658A pdb=" N VAL N 25 " --> pdb=" O GLN N 265 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLN N 265 " --> pdb=" O VAL N 25 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU N 27 " --> pdb=" O VAL N 263 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL N 263 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N THR N 29 " --> pdb=" O GLU N 261 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU N 261 " --> pdb=" O THR N 29 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU N 31 " --> pdb=" O LEU N 259 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU N 259 " --> pdb=" O LEU N 31 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE N 268 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL N 311 " --> pdb=" O ILE N 268 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG N 303 " --> pdb=" O LEU N 310 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 33 through 36 removed outlier: 6.808A pdb=" N THR N 237 " --> pdb=" O SER N 225 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER N 225 " --> pdb=" O THR N 237 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ARG N 239 " --> pdb=" O GLU N 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 39 through 42 removed outlier: 3.765A pdb=" N ARG N 39 " --> pdb=" O GLN N 169 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 49 through 50 Processing sheet with id=AE3, first strand: chain 'N' and resid 275 through 277 Processing sheet with id=AE4, first strand: chain 'B' and resid 331 through 335 removed outlier: 3.616A pdb=" N LEU B 332 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE A 88 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 89 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 93 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 99 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 110 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP A 324 " --> pdb=" O ARG C 98 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE C 88 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY C 116 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN C 97 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 110 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 310 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 124 through 126 removed outlier: 4.183A pdb=" N ILE A 300 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 110 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 99 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 93 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 89 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 94 " --> pdb=" O PRO B 328 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN B 327 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 124 through 125 removed outlier: 4.043A pdb=" N ALA B 110 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU B 99 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE C 300 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TRP C 124 " --> pdb=" O LEU C 302 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 128 through 130 removed outlier: 3.705A pdb=" N VAL F 47 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU F 816 " --> pdb=" O ALA F 823 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLU F 829 " --> pdb=" O ARG F 714 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ARG F 714 " --> pdb=" O GLU F 829 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 128 through 130 removed outlier: 3.705A pdb=" N VAL F 47 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU F 816 " --> pdb=" O ALA F 823 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 172 through 177 removed outlier: 3.615A pdb=" N ASP F 174 " --> pdb=" O LYS F 292 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER F 144 " --> pdb=" O PRO F 285 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET F 138 " --> pdb=" O ILE F 291 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL F 139 " --> pdb=" O PRO F 326 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 172 through 177 removed outlier: 3.615A pdb=" N ASP F 174 " --> pdb=" O LYS F 292 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA F 286 " --> pdb=" O ALA F 279 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA F 279 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN F 278 " --> pdb=" O THR F 613 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR F 613 " --> pdb=" O ASN F 278 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 266 through 272 removed outlier: 3.615A pdb=" N ASP F 267 " --> pdb=" O TRP F 187 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP F 187 " --> pdb=" O ASP F 267 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N TYR F 182 " --> pdb=" O VAL F 767 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG F 769 " --> pdb=" O TYR F 182 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR F 771 " --> pdb=" O MET F 184 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN F 759 " --> pdb=" O VAL F 770 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU F 772 " --> pdb=" O TYR F 757 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR F 757 " --> pdb=" O LEU F 772 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 252 through 253 removed outlier: 3.906A pdb=" N LYS F 252 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 723 through 730 removed outlier: 3.690A pdb=" N GLY F 811 " --> pdb=" O GLU F 723 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN F 725 " --> pdb=" O GLU F 809 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 789 through 791 Processing sheet with id=AF6, first strand: chain 'G' and resid 128 through 131 removed outlier: 3.656A pdb=" N VAL G 47 " --> pdb=" O MET G 88 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER G 79 " --> pdb=" O THR G 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR G 77 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU G 816 " --> pdb=" O ALA G 823 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU G 829 " --> pdb=" O ARG G 714 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ARG G 714 " --> pdb=" O GLU G 829 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 128 through 131 removed outlier: 3.656A pdb=" N VAL G 47 " --> pdb=" O MET G 88 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER G 79 " --> pdb=" O THR G 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR G 77 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU G 816 " --> pdb=" O ALA G 823 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU G 682 " --> pdb=" O ILE G 826 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY G 828 " --> pdb=" O PHE G 680 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE G 680 " --> pdb=" O GLY G 828 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 175 through 177 removed outlier: 3.831A pdb=" N MET G 138 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL G 139 " --> pdb=" O PRO G 326 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 175 through 177 removed outlier: 4.715A pdb=" N ALA G 279 " --> pdb=" O ALA G 286 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER G 624 " --> pdb=" O GLY G 614 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 266 through 272 removed outlier: 3.583A pdb=" N TRP G 187 " --> pdb=" O ASP G 267 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY G 269 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 218 through 219 removed outlier: 4.103A pdb=" N THR G 233 " --> pdb=" O PRO E 724 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU E 728 " --> pdb=" O ILE G 235 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 252 through 253 removed outlier: 3.632A pdb=" N LYS G 252 " --> pdb=" O VAL G 260 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 723 through 730 removed outlier: 3.671A pdb=" N THR G 805 " --> pdb=" O GLU G 729 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 760 through 762 Processing sheet with id=AG6, first strand: chain 'G' and resid 790 through 791 Processing sheet with id=AG7, first strand: chain 'E' and resid 131 through 132 removed outlier: 4.272A pdb=" N ALA E 42 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER E 79 " --> pdb=" O THR E 91 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG E 817 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 172 through 178 removed outlier: 4.437A pdb=" N ASP E 174 " --> pdb=" O LYS E 292 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY E 288 " --> pdb=" O PHE E 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER E 287 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL E 139 " --> pdb=" O PRO E 326 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 172 through 178 removed outlier: 4.437A pdb=" N ASP E 174 " --> pdb=" O LYS E 292 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY E 288 " --> pdb=" O PHE E 178 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA E 286 " --> pdb=" O ALA E 279 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA E 279 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER E 608 " --> pdb=" O MET E 630 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 266 through 272 removed outlier: 7.459A pdb=" N TYR E 182 " --> pdb=" O ARG E 769 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N TYR E 771 " --> pdb=" O TYR E 182 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N MET E 184 " --> pdb=" O TYR E 771 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N GLN E 773 " --> pdb=" O MET E 184 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE E 186 " --> pdb=" O GLN E 773 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 250 through 253 removed outlier: 6.822A pdb=" N VAL E 260 " --> pdb=" O LEU E 251 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 682 through 686 removed outlier: 3.664A pdb=" N SER E 857 " --> pdb=" O PHE E 683 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 712 through 713 Processing sheet with id=AH5, first strand: chain 'E' and resid 789 through 791 2840 hydrogen bonds defined for protein. 8298 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: 24.65 Time building geometry restraints manager: 18.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14591 1.34 - 1.46: 7987 1.46 - 1.57: 26995 1.57 - 1.69: 0 1.69 - 1.81: 270 Bond restraints: 49843 Sorted by residual: bond pdb=" C ALA F 539 " pdb=" N PRO F 540 " ideal model delta sigma weight residual 1.336 1.393 -0.057 1.20e-02 6.94e+03 2.22e+01 bond pdb=" C LEU F 454 " pdb=" N PRO F 455 " ideal model delta sigma weight residual 1.337 1.380 -0.044 9.80e-03 1.04e+04 1.99e+01 bond pdb=" C VAL F 985 " pdb=" N PRO F 986 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.49e+00 bond pdb=" CG LEU C 389 " pdb=" CD1 LEU C 389 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.69e+00 bond pdb=" CB VAL E 770 " pdb=" CG2 VAL E 770 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.64e+00 ... (remaining 49838 not shown) Histogram of bond angle deviations from ideal: 95.41 - 103.54: 656 103.54 - 111.66: 21402 111.66 - 119.78: 21990 119.78 - 127.91: 23401 127.91 - 136.03: 272 Bond angle restraints: 67721 Sorted by residual: angle pdb=" N THR E 115 " pdb=" CA THR E 115 " pdb=" C THR E 115 " ideal model delta sigma weight residual 113.57 121.19 -7.62 1.38e+00 5.25e-01 3.05e+01 angle pdb=" C VAL E 903 " pdb=" N VAL E 904 " pdb=" CA VAL E 904 " ideal model delta sigma weight residual 120.33 124.44 -4.11 8.00e-01 1.56e+00 2.63e+01 angle pdb=" CA LYS L 136 " pdb=" CB LYS L 136 " pdb=" CG LYS L 136 " ideal model delta sigma weight residual 114.10 123.01 -8.91 2.00e+00 2.50e-01 1.98e+01 angle pdb=" N GLU F 314 " pdb=" CA GLU F 314 " pdb=" C GLU F 314 " ideal model delta sigma weight residual 109.81 119.25 -9.44 2.21e+00 2.05e-01 1.83e+01 angle pdb=" C GLY E 506 " pdb=" N GLU E 507 " pdb=" CA GLU E 507 " ideal model delta sigma weight residual 121.54 129.57 -8.03 1.91e+00 2.74e-01 1.77e+01 ... (remaining 67716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 28127 16.08 - 32.16: 1519 32.16 - 48.24: 429 48.24 - 64.31: 16 64.31 - 80.39: 61 Dihedral angle restraints: 30152 sinusoidal: 11683 harmonic: 18469 Sorted by residual: dihedral pdb=" CA ASP K 171 " pdb=" C ASP K 171 " pdb=" N PRO K 172 " pdb=" CA PRO K 172 " ideal model delta harmonic sigma weight residual 180.00 140.63 39.37 0 5.00e+00 4.00e-02 6.20e+01 dihedral pdb=" CA ASP M 171 " pdb=" C ASP M 171 " pdb=" N PRO M 172 " pdb=" CA PRO M 172 " ideal model delta harmonic sigma weight residual 180.00 141.03 38.97 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CA ASP J 171 " pdb=" C ASP J 171 " pdb=" N PRO J 172 " pdb=" CA PRO J 172 " ideal model delta harmonic sigma weight residual 180.00 149.24 30.76 0 5.00e+00 4.00e-02 3.79e+01 ... (remaining 30149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 6010 0.064 - 0.127: 1581 0.127 - 0.191: 259 0.191 - 0.255: 50 0.255 - 0.318: 8 Chirality restraints: 7908 Sorted by residual: chirality pdb=" CA PHE I 224 " pdb=" N PHE I 224 " pdb=" C PHE I 224 " pdb=" CB PHE I 224 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CB ILE E 78 " pdb=" CA ILE E 78 " pdb=" CG1 ILE E 78 " pdb=" CG2 ILE E 78 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB VAL F 821 " pdb=" CA VAL F 821 " pdb=" CG1 VAL F 821 " pdb=" CG2 VAL F 821 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 7905 not shown) Planarity restraints: 8856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP K 171 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.71e+01 pdb=" N PRO K 172 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO K 172 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO K 172 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP M 171 " -0.061 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO M 172 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO M 172 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO M 172 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 171 " 0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO J 172 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO J 172 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO J 172 " 0.048 5.00e-02 4.00e+02 ... (remaining 8853 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 2 2.04 - 2.75: 6155 2.75 - 3.47: 66857 3.47 - 4.18: 111148 4.18 - 4.90: 200334 Nonbonded interactions: 384496 Sorted by model distance: nonbonded pdb=" OE1 GLU J 190 " pdb=" NE2 GLN J 195 " model vdw 1.322 2.520 nonbonded pdb=" OE2 GLU J 190 " pdb=" CG GLN J 195 " model vdw 1.827 3.440 nonbonded pdb=" CD GLU J 190 " pdb=" NE2 GLN J 195 " model vdw 2.163 3.350 nonbonded pdb=" OD1 ASP F 153 " pdb=" OH TYR F 182 " model vdw 2.242 2.440 nonbonded pdb=" OG SER B 134 " pdb=" O ALA B 287 " model vdw 2.245 2.440 ... (remaining 384491 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' } ncs_group { reference = (chain 'E' and (resid 1 through 499 or resid 506 through 1030)) selection = chain 'F' selection = (chain 'G' and (resid 1 through 499 or resid 506 through 1030)) } ncs_group { reference = (chain 'I' and (resid 12 through 338 or (resid 339 and (name N or name CA or nam \ e C or name CB or name CG or name CD )) or resid 340)) selection = (chain 'J' and (resid 12 through 338 or (resid 339 and (name N or name CA or nam \ e C or name CB or name CG or name CD )) or resid 340)) selection = (chain 'K' and (resid 12 through 338 or (resid 339 and (name N or name CA or nam \ e C or name CB or name CG or name CD )) or resid 340)) selection = (chain 'L' and (resid 12 through 338 or (resid 339 and (name N or name CA or nam \ e C or name CB or name CG or name CD )) or resid 340)) selection = (chain 'M' and (resid 12 through 338 or (resid 339 and (name N or name CA or nam \ e C or name CB or name CG or name CD )) or resid 340)) selection = (chain 'N' and resid 12 through 340) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 15.210 Check model and map are aligned: 0.790 Set scattering table: 0.480 Process input model: 130.740 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 : 0.007 0.083 49843 Z= 0.424 Angle : 1.042 15.222 67721 Z= 0.534 Chirality : 0.060 0.318 7908 Planarity : 0.008 0.104 8856 Dihedral : 11.565 80.392 18294 Min Nonbonded Distance : 1.322 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.35 % Allowed : 6.40 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 1.04 % 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: -3.61 (0.08), residues: 6415 helix: -1.95 (0.07), residues: 2813 sheet: -2.77 (0.14), residues: 1002 loop : -2.56 (0.10), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP M 309 HIS 0.015 0.003 HIS A 280 PHE 0.052 0.003 PHE I 224 TYR 0.053 0.003 TYR E 467 ARG 0.014 0.001 ARG N 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 586 time to evaluate : 5.135 Fit side-chains TARDY: cannot create tardy model for: "ASP J 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP K 72 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP M 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP N 72 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 99 LEU cc_start: 0.7986 (tt) cc_final: 0.7307 (mt) REVERT: I 205 LYS cc_start: 0.8225 (mttt) cc_final: 0.7976 (mtmt) REVERT: J 14 GLU cc_start: 0.7239 (tt0) cc_final: 0.6950 (tt0) REVERT: J 152 GLU cc_start: 0.7593 (mp0) cc_final: 0.7231 (mp0) REVERT: J 186 ARG cc_start: 0.7304 (ttp-170) cc_final: 0.6623 (ttm-80) REVERT: J 205 LYS cc_start: 0.7675 (mmtt) cc_final: 0.6915 (mttt) REVERT: K 131 ASN cc_start: 0.8316 (t0) cc_final: 0.7717 (m-40) REVERT: K 191 LEU cc_start: 0.8481 (mm) cc_final: 0.8185 (mp) REVERT: L 324 GLU cc_start: 0.8074 (tt0) cc_final: 0.7654 (tt0) REVERT: M 58 GLU cc_start: 0.6413 (pm20) cc_final: 0.6057 (pt0) REVERT: M 98 LYS cc_start: 0.8424 (ttmt) cc_final: 0.8222 (tttp) REVERT: N 14 GLU cc_start: 0.7523 (pp20) cc_final: 0.6964 (pt0) REVERT: N 21 GLU cc_start: 0.7570 (pp20) cc_final: 0.7354 (pt0) REVERT: N 221 ARG cc_start: 0.8162 (ttp-170) cc_final: 0.7499 (ttt90) REVERT: N 324 GLU cc_start: 0.7441 (pm20) cc_final: 0.7172 (pt0) REVERT: B 283 MET cc_start: 0.7200 (mmt) cc_final: 0.6971 (mmp) REVERT: C 1 CYS cc_start: 0.6680 (p) cc_final: 0.5854 (m) REVERT: C 226 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7446 (tp) REVERT: C 444 LYS cc_start: 0.7901 (tmmm) cc_final: 0.7593 (ttpt) REVERT: F 69 MET cc_start: 0.8661 (mmp) cc_final: 0.8337 (mmt) REVERT: F 164 ASP cc_start: 0.8012 (m-30) cc_final: 0.7771 (m-30) REVERT: F 350 LEU cc_start: 0.4516 (mt) cc_final: 0.4115 (mt) REVERT: F 447 MET cc_start: 0.3214 (mtp) cc_final: 0.2926 (mtp) REVERT: F 519 MET cc_start: 0.0264 (tmt) cc_final: -0.0158 (tmt) REVERT: F 563 PHE cc_start: 0.6946 (t80) cc_final: 0.6709 (t80) REVERT: F 568 ASP cc_start: 0.7503 (t0) cc_final: 0.7170 (t0) REVERT: F 767 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8203 (p) REVERT: F 787 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8361 (mttm) REVERT: F 792 ASN cc_start: 0.8288 (t0) cc_final: 0.8078 (t0) REVERT: F 824 MET cc_start: 0.7820 (mpt) cc_final: 0.7373 (mmm) REVERT: F 1015 LEU cc_start: 0.5659 (tp) cc_final: 0.5312 (tp) REVERT: G 20 MET cc_start: 0.4973 (mmt) cc_final: 0.4616 (ttm) REVERT: G 456 MET cc_start: 0.7911 (tmt) cc_final: 0.7578 (ttp) REVERT: G 519 MET cc_start: 0.3354 (ppp) cc_final: 0.2984 (tpt) REVERT: G 714 ARG cc_start: 0.8076 (ttt180) cc_final: 0.7602 (tpp80) REVERT: G 780 MET cc_start: 0.8867 (mmp) cc_final: 0.8458 (mmp) REVERT: G 807 LYS cc_start: 0.8592 (pttp) cc_final: 0.8381 (pttm) REVERT: E 110 LYS cc_start: 0.7565 (mmtp) cc_final: 0.6958 (mmmm) REVERT: E 134 LYS cc_start: 0.7754 (mmmm) cc_final: 0.7200 (mppt) REVERT: E 388 PHE cc_start: 0.7844 (m-10) cc_final: 0.7575 (m-80) REVERT: E 420 MET cc_start: 0.6620 (ttp) cc_final: 0.6183 (mtp) REVERT: E 594 MET cc_start: 0.8004 (ttm) cc_final: 0.7688 (ttp) REVERT: E 784 ASP cc_start: 0.8091 (t0) cc_final: 0.7492 (t0) outliers start: 18 outliers final: 5 residues processed: 601 average time/residue: 0.6171 time to fit residues: 604.2752 Evaluate side-chains 402 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 395 time to evaluate : 4.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 767 VAL Chi-restraints excluded: chain F residue 964 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 540 optimal weight: 4.9990 chunk 485 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 327 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 501 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 305 optimal weight: 0.1980 chunk 373 optimal weight: 0.9980 chunk 581 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 23 GLN I 169 GLN I 289 ASN I 292 ASN J 84 GLN J 247 ASN J 258 GLN K 28 ASN K 46 GLN K 168 GLN K 256 HIS K 291 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 120 GLN L 282 GLN ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 215 GLN M 260 GLN N 120 GLN N 168 GLN N 256 HIS N 272 GLN A 59 ASN A 114 GLN A 232 ASN A 354 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN B 59 ASN B 232 ASN B 327 GLN B 354 ASN C 20 GLN C 327 GLN C 354 ASN ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN F 415 ASN F 469 GLN F 508 HIS ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 801 ASN ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 248 ASN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN ** G 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 685 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN E 439 GLN E 537 HIS E 588 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 49843 Z= 0.265 Angle : 0.661 14.287 67721 Z= 0.333 Chirality : 0.045 0.227 7908 Planarity : 0.005 0.080 8856 Dihedral : 5.433 57.059 6935 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.63 % Allowed : 9.53 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.10), residues: 6415 helix: 0.08 (0.09), residues: 2850 sheet: -2.36 (0.15), residues: 984 loop : -2.12 (0.11), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 309 HIS 0.007 0.001 HIS A 280 PHE 0.036 0.002 PHE I 224 TYR 0.023 0.002 TYR F 49 ARG 0.007 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 396 time to evaluate : 5.199 Fit side-chains TARDY: cannot create tardy model for: "ASP J 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP K 72 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP N 72 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: I 99 LEU cc_start: 0.8034 (tt) cc_final: 0.7312 (mt) REVERT: J 14 GLU cc_start: 0.7236 (tt0) cc_final: 0.6986 (tt0) REVERT: J 152 GLU cc_start: 0.7562 (mp0) cc_final: 0.7262 (mp0) REVERT: J 186 ARG cc_start: 0.7248 (ttp-170) cc_final: 0.6491 (ttm-80) REVERT: J 205 LYS cc_start: 0.7415 (mmtt) cc_final: 0.6742 (mttt) REVERT: K 131 ASN cc_start: 0.8343 (t0) cc_final: 0.7811 (m-40) REVERT: K 189 ARG cc_start: 0.6720 (mtm110) cc_final: 0.5613 (ttt90) REVERT: K 191 LEU cc_start: 0.8420 (mm) cc_final: 0.8067 (mp) REVERT: L 190 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: L 246 ASN cc_start: 0.8451 (p0) cc_final: 0.7689 (m-40) REVERT: L 300 LYS cc_start: 0.7533 (ptmm) cc_final: 0.6933 (mmtt) REVERT: M 98 LYS cc_start: 0.8413 (ttmt) cc_final: 0.8134 (tttp) REVERT: M 196 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7399 (tt) REVERT: A 111 ILE cc_start: 0.7024 (mp) cc_final: 0.6528 (pt) REVERT: A 168 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7607 (tt) REVERT: A 282 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6940 (tp) REVERT: B 234 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7757 (tp) REVERT: B 283 MET cc_start: 0.7181 (mmt) cc_final: 0.6285 (mtm) REVERT: C 1 CYS cc_start: 0.6399 (p) cc_final: 0.5503 (m) REVERT: C 168 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7269 (tp) REVERT: C 175 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7888 (tp) REVERT: C 220 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8114 (tp) REVERT: C 226 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7538 (tp) REVERT: C 428 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8419 (tt) REVERT: C 444 LYS cc_start: 0.8061 (tmmm) cc_final: 0.7562 (tttt) REVERT: F 69 MET cc_start: 0.8748 (mmp) cc_final: 0.8352 (mmt) REVERT: F 447 MET cc_start: 0.3365 (mtp) cc_final: 0.2992 (mtp) REVERT: F 519 MET cc_start: -0.0087 (tmt) cc_final: -0.0475 (tmt) REVERT: F 563 PHE cc_start: 0.6988 (t80) cc_final: 0.6736 (t80) REVERT: F 605 SER cc_start: 0.8303 (m) cc_final: 0.8012 (t) REVERT: F 931 LEU cc_start: 0.6387 (OUTLIER) cc_final: 0.5953 (mm) REVERT: G 192 LYS cc_start: 0.7901 (mtpt) cc_final: 0.7586 (mtmt) REVERT: G 552 MET cc_start: 0.3817 (ttt) cc_final: 0.3422 (ttm) REVERT: G 751 ILE cc_start: 0.8346 (tt) cc_final: 0.8074 (tt) REVERT: G 780 MET cc_start: 0.8816 (mmp) cc_final: 0.8371 (mmp) REVERT: G 920 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.6062 (mp) REVERT: E 110 LYS cc_start: 0.7572 (mmtp) cc_final: 0.7101 (mmtp) REVERT: E 134 LYS cc_start: 0.7742 (mmmm) cc_final: 0.7181 (mppt) REVERT: E 358 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.5836 (t80) REVERT: E 404 LEU cc_start: 0.6232 (mt) cc_final: 0.5796 (mt) REVERT: E 626 MET cc_start: 0.7427 (ttm) cc_final: 0.7200 (ttt) REVERT: E 731 ASP cc_start: 0.8019 (p0) cc_final: 0.7790 (p0) REVERT: E 784 ASP cc_start: 0.8118 (t0) cc_final: 0.7435 (t0) REVERT: E 881 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6292 (tp) REVERT: E 968 MET cc_start: 0.5722 (mmm) cc_final: 0.4733 (ptm) outliers start: 137 outliers final: 52 residues processed: 513 average time/residue: 0.5656 time to fit residues: 497.3681 Evaluate side-chains 414 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 348 time to evaluate : 5.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 292 ASN Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 233 THR Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 391 ASN Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 862 SER Chi-restraints excluded: chain F residue 931 LEU Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 612 VAL Chi-restraints excluded: chain G residue 750 SER Chi-restraints excluded: chain G residue 756 SER Chi-restraints excluded: chain G residue 887 LEU Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 568 ASP Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 868 SER Chi-restraints excluded: chain E residue 879 SER Chi-restraints excluded: chain E residue 881 LEU Chi-restraints excluded: chain E residue 890 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 322 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 483 optimal weight: 4.9990 chunk 395 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 582 optimal weight: 2.9990 chunk 628 optimal weight: 5.9990 chunk 518 optimal weight: 0.7980 chunk 577 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 467 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 247 ASN I 260 GLN I 292 ASN J 109 GLN J 120 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 GLN ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 215 GLN N 84 GLN N 127 GLN N 169 GLN A 48 GLN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN B 27 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 ASN G 248 ASN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 685 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 998 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 49843 Z= 0.327 Angle : 0.674 13.921 67721 Z= 0.337 Chirality : 0.046 0.424 7908 Planarity : 0.005 0.099 8856 Dihedral : 5.222 56.628 6928 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.84 % Allowed : 10.78 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -1.22 (0.10), residues: 6415 helix: 0.72 (0.09), residues: 2838 sheet: -2.19 (0.15), residues: 1001 loop : -1.95 (0.11), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 324 HIS 0.006 0.001 HIS F 999 PHE 0.034 0.002 PHE I 224 TYR 0.024 0.002 TYR G 182 ARG 0.007 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 385 time to evaluate : 5.231 Fit side-chains TARDY: cannot create tardy model for: "ASP J 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP K 72 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP N 72 " (corrupted residue). Skipping it. REVERT: I 99 LEU cc_start: 0.8064 (tt) cc_final: 0.7248 (mt) REVERT: I 324 GLU cc_start: 0.6132 (mt-10) cc_final: 0.5060 (tm-30) REVERT: J 14 GLU cc_start: 0.7268 (tt0) cc_final: 0.6964 (tt0) REVERT: J 87 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7523 (tp) REVERT: J 186 ARG cc_start: 0.7275 (ttp-170) cc_final: 0.6534 (ttm-80) REVERT: J 205 LYS cc_start: 0.7506 (mmtt) cc_final: 0.6793 (mttt) REVERT: K 131 ASN cc_start: 0.8315 (t0) cc_final: 0.7875 (m-40) REVERT: K 189 ARG cc_start: 0.6838 (mtm110) cc_final: 0.6564 (mtm110) REVERT: K 191 LEU cc_start: 0.8438 (mm) cc_final: 0.8059 (mp) REVERT: L 15 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8400 (m) REVERT: L 47 VAL cc_start: 0.8262 (OUTLIER) cc_final: 0.8051 (m) REVERT: L 110 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7307 (pt0) REVERT: L 246 ASN cc_start: 0.8319 (p0) cc_final: 0.7876 (m-40) REVERT: L 300 LYS cc_start: 0.7528 (ptmm) cc_final: 0.7092 (mmtt) REVERT: M 58 GLU cc_start: 0.6932 (pm20) cc_final: 0.6577 (pt0) REVERT: M 98 LYS cc_start: 0.8383 (ttmt) cc_final: 0.8053 (tttp) REVERT: M 196 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7353 (tt) REVERT: N 87 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7771 (tp) REVERT: N 98 LYS cc_start: 0.7987 (tppt) cc_final: 0.7695 (ttmt) REVERT: A 111 ILE cc_start: 0.7119 (mp) cc_final: 0.6648 (pt) REVERT: A 157 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6690 (tt) REVERT: A 168 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7614 (tt) REVERT: A 220 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7215 (tp) REVERT: A 282 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7003 (tp) REVERT: A 421 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8148 (tp) REVERT: B 49 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7280 (tt) REVERT: B 144 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8063 (mt) REVERT: B 220 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7690 (tp) REVERT: B 226 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7207 (tp) REVERT: B 234 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7745 (tp) REVERT: B 283 MET cc_start: 0.7171 (mmt) cc_final: 0.6326 (mtm) REVERT: C 1 CYS cc_start: 0.6265 (p) cc_final: 0.5366 (m) REVERT: C 168 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7301 (tp) REVERT: C 175 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7954 (tp) REVERT: C 220 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8134 (tp) REVERT: C 226 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7531 (tp) REVERT: C 414 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7549 (tm) REVERT: C 428 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8440 (tt) REVERT: F 69 MET cc_start: 0.8707 (mmp) cc_final: 0.8353 (mmt) REVERT: F 447 MET cc_start: 0.3502 (mtp) cc_final: 0.3184 (mtp) REVERT: F 519 MET cc_start: 0.0283 (tmt) cc_final: -0.0157 (tmt) REVERT: F 563 PHE cc_start: 0.6886 (t80) cc_final: 0.6546 (t80) REVERT: F 622 GLN cc_start: 0.8149 (tt0) cc_final: 0.7753 (tt0) REVERT: G 20 MET cc_start: 0.5533 (ttm) cc_final: 0.5181 (mtm) REVERT: G 127 ILE cc_start: 0.8401 (mm) cc_final: 0.8048 (mm) REVERT: G 344 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.5507 (tt) REVERT: G 552 MET cc_start: 0.4211 (ttt) cc_final: 0.3976 (mtp) REVERT: G 630 MET cc_start: 0.7364 (mmm) cc_final: 0.6855 (mmt) REVERT: G 751 ILE cc_start: 0.8455 (tt) cc_final: 0.8200 (tt) REVERT: G 780 MET cc_start: 0.8815 (mmp) cc_final: 0.8408 (mmp) REVERT: G 865 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6377 (mt-10) REVERT: E 17 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7506 (pp) REVERT: E 110 LYS cc_start: 0.7651 (mmtp) cc_final: 0.7054 (mmtp) REVERT: E 134 LYS cc_start: 0.7762 (mmmm) cc_final: 0.7490 (mtpp) REVERT: E 149 MET cc_start: 0.7701 (ptp) cc_final: 0.7471 (ptp) REVERT: E 250 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8140 (pp) REVERT: E 358 PHE cc_start: 0.6615 (OUTLIER) cc_final: 0.5151 (t80) REVERT: E 404 LEU cc_start: 0.6168 (mt) cc_final: 0.5953 (mt) REVERT: E 414 GLU cc_start: 0.7479 (tm-30) cc_final: 0.6814 (tm-30) REVERT: E 544 ILE cc_start: 0.5464 (OUTLIER) cc_final: 0.5179 (tt) REVERT: E 745 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7688 (mt) REVERT: E 784 ASP cc_start: 0.8258 (t0) cc_final: 0.7663 (t0) REVERT: E 881 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6306 (tp) REVERT: E 893 SER cc_start: 0.8291 (t) cc_final: 0.8081 (m) REVERT: E 968 MET cc_start: 0.5878 (mmm) cc_final: 0.4967 (ptm) outliers start: 200 outliers final: 98 residues processed: 551 average time/residue: 0.5257 time to fit residues: 505.8665 Evaluate side-chains 486 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 358 time to evaluate : 4.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 110 GLN Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 310 LEU Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 233 THR Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 391 ASN Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 496 MET Chi-restraints excluded: chain F residue 571 VAL Chi-restraints excluded: chain F residue 740 VAL Chi-restraints excluded: chain F residue 758 VAL Chi-restraints excluded: chain F residue 862 SER Chi-restraints excluded: chain F residue 921 SER Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 612 VAL Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain G residue 682 LEU Chi-restraints excluded: chain G residue 750 SER Chi-restraints excluded: chain G residue 756 SER Chi-restraints excluded: chain G residue 847 VAL Chi-restraints excluded: chain G residue 865 GLU Chi-restraints excluded: chain G residue 984 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 568 ASP Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 745 ILE Chi-restraints excluded: chain E residue 868 SER Chi-restraints excluded: chain E residue 879 SER Chi-restraints excluded: chain E residue 881 LEU Chi-restraints excluded: chain E residue 890 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 575 optimal weight: 4.9990 chunk 437 optimal weight: 2.9990 chunk 302 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 277 optimal weight: 4.9990 chunk 390 optimal weight: 0.9980 chunk 584 optimal weight: 4.9990 chunk 618 optimal weight: 4.9990 chunk 305 optimal weight: 0.8980 chunk 553 optimal weight: 5.9990 chunk 166 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 46 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 215 GLN N 91 GLN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN F 927 GLN G 67 GLN G 74 ASN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 248 ASN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 308 GLN G 312 ASN G 685 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 GLN ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 49843 Z= 0.196 Angle : 0.587 12.346 67721 Z= 0.290 Chirality : 0.043 0.198 7908 Planarity : 0.004 0.082 8856 Dihedral : 4.838 57.721 6928 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.96 % Allowed : 11.95 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.10), residues: 6415 helix: 1.33 (0.10), residues: 2862 sheet: -1.96 (0.15), residues: 986 loop : -1.70 (0.11), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 309 HIS 0.004 0.001 HIS B 280 PHE 0.019 0.001 PHE I 224 TYR 0.024 0.002 TYR G 182 ARG 0.006 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 381 time to evaluate : 5.754 Fit side-chains TARDY: cannot create tardy model for: "ASP J 72 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP K 72 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP N 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL C 455 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: I 99 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7233 (mt) REVERT: I 324 GLU cc_start: 0.6184 (mt-10) cc_final: 0.5954 (mm-30) REVERT: J 14 GLU cc_start: 0.7143 (tt0) cc_final: 0.6856 (tt0) REVERT: J 87 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7390 (tp) REVERT: J 152 GLU cc_start: 0.7498 (mp0) cc_final: 0.7172 (mp0) REVERT: J 186 ARG cc_start: 0.7304 (ttp-170) cc_final: 0.6556 (ttm-80) REVERT: J 205 LYS cc_start: 0.7591 (mmtt) cc_final: 0.6910 (mttt) REVERT: J 237 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8275 (m) REVERT: K 131 ASN cc_start: 0.8243 (t0) cc_final: 0.7818 (m-40) REVERT: K 135 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8491 (m) REVERT: K 191 LEU cc_start: 0.8330 (mm) cc_final: 0.7971 (mp) REVERT: L 190 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: L 246 ASN cc_start: 0.8089 (p0) cc_final: 0.7827 (m-40) REVERT: L 300 LYS cc_start: 0.7441 (ptmm) cc_final: 0.7111 (mmtt) REVERT: M 58 GLU cc_start: 0.6803 (pm20) cc_final: 0.6535 (pt0) REVERT: M 98 LYS cc_start: 0.8383 (ttmt) cc_final: 0.8052 (tttp) REVERT: M 196 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7432 (tt) REVERT: N 87 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7713 (tp) REVERT: N 98 LYS cc_start: 0.7964 (tppt) cc_final: 0.7743 (ttmt) REVERT: A 111 ILE cc_start: 0.7092 (mp) cc_final: 0.6640 (pt) REVERT: A 157 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6556 (tt) REVERT: A 168 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7621 (tt) REVERT: A 220 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7263 (tp) REVERT: A 282 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6988 (tp) REVERT: A 316 LEU cc_start: 0.5106 (OUTLIER) cc_final: 0.4817 (mt) REVERT: A 428 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7787 (tp) REVERT: A 433 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7734 (tp) REVERT: B 220 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7661 (tp) REVERT: B 226 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7367 (tp) REVERT: B 230 ASP cc_start: 0.7106 (m-30) cc_final: 0.6889 (m-30) REVERT: B 234 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7638 (tp) REVERT: B 283 MET cc_start: 0.7151 (mmt) cc_final: 0.6312 (mtm) REVERT: B 428 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7798 (tp) REVERT: B 433 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8386 (tp) REVERT: C 1 CYS cc_start: 0.6318 (p) cc_final: 0.5433 (m) REVERT: C 168 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7198 (tp) REVERT: C 175 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7962 (tp) REVERT: C 414 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7334 (tm) REVERT: F 43 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8052 (mt) REVERT: F 69 MET cc_start: 0.8683 (mmp) cc_final: 0.8296 (mmt) REVERT: F 447 MET cc_start: 0.3283 (mtp) cc_final: 0.2958 (mtp) REVERT: F 563 PHE cc_start: 0.6909 (t80) cc_final: 0.6621 (t80) REVERT: G 13 TRP cc_start: 0.6588 (OUTLIER) cc_final: 0.5472 (t60) REVERT: G 20 MET cc_start: 0.5450 (ttm) cc_final: 0.5188 (mtm) REVERT: G 274 ASP cc_start: 0.6844 (t0) cc_final: 0.6505 (t0) REVERT: G 344 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.5481 (tt) REVERT: G 478 MET cc_start: 0.6574 (tpt) cc_final: 0.6234 (tpt) REVERT: G 513 PHE cc_start: 0.5465 (m-80) cc_final: 0.5086 (m-10) REVERT: G 552 MET cc_start: 0.4181 (ttt) cc_final: 0.3965 (mtp) REVERT: G 630 MET cc_start: 0.7274 (mmm) cc_final: 0.6912 (mmt) REVERT: G 751 ILE cc_start: 0.8463 (tt) cc_final: 0.8186 (tt) REVERT: G 780 MET cc_start: 0.8839 (mmp) cc_final: 0.8409 (mmp) REVERT: G 865 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6256 (mt-10) REVERT: E 17 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7346 (pp) REVERT: E 110 LYS cc_start: 0.7588 (mmtp) cc_final: 0.6994 (mmtp) REVERT: E 134 LYS cc_start: 0.7768 (mmmm) cc_final: 0.7539 (mtpp) REVERT: E 250 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8049 (pp) REVERT: E 358 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.5173 (t80) REVERT: E 414 GLU cc_start: 0.7519 (tm-30) cc_final: 0.6861 (tm-30) REVERT: E 544 ILE cc_start: 0.5389 (OUTLIER) cc_final: 0.5073 (tt) REVERT: E 620 ARG cc_start: 0.8352 (mtt-85) cc_final: 0.8126 (mtp-110) REVERT: E 731 ASP cc_start: 0.8102 (p0) cc_final: 0.7382 (p0) REVERT: E 784 ASP cc_start: 0.8183 (t0) cc_final: 0.7580 (t0) REVERT: E 881 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6233 (tp) outliers start: 206 outliers final: 99 residues processed: 555 average time/residue: 0.5490 time to fit residues: 541.8017 Evaluate side-chains 479 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 349 time to evaluate : 5.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain I residue 229 VAL Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 193 SER Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 233 THR Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 496 MET Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 571 VAL Chi-restraints excluded: chain F residue 605 SER Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 758 VAL Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain G residue 13 TRP Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 548 ILE Chi-restraints excluded: chain G residue 612 VAL Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain G residue 682 LEU Chi-restraints excluded: chain G residue 756 SER Chi-restraints excluded: chain G residue 865 GLU Chi-restraints excluded: chain G residue 887 LEU Chi-restraints excluded: chain G residue 984 VAL Chi-restraints excluded: chain G residue 985 VAL Chi-restraints excluded: chain G residue 1005 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 568 ASP Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain E residue 868 SER Chi-restraints excluded: chain E residue 879 SER Chi-restraints excluded: chain E residue 881 LEU Chi-restraints excluded: chain E residue 921 SER Chi-restraints excluded: chain E residue 934 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 515 optimal weight: 0.9990 chunk 351 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 460 optimal weight: 3.9990 chunk 255 optimal weight: 6.9990 chunk 527 optimal weight: 1.9990 chunk 427 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 315 optimal weight: 0.9980 chunk 555 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 110 GLN ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 248 ASN G 308 GLN G 312 ASN G 685 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 49843 Z= 0.305 Angle : 0.645 12.789 67721 Z= 0.319 Chirality : 0.045 0.236 7908 Planarity : 0.005 0.103 8856 Dihedral : 4.914 59.328 6926 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.75 % Allowed : 12.74 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.10), residues: 6415 helix: 1.35 (0.10), residues: 2848 sheet: -1.93 (0.15), residues: 1039 loop : -1.62 (0.11), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 324 HIS 0.005 0.001 HIS B 280 PHE 0.024 0.002 PHE I 224 TYR 0.023 0.002 TYR L 76 ARG 0.008 0.000 ARG F 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 382 time to evaluate : 4.806 Fit side-chains TARDY: cannot create tardy model for: "ASP J 72 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP K 72 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP N 72 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: I 99 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7235 (mt) REVERT: I 272 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6533 (tt0) REVERT: I 324 GLU cc_start: 0.6225 (mt-10) cc_final: 0.5969 (mm-30) REVERT: J 23 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.6715 (pp30) REVERT: J 87 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7483 (tp) REVERT: J 186 ARG cc_start: 0.7294 (ttp-170) cc_final: 0.6570 (ttm-80) REVERT: J 205 LYS cc_start: 0.7567 (mmtt) cc_final: 0.6870 (mttp) REVERT: J 237 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8333 (m) REVERT: J 258 GLN cc_start: 0.7532 (mm-40) cc_final: 0.7262 (mt0) REVERT: K 131 ASN cc_start: 0.8317 (t0) cc_final: 0.7814 (m-40) REVERT: K 135 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8548 (m) REVERT: K 187 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6716 (tp) REVERT: K 191 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8011 (mp) REVERT: L 110 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7318 (pt0) REVERT: L 190 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: L 300 LYS cc_start: 0.7443 (ptmm) cc_final: 0.7111 (mmtt) REVERT: M 98 LYS cc_start: 0.8371 (ttmt) cc_final: 0.8052 (tttp) REVERT: M 196 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7547 (tt) REVERT: M 228 SER cc_start: 0.8267 (t) cc_final: 0.7752 (p) REVERT: N 87 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7781 (tp) REVERT: N 98 LYS cc_start: 0.8070 (tppt) cc_final: 0.7387 (ttpp) REVERT: A 111 ILE cc_start: 0.7134 (mp) cc_final: 0.6695 (pt) REVERT: A 157 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6588 (tt) REVERT: A 168 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7611 (tt) REVERT: A 220 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7235 (tp) REVERT: A 282 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7142 (tp) REVERT: A 283 MET cc_start: 0.7491 (mmm) cc_final: 0.7197 (mmm) REVERT: A 316 LEU cc_start: 0.5154 (OUTLIER) cc_final: 0.4868 (mt) REVERT: A 391 LYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6855 (ttmm) REVERT: A 428 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7829 (tp) REVERT: A 433 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7828 (tp) REVERT: B 220 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7826 (tp) REVERT: B 226 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7363 (tp) REVERT: B 234 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7685 (tp) REVERT: B 283 MET cc_start: 0.7204 (mmt) cc_final: 0.6429 (mtm) REVERT: B 428 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7790 (tp) REVERT: B 433 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8400 (tp) REVERT: C 1 CYS cc_start: 0.6443 (p) cc_final: 0.5765 (m) REVERT: C 168 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7281 (tp) REVERT: C 175 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7973 (tp) REVERT: C 187 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7379 (ttmt) REVERT: C 220 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8143 (tp) REVERT: C 414 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7435 (tm) REVERT: C 428 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8337 (tt) REVERT: F 43 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8111 (mt) REVERT: F 69 MET cc_start: 0.8670 (mmp) cc_final: 0.8331 (mmt) REVERT: F 256 ASP cc_start: 0.8492 (t0) cc_final: 0.8159 (t0) REVERT: F 267 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7650 (p0) REVERT: F 447 MET cc_start: 0.3325 (mtp) cc_final: 0.2992 (mtp) REVERT: F 519 MET cc_start: 0.0218 (tmt) cc_final: -0.0244 (tmt) REVERT: F 563 PHE cc_start: 0.6910 (t80) cc_final: 0.6586 (t80) REVERT: F 622 GLN cc_start: 0.8206 (tt0) cc_final: 0.7801 (tt0) REVERT: G 13 TRP cc_start: 0.6629 (OUTLIER) cc_final: 0.5536 (t60) REVERT: G 127 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8148 (mm) REVERT: G 274 ASP cc_start: 0.6957 (t0) cc_final: 0.6585 (t0) REVERT: G 344 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.5453 (tt) REVERT: G 513 PHE cc_start: 0.5510 (m-80) cc_final: 0.5023 (m-10) REVERT: G 751 ILE cc_start: 0.8502 (tt) cc_final: 0.8223 (tt) REVERT: G 780 MET cc_start: 0.8816 (mmp) cc_final: 0.8415 (mmp) REVERT: G 865 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6218 (mt-10) REVERT: G 1019 TRP cc_start: 0.5667 (m100) cc_final: 0.5407 (m100) REVERT: E 17 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7344 (pp) REVERT: E 110 LYS cc_start: 0.7582 (mmtp) cc_final: 0.7014 (mmtp) REVERT: E 134 LYS cc_start: 0.7825 (mmmm) cc_final: 0.7569 (mtpp) REVERT: E 149 MET cc_start: 0.7772 (ptm) cc_final: 0.7457 (ptp) REVERT: E 250 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8144 (pp) REVERT: E 293 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6716 (pp) REVERT: E 358 PHE cc_start: 0.6763 (OUTLIER) cc_final: 0.5264 (t80) REVERT: E 435 MET cc_start: 0.4844 (mmp) cc_final: 0.4526 (mmt) REVERT: E 544 ILE cc_start: 0.5525 (OUTLIER) cc_final: 0.5258 (tt) REVERT: E 626 MET cc_start: 0.7758 (ttm) cc_final: 0.7203 (ttp) REVERT: E 731 ASP cc_start: 0.8033 (p0) cc_final: 0.7367 (p0) REVERT: E 816 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6981 (tp30) REVERT: E 840 MET cc_start: 0.7895 (ttm) cc_final: 0.7232 (mtp) REVERT: E 881 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6290 (tp) REVERT: E 970 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7335 (tt) outliers start: 247 outliers final: 144 residues processed: 579 average time/residue: 0.5542 time to fit residues: 557.6621 Evaluate side-chains 551 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 363 time to evaluate : 5.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain I residue 272 GLN Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 23 GLN Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 110 GLN Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 316 ASN Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain M residue 193 SER Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 233 THR Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 279 LEU Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 391 ASN Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 496 MET Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 571 VAL Chi-restraints excluded: chain F residue 594 MET Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 740 VAL Chi-restraints excluded: chain F residue 862 SER Chi-restraints excluded: chain F residue 987 LEU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain G residue 13 TRP Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 149 MET Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 548 ILE Chi-restraints excluded: chain G residue 612 VAL Chi-restraints excluded: chain G residue 613 THR Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain G residue 682 LEU Chi-restraints excluded: chain G residue 750 SER Chi-restraints excluded: chain G residue 756 SER Chi-restraints excluded: chain G residue 847 VAL Chi-restraints excluded: chain G residue 865 GLU Chi-restraints excluded: chain G residue 887 LEU Chi-restraints excluded: chain G residue 958 ILE Chi-restraints excluded: chain G residue 984 VAL Chi-restraints excluded: chain G residue 985 VAL Chi-restraints excluded: chain G residue 1005 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 568 ASP Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 745 ILE Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain E residue 854 VAL Chi-restraints excluded: chain E residue 868 SER Chi-restraints excluded: chain E residue 879 SER Chi-restraints excluded: chain E residue 881 LEU Chi-restraints excluded: chain E residue 921 SER Chi-restraints excluded: chain E residue 970 LEU Chi-restraints excluded: chain E residue 1001 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 208 optimal weight: 3.9990 chunk 557 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 363 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 619 optimal weight: 0.0040 chunk 514 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 325 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 342 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 ASN G 248 ASN G 308 GLN G 312 ASN G 685 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 49843 Z= 0.169 Angle : 0.566 10.651 67721 Z= 0.278 Chirality : 0.042 0.207 7908 Planarity : 0.004 0.095 8856 Dihedral : 4.613 59.871 6926 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.81 % Allowed : 14.24 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.11), residues: 6415 helix: 1.80 (0.10), residues: 2842 sheet: -1.80 (0.15), residues: 1015 loop : -1.47 (0.11), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 309 HIS 0.004 0.001 HIS B 280 PHE 0.024 0.001 PHE I 224 TYR 0.024 0.001 TYR J 76 ARG 0.006 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 363 time to evaluate : 5.659 Fit side-chains TARDY: cannot create tardy model for: "ASP J 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP K 72 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP N 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL C 455 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: I 99 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7240 (mt) REVERT: I 320 LYS cc_start: 0.6251 (mttm) cc_final: 0.5795 (ttmt) REVERT: I 324 GLU cc_start: 0.6289 (mt-10) cc_final: 0.6086 (mm-30) REVERT: J 87 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7322 (tp) REVERT: J 152 GLU cc_start: 0.7485 (mp0) cc_final: 0.7198 (mp0) REVERT: J 186 ARG cc_start: 0.7295 (ttp-170) cc_final: 0.6538 (ttm-80) REVERT: J 205 LYS cc_start: 0.7511 (mmtt) cc_final: 0.6830 (mttp) REVERT: J 237 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8243 (m) REVERT: K 131 ASN cc_start: 0.8234 (t0) cc_final: 0.7807 (m-40) REVERT: K 135 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8507 (m) REVERT: K 191 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7957 (mp) REVERT: L 93 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7899 (tp40) REVERT: L 190 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: L 300 LYS cc_start: 0.7395 (ptmm) cc_final: 0.7071 (mmtt) REVERT: M 58 GLU cc_start: 0.6755 (pm20) cc_final: 0.6287 (pt0) REVERT: M 98 LYS cc_start: 0.8336 (ttmt) cc_final: 0.7995 (tttp) REVERT: M 196 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7471 (tt) REVERT: N 87 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7701 (tp) REVERT: N 98 LYS cc_start: 0.8005 (tppt) cc_final: 0.7652 (ttmt) REVERT: A 111 ILE cc_start: 0.7086 (mp) cc_final: 0.6685 (pt) REVERT: A 220 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7254 (tp) REVERT: A 283 MET cc_start: 0.7416 (mmm) cc_final: 0.7084 (mmm) REVERT: A 316 LEU cc_start: 0.5022 (OUTLIER) cc_final: 0.4762 (mt) REVERT: A 428 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7766 (tp) REVERT: A 433 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7788 (tp) REVERT: B 220 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7638 (tp) REVERT: B 283 MET cc_start: 0.7142 (mmt) cc_final: 0.6338 (mtm) REVERT: B 428 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7773 (tp) REVERT: B 433 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8400 (tp) REVERT: C 1 CYS cc_start: 0.6466 (p) cc_final: 0.5763 (m) REVERT: C 168 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7210 (tp) REVERT: C 175 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8094 (tt) REVERT: C 187 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7321 (ttmt) REVERT: C 220 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8140 (tp) REVERT: C 414 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7282 (tm) REVERT: C 428 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8383 (tt) REVERT: F 69 MET cc_start: 0.8664 (mmp) cc_final: 0.8331 (mmt) REVERT: F 447 MET cc_start: 0.3255 (mtp) cc_final: 0.2970 (mtp) REVERT: F 563 PHE cc_start: 0.6898 (t80) cc_final: 0.6695 (t80) REVERT: F 594 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7706 (ttp) REVERT: G 13 TRP cc_start: 0.6559 (OUTLIER) cc_final: 0.5412 (t60) REVERT: G 127 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8135 (mm) REVERT: G 192 LYS cc_start: 0.7880 (mtpt) cc_final: 0.7425 (mtmt) REVERT: G 344 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.5588 (tt) REVERT: G 513 PHE cc_start: 0.5483 (m-80) cc_final: 0.5024 (m-10) REVERT: G 630 MET cc_start: 0.7278 (mmm) cc_final: 0.6736 (mmp) REVERT: G 751 ILE cc_start: 0.8458 (tt) cc_final: 0.8181 (tt) REVERT: G 780 MET cc_start: 0.8798 (mmp) cc_final: 0.8405 (mmp) REVERT: G 865 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6190 (mt-10) REVERT: G 1019 TRP cc_start: 0.5567 (m100) cc_final: 0.5294 (m100) REVERT: E 17 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7306 (pp) REVERT: E 110 LYS cc_start: 0.7523 (mmtp) cc_final: 0.6990 (mmtp) REVERT: E 134 LYS cc_start: 0.7823 (mmmm) cc_final: 0.7598 (mtpp) REVERT: E 250 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8041 (pp) REVERT: E 287 SER cc_start: 0.9333 (p) cc_final: 0.9119 (m) REVERT: E 358 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.5293 (t80) REVERT: E 414 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7015 (mm-30) REVERT: E 544 ILE cc_start: 0.5437 (OUTLIER) cc_final: 0.5190 (tt) REVERT: E 620 ARG cc_start: 0.8325 (mtt-85) cc_final: 0.8107 (mtp-110) REVERT: E 626 MET cc_start: 0.7664 (ttm) cc_final: 0.7306 (ttp) REVERT: E 731 ASP cc_start: 0.7799 (p0) cc_final: 0.7242 (p0) REVERT: E 745 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7557 (mt) REVERT: E 784 ASP cc_start: 0.8469 (t0) cc_final: 0.7812 (t0) REVERT: E 881 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6244 (tp) outliers start: 198 outliers final: 118 residues processed: 526 average time/residue: 0.5390 time to fit residues: 495.9091 Evaluate side-chains 488 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 337 time to evaluate : 5.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain I residue 229 VAL Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 233 THR Chi-restraints excluded: chain N residue 279 LEU Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 571 VAL Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 594 MET Chi-restraints excluded: chain F residue 605 SER Chi-restraints excluded: chain F residue 740 VAL Chi-restraints excluded: chain F residue 758 VAL Chi-restraints excluded: chain F residue 985 VAL Chi-restraints excluded: chain F residue 987 LEU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain G residue 13 TRP Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 571 VAL Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain G residue 682 LEU Chi-restraints excluded: chain G residue 756 SER Chi-restraints excluded: chain G residue 847 VAL Chi-restraints excluded: chain G residue 865 GLU Chi-restraints excluded: chain G residue 887 LEU Chi-restraints excluded: chain G residue 984 VAL Chi-restraints excluded: chain G residue 985 VAL Chi-restraints excluded: chain G residue 1005 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 568 ASP Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 745 ILE Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain E residue 868 SER Chi-restraints excluded: chain E residue 879 SER Chi-restraints excluded: chain E residue 881 LEU Chi-restraints excluded: chain E residue 921 SER Chi-restraints excluded: chain E residue 966 CYS Chi-restraints excluded: chain E residue 1001 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 597 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 352 optimal weight: 3.9990 chunk 452 optimal weight: 3.9990 chunk 350 optimal weight: 3.9990 chunk 521 optimal weight: 9.9990 chunk 345 optimal weight: 0.9990 chunk 616 optimal weight: 4.9990 chunk 386 optimal weight: 0.6980 chunk 376 optimal weight: 5.9990 chunk 284 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 84 GLN ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 GLN N 342 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 ASN G 248 ASN G 312 ASN G 685 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 927 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 49843 Z= 0.412 Angle : 0.707 13.203 67721 Z= 0.352 Chirality : 0.048 0.238 7908 Planarity : 0.005 0.112 8856 Dihedral : 5.029 59.603 6925 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.57 % Allowed : 14.15 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.10), residues: 6415 helix: 1.33 (0.10), residues: 2832 sheet: -1.87 (0.15), residues: 1043 loop : -1.59 (0.11), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 324 HIS 0.006 0.001 HIS G 999 PHE 0.030 0.002 PHE I 224 TYR 0.031 0.002 TYR G 182 ARG 0.008 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 394 time to evaluate : 5.001 Fit side-chains TARDY: cannot create tardy model for: "ASP J 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP K 72 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL C 455 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: I 28 ASN cc_start: 0.8466 (p0) cc_final: 0.7904 (p0) REVERT: I 99 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7378 (mt) REVERT: I 272 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6111 (mm110) REVERT: I 324 GLU cc_start: 0.6294 (mt-10) cc_final: 0.6067 (mm-30) REVERT: J 23 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7314 (pt0) REVERT: J 87 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7529 (tp) REVERT: J 186 ARG cc_start: 0.7271 (ttp-170) cc_final: 0.6582 (ttm-80) REVERT: J 205 LYS cc_start: 0.7637 (mmtt) cc_final: 0.6856 (mttm) REVERT: J 237 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8378 (m) REVERT: J 295 GLU cc_start: 0.8242 (tt0) cc_final: 0.7957 (tt0) REVERT: J 337 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8462 (p) REVERT: K 131 ASN cc_start: 0.8385 (t0) cc_final: 0.7839 (m-40) REVERT: K 191 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8085 (mp) REVERT: K 297 ARG cc_start: 0.7328 (mtm180) cc_final: 0.6491 (mtm180) REVERT: L 93 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7970 (tp40) REVERT: L 190 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: L 278 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.6899 (m-30) REVERT: L 300 LYS cc_start: 0.7369 (ptmm) cc_final: 0.7147 (mmtt) REVERT: M 58 GLU cc_start: 0.6852 (pm20) cc_final: 0.6436 (pt0) REVERT: M 98 LYS cc_start: 0.8339 (ttmt) cc_final: 0.8006 (tttp) REVERT: M 228 SER cc_start: 0.8337 (t) cc_final: 0.7856 (p) REVERT: M 248 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6517 (mm-30) REVERT: N 87 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7847 (tp) REVERT: N 98 LYS cc_start: 0.8174 (tppt) cc_final: 0.7464 (ttpp) REVERT: A 111 ILE cc_start: 0.7233 (mp) cc_final: 0.6837 (pt) REVERT: A 168 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7625 (tt) REVERT: A 220 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7271 (tp) REVERT: A 283 MET cc_start: 0.7561 (mmm) cc_final: 0.7157 (mmm) REVERT: A 316 LEU cc_start: 0.5371 (OUTLIER) cc_final: 0.5102 (mt) REVERT: A 391 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6859 (ttmm) REVERT: A 428 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7827 (tp) REVERT: A 433 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7857 (tp) REVERT: B 220 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7821 (tp) REVERT: B 226 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7107 (tp) REVERT: B 234 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7761 (tp) REVERT: B 283 MET cc_start: 0.7188 (mmt) cc_final: 0.6453 (mtm) REVERT: B 428 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7814 (tp) REVERT: B 433 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8426 (tp) REVERT: C 1 CYS cc_start: 0.6487 (p) cc_final: 0.5785 (m) REVERT: C 168 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7319 (tp) REVERT: C 175 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8008 (tp) REVERT: C 187 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7432 (ttmt) REVERT: C 220 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8162 (tp) REVERT: C 414 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7514 (tm) REVERT: C 428 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8299 (tt) REVERT: F 43 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8202 (mt) REVERT: F 69 MET cc_start: 0.8670 (mmp) cc_final: 0.8347 (mmt) REVERT: F 447 MET cc_start: 0.3483 (mtp) cc_final: 0.3155 (mtp) REVERT: F 563 PHE cc_start: 0.7091 (t80) cc_final: 0.6743 (t80) REVERT: G 13 TRP cc_start: 0.6653 (OUTLIER) cc_final: 0.5373 (t60) REVERT: G 127 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8106 (mm) REVERT: G 344 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.5619 (tt) REVERT: G 513 PHE cc_start: 0.5628 (m-80) cc_final: 0.5099 (m-80) REVERT: G 630 MET cc_start: 0.7279 (mmm) cc_final: 0.6730 (mmp) REVERT: G 714 ARG cc_start: 0.8053 (ttt180) cc_final: 0.7515 (tpp80) REVERT: G 751 ILE cc_start: 0.8553 (tt) cc_final: 0.8268 (tt) REVERT: G 780 MET cc_start: 0.8791 (mmp) cc_final: 0.8365 (mmp) REVERT: G 865 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6238 (mt-10) REVERT: G 1009 MET cc_start: 0.6710 (tmm) cc_final: 0.6334 (tmm) REVERT: G 1019 TRP cc_start: 0.5739 (m100) cc_final: 0.5373 (m100) REVERT: E 110 LYS cc_start: 0.7636 (mmtp) cc_final: 0.7036 (mmtp) REVERT: E 134 LYS cc_start: 0.7778 (mmmm) cc_final: 0.7549 (mtpp) REVERT: E 149 MET cc_start: 0.7846 (ptm) cc_final: 0.7523 (ptp) REVERT: E 250 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8285 (pp) REVERT: E 293 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6931 (pp) REVERT: E 358 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.5207 (t80) REVERT: E 544 ILE cc_start: 0.5604 (OUTLIER) cc_final: 0.5349 (tt) REVERT: E 626 MET cc_start: 0.7811 (ttm) cc_final: 0.7361 (ttp) REVERT: E 784 ASP cc_start: 0.8567 (t0) cc_final: 0.7898 (t0) REVERT: E 810 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7449 (t80) REVERT: E 881 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6272 (tp) REVERT: E 970 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7452 (tt) outliers start: 238 outliers final: 152 residues processed: 590 average time/residue: 0.5668 time to fit residues: 573.2450 Evaluate side-chains 562 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 370 time to evaluate : 5.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain I residue 272 GLN Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 23 GLN Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 323 THR Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain J residue 337 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 316 ASN Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain M residue 193 SER Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 310 LEU Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 233 THR Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 279 LEU Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 391 ASN Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 571 VAL Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 594 MET Chi-restraints excluded: chain F residue 605 SER Chi-restraints excluded: chain F residue 630 MET Chi-restraints excluded: chain F residue 740 VAL Chi-restraints excluded: chain F residue 758 VAL Chi-restraints excluded: chain F residue 862 SER Chi-restraints excluded: chain F residue 985 VAL Chi-restraints excluded: chain F residue 987 LEU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain G residue 13 TRP Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 149 MET Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 547 VAL Chi-restraints excluded: chain G residue 554 TRP Chi-restraints excluded: chain G residue 571 VAL Chi-restraints excluded: chain G residue 613 THR Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain G residue 682 LEU Chi-restraints excluded: chain G residue 750 SER Chi-restraints excluded: chain G residue 756 SER Chi-restraints excluded: chain G residue 847 VAL Chi-restraints excluded: chain G residue 865 GLU Chi-restraints excluded: chain G residue 887 LEU Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 984 VAL Chi-restraints excluded: chain G residue 985 VAL Chi-restraints excluded: chain G residue 1005 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 568 ASP Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 745 ILE Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain E residue 810 TYR Chi-restraints excluded: chain E residue 847 VAL Chi-restraints excluded: chain E residue 854 VAL Chi-restraints excluded: chain E residue 868 SER Chi-restraints excluded: chain E residue 879 SER Chi-restraints excluded: chain E residue 881 LEU Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 921 SER Chi-restraints excluded: chain E residue 966 CYS Chi-restraints excluded: chain E residue 970 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 381 optimal weight: 4.9990 chunk 246 optimal weight: 0.7980 chunk 368 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 392 optimal weight: 4.9990 chunk 420 optimal weight: 0.6980 chunk 304 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 484 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 342 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 ASN G 248 ASN G 685 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 49843 Z= 0.173 Angle : 0.573 13.918 67721 Z= 0.280 Chirality : 0.042 0.258 7908 Planarity : 0.004 0.115 8856 Dihedral : 4.570 58.829 6925 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.48 % Allowed : 15.45 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.11), residues: 6415 helix: 1.92 (0.10), residues: 2830 sheet: -1.71 (0.15), residues: 1041 loop : -1.41 (0.11), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 309 HIS 0.004 0.001 HIS B 280 PHE 0.023 0.001 PHE I 224 TYR 0.022 0.001 TYR G 182 ARG 0.010 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 343 time to evaluate : 5.167 Fit side-chains TARDY: cannot create tardy model for: "ASP J 72 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP K 72 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL C 455 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: I 28 ASN cc_start: 0.8402 (p0) cc_final: 0.7865 (p0) REVERT: I 99 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7228 (mt) REVERT: I 272 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6574 (tt0) REVERT: I 320 LYS cc_start: 0.6292 (mttm) cc_final: 0.5837 (ttmt) REVERT: I 324 GLU cc_start: 0.6348 (mt-10) cc_final: 0.6139 (mm-30) REVERT: J 23 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.6782 (pp30) REVERT: J 87 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7304 (tp) REVERT: J 186 ARG cc_start: 0.7283 (ttp-170) cc_final: 0.6549 (ttm-80) REVERT: J 205 LYS cc_start: 0.7592 (mmtt) cc_final: 0.6831 (mttm) REVERT: J 237 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8280 (m) REVERT: K 131 ASN cc_start: 0.8195 (t0) cc_final: 0.7849 (m-40) REVERT: K 191 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7942 (mp) REVERT: L 93 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.8014 (tp40) REVERT: L 190 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: L 278 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.6857 (m-30) REVERT: L 300 LYS cc_start: 0.7313 (ptmm) cc_final: 0.7040 (mmtt) REVERT: M 58 GLU cc_start: 0.6719 (pm20) cc_final: 0.6385 (pt0) REVERT: M 98 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7967 (tttp) REVERT: M 228 SER cc_start: 0.8257 (t) cc_final: 0.7766 (p) REVERT: N 14 GLU cc_start: 0.7535 (pp20) cc_final: 0.6339 (tt0) REVERT: N 87 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7634 (tp) REVERT: N 98 LYS cc_start: 0.8045 (tppt) cc_final: 0.7649 (ttmt) REVERT: A 111 ILE cc_start: 0.7168 (mp) cc_final: 0.6792 (pt) REVERT: A 168 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7588 (tt) REVERT: A 220 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7239 (tp) REVERT: A 283 MET cc_start: 0.7416 (mmm) cc_final: 0.7046 (mmm) REVERT: A 316 LEU cc_start: 0.5086 (OUTLIER) cc_final: 0.4871 (mt) REVERT: A 391 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6818 (ttmm) REVERT: A 428 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7789 (tp) REVERT: A 433 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7822 (tp) REVERT: B 220 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7645 (tp) REVERT: B 234 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7627 (tp) REVERT: B 283 MET cc_start: 0.7134 (mmt) cc_final: 0.6361 (mtm) REVERT: B 341 ARG cc_start: 0.6025 (tpt90) cc_final: 0.5333 (mtp180) REVERT: B 428 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7768 (tp) REVERT: B 433 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8437 (tp) REVERT: C 1 CYS cc_start: 0.6432 (p) cc_final: 0.5719 (m) REVERT: C 144 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7749 (mt) REVERT: C 168 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7250 (tp) REVERT: C 175 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8133 (tt) REVERT: C 187 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7357 (ttmt) REVERT: C 220 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8145 (tp) REVERT: C 414 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7267 (tm) REVERT: C 428 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8428 (tp) REVERT: F 43 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8143 (mt) REVERT: F 69 MET cc_start: 0.8590 (mmp) cc_final: 0.8260 (mmt) REVERT: F 447 MET cc_start: 0.3360 (mtp) cc_final: 0.3036 (mtp) REVERT: F 563 PHE cc_start: 0.7027 (t80) cc_final: 0.6735 (t80) REVERT: F 594 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7615 (ttp) REVERT: F 878 LEU cc_start: 0.5702 (mt) cc_final: 0.4928 (mm) REVERT: G 13 TRP cc_start: 0.6562 (OUTLIER) cc_final: 0.5356 (t60) REVERT: G 127 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8104 (mm) REVERT: G 192 LYS cc_start: 0.7844 (mtpt) cc_final: 0.7419 (mtmt) REVERT: G 344 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.5599 (tt) REVERT: G 630 MET cc_start: 0.7191 (mmm) cc_final: 0.6692 (mmt) REVERT: G 751 ILE cc_start: 0.8448 (tt) cc_final: 0.8119 (tt) REVERT: G 780 MET cc_start: 0.8870 (mmp) cc_final: 0.8480 (mmp) REVERT: G 862 SER cc_start: 0.8335 (m) cc_final: 0.7899 (p) REVERT: G 865 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6147 (mt-10) REVERT: G 1009 MET cc_start: 0.6708 (tmm) cc_final: 0.6321 (tmm) REVERT: E 110 LYS cc_start: 0.7525 (mmtp) cc_final: 0.6971 (mmtp) REVERT: E 250 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8060 (pp) REVERT: E 358 PHE cc_start: 0.6817 (OUTLIER) cc_final: 0.5485 (t80) REVERT: E 544 ILE cc_start: 0.5552 (OUTLIER) cc_final: 0.5310 (tt) REVERT: E 626 MET cc_start: 0.7685 (ttm) cc_final: 0.7348 (ttp) REVERT: E 731 ASP cc_start: 0.8169 (p0) cc_final: 0.7656 (p0) REVERT: E 745 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7517 (mt) REVERT: E 810 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.7263 (t80) REVERT: E 865 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6481 (mt-10) REVERT: E 881 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6258 (tp) REVERT: E 970 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7503 (tt) outliers start: 181 outliers final: 117 residues processed: 493 average time/residue: 0.5595 time to fit residues: 475.8789 Evaluate side-chains 494 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 336 time to evaluate : 5.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain I residue 272 GLN Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain J residue 23 GLN Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 268 ILE Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 ASN Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 571 VAL Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 594 MET Chi-restraints excluded: chain F residue 605 SER Chi-restraints excluded: chain F residue 740 VAL Chi-restraints excluded: chain F residue 758 VAL Chi-restraints excluded: chain F residue 985 VAL Chi-restraints excluded: chain F residue 987 LEU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain G residue 13 TRP Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 554 TRP Chi-restraints excluded: chain G residue 555 MET Chi-restraints excluded: chain G residue 613 THR Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain G residue 682 LEU Chi-restraints excluded: chain G residue 756 SER Chi-restraints excluded: chain G residue 847 VAL Chi-restraints excluded: chain G residue 865 GLU Chi-restraints excluded: chain G residue 887 LEU Chi-restraints excluded: chain G residue 984 VAL Chi-restraints excluded: chain G residue 985 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 568 ASP Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 745 ILE Chi-restraints excluded: chain E residue 810 TYR Chi-restraints excluded: chain E residue 865 GLU Chi-restraints excluded: chain E residue 868 SER Chi-restraints excluded: chain E residue 879 SER Chi-restraints excluded: chain E residue 881 LEU Chi-restraints excluded: chain E residue 966 CYS Chi-restraints excluded: chain E residue 970 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 561 optimal weight: 0.7980 chunk 590 optimal weight: 3.9990 chunk 539 optimal weight: 0.9980 chunk 574 optimal weight: 1.9990 chunk 345 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 451 optimal weight: 0.6980 chunk 176 optimal weight: 0.1980 chunk 519 optimal weight: 0.6980 chunk 543 optimal weight: 0.7980 chunk 572 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 110 GLN ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 GLN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN G 67 GLN G 112 GLN G 161 ASN G 248 ASN G 273 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 49843 Z= 0.169 Angle : 0.561 13.755 67721 Z= 0.273 Chirality : 0.042 0.292 7908 Planarity : 0.004 0.109 8856 Dihedral : 4.383 55.097 6925 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.56 % Allowed : 15.39 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.11), residues: 6415 helix: 2.11 (0.10), residues: 2834 sheet: -1.64 (0.15), residues: 1016 loop : -1.29 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 309 HIS 0.004 0.001 HIS A 280 PHE 0.021 0.001 PHE I 224 TYR 0.021 0.001 TYR G 182 ARG 0.009 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 348 time to evaluate : 4.970 Fit side-chains TARDY: cannot create tardy model for: "ASP J 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP K 72 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL C 455 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: I 28 ASN cc_start: 0.8387 (p0) cc_final: 0.7866 (p0) REVERT: I 99 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7278 (mt) REVERT: I 272 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6546 (tt0) REVERT: I 320 LYS cc_start: 0.6147 (mttm) cc_final: 0.5729 (ttmt) REVERT: J 23 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.6862 (pp30) REVERT: J 87 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7313 (tp) REVERT: J 152 GLU cc_start: 0.7458 (mp0) cc_final: 0.7200 (mp0) REVERT: J 186 ARG cc_start: 0.7311 (ttp-170) cc_final: 0.6561 (ttm-80) REVERT: J 205 LYS cc_start: 0.7507 (mmtt) cc_final: 0.6763 (mttm) REVERT: J 237 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8251 (m) REVERT: K 131 ASN cc_start: 0.8213 (t0) cc_final: 0.7804 (m-40) REVERT: K 191 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7925 (mp) REVERT: L 190 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: L 278 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.6824 (m-30) REVERT: M 58 GLU cc_start: 0.6668 (pm20) cc_final: 0.6392 (pt0) REVERT: M 98 LYS cc_start: 0.8296 (ttmt) cc_final: 0.7963 (tttp) REVERT: N 14 GLU cc_start: 0.7399 (pp20) cc_final: 0.6403 (tt0) REVERT: N 87 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7689 (tp) REVERT: N 98 LYS cc_start: 0.8058 (tppt) cc_final: 0.7321 (ttpp) REVERT: A 111 ILE cc_start: 0.7173 (mp) cc_final: 0.6798 (pt) REVERT: A 168 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7606 (tt) REVERT: A 220 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7266 (tp) REVERT: A 283 MET cc_start: 0.7445 (mmm) cc_final: 0.7080 (mmm) REVERT: A 316 LEU cc_start: 0.4883 (OUTLIER) cc_final: 0.4439 (mt) REVERT: A 428 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7813 (tp) REVERT: A 433 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7812 (tp) REVERT: B 168 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7313 (tp) REVERT: B 220 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7646 (tp) REVERT: B 234 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7572 (tp) REVERT: B 283 MET cc_start: 0.7082 (mmt) cc_final: 0.6325 (mtm) REVERT: B 341 ARG cc_start: 0.5992 (tpt90) cc_final: 0.5285 (mtp180) REVERT: B 428 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7787 (tp) REVERT: B 433 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8425 (tp) REVERT: C 1 CYS cc_start: 0.6510 (p) cc_final: 0.5771 (m) REVERT: C 168 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7268 (tp) REVERT: C 175 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8142 (tt) REVERT: C 187 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7364 (ttmt) REVERT: C 220 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8149 (tp) REVERT: C 414 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7136 (tm) REVERT: C 428 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8463 (tp) REVERT: C 444 LYS cc_start: 0.8090 (tmmm) cc_final: 0.7753 (ttpt) REVERT: F 43 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8146 (mt) REVERT: F 69 MET cc_start: 0.8583 (mmp) cc_final: 0.8228 (mmt) REVERT: F 89 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8137 (p) REVERT: F 267 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7584 (p0) REVERT: F 447 MET cc_start: 0.3369 (mtp) cc_final: 0.3063 (mtp) REVERT: F 563 PHE cc_start: 0.7072 (t80) cc_final: 0.6797 (t80) REVERT: F 594 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7725 (ttp) REVERT: G 13 TRP cc_start: 0.6513 (OUTLIER) cc_final: 0.5391 (t60) REVERT: G 127 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8093 (mm) REVERT: G 274 ASP cc_start: 0.6907 (t0) cc_final: 0.6603 (t0) REVERT: G 344 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.5582 (tt) REVERT: G 486 LEU cc_start: 0.6627 (tt) cc_final: 0.5970 (mt) REVERT: G 630 MET cc_start: 0.7205 (mmm) cc_final: 0.6728 (mmt) REVERT: G 751 ILE cc_start: 0.8429 (tt) cc_final: 0.8135 (tt) REVERT: G 780 MET cc_start: 0.8825 (mmp) cc_final: 0.8553 (mmp) REVERT: G 865 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6097 (mt-10) REVERT: G 1009 MET cc_start: 0.6725 (tmm) cc_final: 0.6299 (tmm) REVERT: E 110 LYS cc_start: 0.7534 (mmtp) cc_final: 0.6943 (mmtp) REVERT: E 149 MET cc_start: 0.7748 (ptm) cc_final: 0.7425 (ptp) REVERT: E 250 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8034 (pp) REVERT: E 293 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6723 (pp) REVERT: E 358 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.5504 (t80) REVERT: E 414 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7233 (mm-30) REVERT: E 544 ILE cc_start: 0.5644 (OUTLIER) cc_final: 0.5417 (tt) REVERT: E 626 MET cc_start: 0.7675 (ttm) cc_final: 0.7407 (ttp) REVERT: E 731 ASP cc_start: 0.8114 (p0) cc_final: 0.7605 (p0) REVERT: E 745 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7453 (mt) REVERT: E 810 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7254 (t80) REVERT: E 865 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6438 (mt-10) REVERT: E 881 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6212 (tp) REVERT: E 970 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7490 (tt) outliers start: 185 outliers final: 124 residues processed: 499 average time/residue: 0.5588 time to fit residues: 482.8312 Evaluate side-chains 503 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 337 time to evaluate : 5.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 229 VAL Chi-restraints excluded: chain I residue 272 GLN Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 23 GLN Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 268 ILE Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 316 ASN Chi-restraints excluded: chain L residue 322 ILE Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 ASN Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 233 THR Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 571 VAL Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 594 MET Chi-restraints excluded: chain F residue 605 SER Chi-restraints excluded: chain F residue 740 VAL Chi-restraints excluded: chain F residue 758 VAL Chi-restraints excluded: chain F residue 985 VAL Chi-restraints excluded: chain F residue 987 LEU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain G residue 13 TRP Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 554 TRP Chi-restraints excluded: chain G residue 555 MET Chi-restraints excluded: chain G residue 613 THR Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain G residue 682 LEU Chi-restraints excluded: chain G residue 756 SER Chi-restraints excluded: chain G residue 847 VAL Chi-restraints excluded: chain G residue 865 GLU Chi-restraints excluded: chain G residue 887 LEU Chi-restraints excluded: chain G residue 984 VAL Chi-restraints excluded: chain G residue 985 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 745 ILE Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain E residue 810 TYR Chi-restraints excluded: chain E residue 865 GLU Chi-restraints excluded: chain E residue 879 SER Chi-restraints excluded: chain E residue 881 LEU Chi-restraints excluded: chain E residue 921 SER Chi-restraints excluded: chain E residue 966 CYS Chi-restraints excluded: chain E residue 970 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 377 optimal weight: 0.0270 chunk 607 optimal weight: 1.9990 chunk 371 optimal weight: 3.9990 chunk 288 optimal weight: 0.0770 chunk 422 optimal weight: 5.9990 chunk 637 optimal weight: 5.9990 chunk 586 optimal weight: 0.7980 chunk 507 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 392 optimal weight: 0.6980 chunk 311 optimal weight: 0.0470 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 104 GLN J 70 GLN M 84 GLN ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 282 GLN M 291 GLN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 GLN G 161 ASN G 248 ASN G 273 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 49843 Z= 0.141 Angle : 0.543 14.776 67721 Z= 0.263 Chirality : 0.041 0.321 7908 Planarity : 0.004 0.110 8856 Dihedral : 4.206 51.863 6925 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.96 % Allowed : 16.18 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.11), residues: 6415 helix: 2.32 (0.10), residues: 2836 sheet: -1.41 (0.16), residues: 992 loop : -1.17 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 309 HIS 0.004 0.001 HIS A 280 PHE 0.023 0.001 PHE F 453 TYR 0.016 0.001 TYR G 182 ARG 0.009 0.000 ARG A 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12830 Ramachandran restraints generated. 6415 Oldfield, 0 Emsley, 6415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 338 time to evaluate : 5.180 Fit side-chains TARDY: cannot create tardy model for: "ASP J 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP K 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 72 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: I 28 ASN cc_start: 0.8349 (p0) cc_final: 0.7837 (p0) REVERT: I 99 LEU cc_start: 0.8028 (tt) cc_final: 0.7346 (mt) REVERT: I 272 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6510 (tt0) REVERT: I 320 LYS cc_start: 0.6094 (mttm) cc_final: 0.5637 (ttmt) REVERT: J 23 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.6728 (pp30) REVERT: J 87 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7288 (tp) REVERT: J 186 ARG cc_start: 0.7317 (ttp-170) cc_final: 0.6545 (ttm-80) REVERT: J 205 LYS cc_start: 0.7505 (mmtt) cc_final: 0.6768 (mttm) REVERT: K 131 ASN cc_start: 0.8165 (t0) cc_final: 0.7788 (m-40) REVERT: K 191 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7804 (mp) REVERT: L 190 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: L 278 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.6803 (m-30) REVERT: M 58 GLU cc_start: 0.6561 (pm20) cc_final: 0.6308 (pt0) REVERT: M 98 LYS cc_start: 0.8306 (ttmt) cc_final: 0.7964 (tttp) REVERT: N 14 GLU cc_start: 0.7355 (pp20) cc_final: 0.6383 (tt0) REVERT: N 87 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7622 (tp) REVERT: N 98 LYS cc_start: 0.8029 (tppt) cc_final: 0.7653 (ttmt) REVERT: A 111 ILE cc_start: 0.7121 (mp) cc_final: 0.6750 (pt) REVERT: A 168 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7584 (tt) REVERT: A 283 MET cc_start: 0.7439 (mmm) cc_final: 0.7093 (mmm) REVERT: A 309 MET cc_start: 0.7811 (mtm) cc_final: 0.7460 (mtp) REVERT: A 428 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7796 (tp) REVERT: A 433 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7805 (tp) REVERT: B 168 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7301 (tp) REVERT: B 185 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.8253 (m-10) REVERT: B 220 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7606 (tp) REVERT: B 234 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7570 (tp) REVERT: B 283 MET cc_start: 0.7027 (mmt) cc_final: 0.6289 (mtm) REVERT: B 341 ARG cc_start: 0.5786 (tpt90) cc_final: 0.5089 (mtp180) REVERT: B 428 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7799 (tp) REVERT: B 433 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8433 (tp) REVERT: C 1 CYS cc_start: 0.6490 (p) cc_final: 0.5738 (m) REVERT: C 168 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7254 (tp) REVERT: C 175 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8163 (tt) REVERT: C 187 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7334 (ttmt) REVERT: C 220 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8130 (tp) REVERT: C 414 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6827 (tm) REVERT: C 428 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8472 (tp) REVERT: C 444 LYS cc_start: 0.8020 (tmmm) cc_final: 0.7684 (ttpt) REVERT: F 69 MET cc_start: 0.8569 (mmp) cc_final: 0.8247 (mmt) REVERT: F 267 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7549 (p0) REVERT: F 447 MET cc_start: 0.3543 (mtp) cc_final: 0.3175 (mtp) REVERT: F 563 PHE cc_start: 0.7087 (t80) cc_final: 0.6854 (t80) REVERT: F 878 LEU cc_start: 0.5635 (mt) cc_final: 0.4877 (mm) REVERT: G 13 TRP cc_start: 0.6482 (OUTLIER) cc_final: 0.5401 (t60) REVERT: G 127 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8063 (mm) REVERT: G 344 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.5604 (tt) REVERT: G 486 LEU cc_start: 0.6517 (tt) cc_final: 0.5978 (mt) REVERT: G 630 MET cc_start: 0.7225 (mmm) cc_final: 0.6780 (mmt) REVERT: G 751 ILE cc_start: 0.8404 (tt) cc_final: 0.8109 (tt) REVERT: G 780 MET cc_start: 0.8904 (mmp) cc_final: 0.8572 (mmm) REVERT: G 797 MET cc_start: 0.8884 (mmm) cc_final: 0.8629 (mmt) REVERT: G 865 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6027 (mt-10) REVERT: G 1009 MET cc_start: 0.6746 (tmm) cc_final: 0.6336 (tmm) REVERT: E 110 LYS cc_start: 0.7507 (mmtp) cc_final: 0.6901 (mmtp) REVERT: E 149 MET cc_start: 0.7701 (ptm) cc_final: 0.7306 (ptp) REVERT: E 250 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7946 (pp) REVERT: E 293 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6682 (pp) REVERT: E 319 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7219 (mm-40) REVERT: E 358 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.5703 (t80) REVERT: E 414 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7279 (mm-30) REVERT: E 544 ILE cc_start: 0.5585 (OUTLIER) cc_final: 0.5373 (tt) REVERT: E 613 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8342 (m) REVERT: E 731 ASP cc_start: 0.7937 (p0) cc_final: 0.7490 (p0) REVERT: E 810 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7298 (t80) REVERT: E 865 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.6337 (mt-10) REVERT: E 881 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6307 (tp) REVERT: E 970 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7480 (tt) outliers start: 154 outliers final: 103 residues processed: 463 average time/residue: 0.5622 time to fit residues: 454.0423 Evaluate side-chains 465 residues out of total 5204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 326 time to evaluate : 5.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 229 VAL Chi-restraints excluded: chain I residue 272 GLN Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 23 GLN Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain J residue 337 THR Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 268 ILE Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 322 ILE Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 ASN Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 233 THR Chi-restraints excluded: chain N residue 239 ARG Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 571 VAL Chi-restraints excluded: chain F residue 605 SER Chi-restraints excluded: chain F residue 740 VAL Chi-restraints excluded: chain F residue 758 VAL Chi-restraints excluded: chain F residue 985 VAL Chi-restraints excluded: chain F residue 987 LEU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain G residue 13 TRP Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 161 ASN Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 456 MET Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 613 THR Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain G residue 847 VAL Chi-restraints excluded: chain G residue 865 GLU Chi-restraints excluded: chain G residue 984 VAL Chi-restraints excluded: chain G residue 985 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain E residue 810 TYR Chi-restraints excluded: chain E residue 865 GLU Chi-restraints excluded: chain E residue 881 LEU Chi-restraints excluded: chain E residue 921 SER Chi-restraints excluded: chain E residue 966 CYS Chi-restraints excluded: chain E residue 970 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 403 optimal weight: 4.9990 chunk 540 optimal weight: 0.3980 chunk 155 optimal weight: 2.9990 chunk 468 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 508 optimal weight: 0.5980 chunk 212 optimal weight: 0.7980 chunk 522 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 282 GLN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.161116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.159376 restraints weight = 54161.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.142381 restraints weight = 94500.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.142723 restraints weight = 76004.292| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.226 49843 Z= 0.196 Angle : 0.624 59.156 67721 Z= 0.327 Chirality : 0.042 0.856 7908 Planarity : 0.004 0.110 8856 Dihedral : 4.200 51.849 6925 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.13 % Allowed : 16.18 % Favored : 80.68 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.11), residues: 6415 helix: 2.32 (0.10), residues: 2836 sheet: -1.42 (0.16), residues: 1016 loop : -1.15 (0.12), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 309 HIS 0.004 0.001 HIS A 280 PHE 0.021 0.001 PHE I 224 TYR 0.017 0.001 TYR G 891 ARG 0.023 0.000 ARG K 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10414.81 seconds wall clock time: 188 minutes 34.32 seconds (11314.32 seconds total)