Starting phenix.real_space_refine on Tue Jul 23 14:57:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8d_37342/07_2024/8w8d_37342.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8d_37342/07_2024/8w8d_37342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8d_37342/07_2024/8w8d_37342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8d_37342/07_2024/8w8d_37342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8d_37342/07_2024/8w8d_37342.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8d_37342/07_2024/8w8d_37342.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 118 5.16 5 C 14487 2.51 5 N 4047 2.21 5 O 4411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 19": "OE1" <-> "OE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "B GLU 5": "OE1" <-> "OE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "C GLU 5": "OE1" <-> "OE2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 5": "OE1" <-> "OE2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D ASP 290": "OD1" <-> "OD2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D GLU 351": "OE1" <-> "OE2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "E GLU 19": "OE1" <-> "OE2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E GLU 333": "OE1" <-> "OE2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "E GLU 351": "OE1" <-> "OE2" Residue "E GLU 375": "OE1" <-> "OE2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F GLU 215": "OE1" <-> "OE2" Residue "F GLU 255": "OE1" <-> "OE2" Residue "F GLU 334": "OE1" <-> "OE2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "F GLU 351": "OE1" <-> "OE2" Residue "F GLU 397": "OE1" <-> "OE2" Residue "c GLU 29": "OE1" <-> "OE2" Residue "c GLU 50": "OE1" <-> "OE2" Residue "c GLU 62": "OE1" <-> "OE2" Residue "b GLU 29": "OE1" <-> "OE2" Residue "b GLU 50": "OE1" <-> "OE2" Residue "b GLU 62": "OE1" <-> "OE2" Residue "d GLU 55": "OE1" <-> "OE2" Residue "d GLU 59": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 23063 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3261 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 Chain: "B" Number of atoms: 3245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3245 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 17, 'TRANS': 394} Chain breaks: 2 Chain: "C" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3261 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 Chain: "D" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3261 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 396} Chain breaks: 1 Chain: "E" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 398} Chain: "F" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3222 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 392} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 587 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain breaks: 1 Chain: "e" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "b" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 578 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain breaks: 1 Chain: "a" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 559 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "f" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 559 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "d" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 625 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 12.40, per 1000 atoms: 0.54 Number of scatterers: 23063 At special positions: 0 Unit cell: (165.41, 142.8, 145.18, 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 118 16.00 O 4411 8.00 N 4047 7.00 C 14487 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: 8.68 Conformation dependent library (CDL) restraints added in 3.8 seconds 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5476 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 28 sheets defined 41.9% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 10 through 21 removed outlier: 4.058A pdb=" N ILE A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 42 removed outlier: 3.647A pdb=" N ILE A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.556A pdb=" N SER A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 removed outlier: 3.706A pdb=" N ILE A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.627A pdb=" N LEU A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 255 removed outlier: 3.704A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.661A pdb=" N LEU A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.615A pdb=" N LYS A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.706A pdb=" N GLU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.824A pdb=" N SER A 363 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 391 through 404 Processing helix chain 'A' and resid 409 through 417 removed outlier: 4.312A pdb=" N PHE A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 10 through 22 Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.985A pdb=" N ALA B 127 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.765A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 165 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.678A pdb=" N LEU B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 235 through 255 removed outlier: 3.882A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.657A pdb=" N LYS B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.549A pdb=" N GLU B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.521A pdb=" N ALA B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.705A pdb=" N LEU B 370 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 391 through 404 removed outlier: 4.009A pdb=" N MET B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 30 through 42 Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.734A pdb=" N SER C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.938A pdb=" N LEU C 136 " --> pdb=" O PHE C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.130A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 removed outlier: 3.638A pdb=" N LEU C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 235 through 255 removed outlier: 3.793A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 278 removed outlier: 3.532A pdb=" N LEU C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 293 Processing helix chain 'C' and resid 294 through 302 removed outlier: 3.577A pdb=" N LYS C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.529A pdb=" N GLU C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 removed outlier: 3.596A pdb=" N ALA C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.507A pdb=" N LEU C 370 " --> pdb=" O LYS C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 388 removed outlier: 3.546A pdb=" N ILE C 386 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS C 388 " --> pdb=" O ARG C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 404 Processing helix chain 'D' and resid 2 through 9 removed outlier: 3.858A pdb=" N THR D 9 " --> pdb=" O GLU D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 20 removed outlier: 3.508A pdb=" N THR D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 42 Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 155 through 166 removed outlier: 4.092A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 removed outlier: 3.577A pdb=" N LEU D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 removed outlier: 3.536A pdb=" N VAL D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET D 219 " --> pdb=" O GLU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 255 removed outlier: 3.598A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 243 " --> pdb=" O HIS D 239 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 275 Processing helix chain 'D' and resid 285 through 289 removed outlier: 3.574A pdb=" N GLY D 288 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 293 Processing helix chain 'D' and resid 294 through 302 removed outlier: 3.531A pdb=" N LYS D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 removed outlier: 3.804A pdb=" N GLU D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 334 " --> pdb=" O VAL D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.579A pdb=" N ALA D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.581A pdb=" N LEU D 370 " --> pdb=" O LYS D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 404 removed outlier: 3.637A pdb=" N ALA D 404 " --> pdb=" O ILE D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 415 removed outlier: 3.555A pdb=" N PHE D 412 " --> pdb=" O THR D 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 30 through 42 Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 132 through 136 removed outlier: 3.706A pdb=" N ASN E 135 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU E 136 " --> pdb=" O PHE E 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 132 through 136' Processing helix chain 'E' and resid 155 through 166 removed outlier: 4.071A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.564A pdb=" N GLN E 189 " --> pdb=" O THR E 185 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN E 190 " --> pdb=" O MET E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 235 through 255 removed outlier: 3.676A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 295 through 302 Processing helix chain 'E' and resid 325 through 335 removed outlier: 3.758A pdb=" N GLU E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.580A pdb=" N ALA E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 388 removed outlier: 4.215A pdb=" N GLN E 378 " --> pdb=" O GLN E 374 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 402 Processing helix chain 'E' and resid 409 through 417 removed outlier: 3.685A pdb=" N PHE E 413 " --> pdb=" O ASP E 410 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLU E 414 " --> pdb=" O ASP E 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 Processing helix chain 'F' and resid 10 through 20 removed outlier: 3.526A pdb=" N THR F 16 " --> pdb=" O SER F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 82 through 90 removed outlier: 3.680A pdb=" N ILE F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 166 removed outlier: 4.191A pdb=" N THR F 158 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 Processing helix chain 'F' and resid 212 through 221 removed outlier: 4.061A pdb=" N ARG F 221 " --> pdb=" O THR F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 256 removed outlier: 3.836A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS F 256 " --> pdb=" O ARG F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 278 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 294 through 303 removed outlier: 3.622A pdb=" N LYS F 298 " --> pdb=" O LEU F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 336 removed outlier: 3.501A pdb=" N GLU F 329 " --> pdb=" O SER F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 352 removed outlier: 3.565A pdb=" N ALA F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 388 Processing helix chain 'F' and resid 391 through 403 removed outlier: 3.753A pdb=" N ASN F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 21 removed outlier: 3.701A pdb=" N LEU c 16 " --> pdb=" O ASP c 12 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN c 21 " --> pdb=" O GLU c 17 " (cutoff:3.500A) Processing helix chain 'e' and resid 11 through 20 Processing helix chain 'e' and resid 21 through 23 No H-bonds generated for 'chain 'e' and resid 21 through 23' Processing helix chain 'e' and resid 66 through 68 No H-bonds generated for 'chain 'e' and resid 66 through 68' Processing helix chain 'b' and resid 12 through 21 removed outlier: 3.655A pdb=" N LEU b 16 " --> pdb=" O ASP b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 22 through 24 No H-bonds generated for 'chain 'b' and resid 22 through 24' Processing helix chain 'a' and resid 9 through 19 removed outlier: 3.631A pdb=" N TYR a 13 " --> pdb=" O ASN a 9 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN a 15 " --> pdb=" O ASP a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 20 through 24 removed outlier: 3.676A pdb=" N LEU a 24 " --> pdb=" O GLN a 21 " (cutoff:3.500A) Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'f' and resid 9 through 20 removed outlier: 3.550A pdb=" N TYR f 13 " --> pdb=" O ASN f 9 " (cutoff:3.500A) Processing helix chain 'f' and resid 66 through 68 No H-bonds generated for 'chain 'f' and resid 66 through 68' Processing helix chain 'd' and resid 9 through 21 removed outlier: 3.630A pdb=" N TYR d 13 " --> pdb=" O ASN d 9 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP d 14 " --> pdb=" O CYS d 10 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN d 21 " --> pdb=" O GLU d 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 22 through 24 No H-bonds generated for 'chain 'd' and resid 22 through 24' Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 57 removed outlier: 3.603A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N TYR A 80 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N LYS A 115 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS A 100 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 116 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N SER A 98 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU A 118 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR A 96 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 4.003A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 318 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 removed outlier: 4.003A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY A 174 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA A 319 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE A 176 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 342 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 364 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 57 removed outlier: 3.585A pdb=" N ILE B 79 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS B 100 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL B 116 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N SER B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU B 118 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR B 96 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 139 removed outlier: 4.131A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE B 316 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 262 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N THR B 318 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU B 264 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N LEU B 320 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 203 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU B 263 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 204 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL B 228 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL B 206 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N SER B 230 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 208 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 removed outlier: 4.131A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY B 174 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA B 319 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE B 176 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 364 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 50 through 57 removed outlier: 3.657A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 113 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS C 100 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL C 116 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N SER C 98 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU C 118 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR C 96 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.937A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU C 204 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N VAL C 228 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL C 206 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N SER C 230 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU C 208 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.937A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY C 174 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA C 319 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE C 176 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET C 341 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 364 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 50 through 57 removed outlier: 3.555A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS D 100 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL D 116 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N SER D 98 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU D 118 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR D 96 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.974A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL D 203 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU D 263 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N MET D 205 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.974A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY D 174 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA D 319 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE D 176 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET D 341 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N HIS D 344 " --> pdb=" O ARG D 362 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ARG D 362 " --> pdb=" O HIS D 344 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 50 through 57 removed outlier: 3.514A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS E 100 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL E 116 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N SER E 98 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU E 118 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR E 96 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 226 through 231 removed outlier: 6.713A pdb=" N LEU E 204 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL E 228 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL E 206 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N SER E 230 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU E 208 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 226 through 231 removed outlier: 6.713A pdb=" N LEU E 204 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL E 228 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL E 206 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N SER E 230 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU E 208 " --> pdb=" O SER E 230 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY E 174 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ALA E 319 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE E 176 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET E 341 " --> pdb=" O ARG E 173 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 50 through 57 removed outlier: 3.653A pdb=" N ILE F 79 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU F 114 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ARG F 102 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL F 116 " --> pdb=" O LYS F 100 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LYS F 100 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU F 118 " --> pdb=" O SER F 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 226 through 231 removed outlier: 6.838A pdb=" N LEU F 204 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N VAL F 228 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL F 203 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU F 263 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET F 205 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 318 " --> pdb=" O LEU F 264 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 226 through 231 removed outlier: 6.838A pdb=" N LEU F 204 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N VAL F 228 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL F 203 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU F 263 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET F 205 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 318 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY F 174 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ALA F 319 " --> pdb=" O GLY F 174 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE F 176 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU F 342 " --> pdb=" O GLY F 364 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY F 364 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 25 through 26 Processing sheet with id=AC2, first strand: chain 'c' and resid 42 through 45 Processing sheet with id=AC3, first strand: chain 'c' and resid 71 through 72 removed outlier: 3.774A pdb=" N PHE c 71 " --> pdb=" O THR c 78 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 25 through 27 Processing sheet with id=AC5, first strand: chain 'e' and resid 42 through 46 Processing sheet with id=AC6, first strand: chain 'b' and resid 42 through 45 Processing sheet with id=AC7, first strand: chain 'a' and resid 39 through 46 removed outlier: 4.991A pdb=" N ALA a 40 " --> pdb=" O GLU a 55 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU a 55 " --> pdb=" O ALA a 40 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP a 42 " --> pdb=" O VAL a 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'f' and resid 25 through 27 Processing sheet with id=AC9, first strand: chain 'f' and resid 42 through 46 removed outlier: 3.634A pdb=" N LEU f 52 " --> pdb=" O LEU f 63 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU f 63 " --> pdb=" O LEU f 52 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL f 54 " --> pdb=" O ARG f 61 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 40 through 45 948 hydrogen bonds defined for protein. 2670 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: 7.21 Time building geometry restraints manager: 9.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5490 1.33 - 1.45: 4211 1.45 - 1.58: 13443 1.58 - 1.70: 1 1.70 - 1.82: 218 Bond restraints: 23363 Sorted by residual: bond pdb=" N GLU D 234 " pdb=" CA GLU D 234 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.64e+01 bond pdb=" N VAL D 277 " pdb=" CA VAL D 277 " ideal model delta sigma weight residual 1.459 1.494 -0.035 9.10e-03 1.21e+04 1.50e+01 bond pdb=" C MET F 1 " pdb=" N ASN F 2 " ideal model delta sigma weight residual 1.331 1.378 -0.047 1.29e-02 6.01e+03 1.30e+01 bond pdb=" N ILE D 209 " pdb=" CA ILE D 209 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.19e-02 7.06e+03 1.26e+01 bond pdb=" N GLY F 46 " pdb=" CA GLY F 46 " ideal model delta sigma weight residual 1.444 1.477 -0.033 9.30e-03 1.16e+04 1.24e+01 ... (remaining 23358 not shown) Histogram of bond angle deviations from ideal: 87.64 - 97.73: 15 97.73 - 107.82: 834 107.82 - 117.91: 17190 117.91 - 128.00: 13319 128.00 - 138.09: 120 Bond angle restraints: 31478 Sorted by residual: angle pdb=" N GLY B 150 " pdb=" CA GLY B 150 " pdb=" C GLY B 150 " ideal model delta sigma weight residual 115.21 138.09 -22.88 1.30e+00 5.92e-01 3.10e+02 angle pdb=" N MET F 405 " pdb=" CA MET F 405 " pdb=" C MET F 405 " ideal model delta sigma weight residual 111.56 137.83 -26.27 1.53e+00 4.27e-01 2.95e+02 angle pdb=" N THR d 78 " pdb=" CA THR d 78 " pdb=" C THR d 78 " ideal model delta sigma weight residual 110.30 132.31 -22.01 1.50e+00 4.44e-01 2.15e+02 angle pdb=" C ARG B 149 " pdb=" CA ARG B 149 " pdb=" CB ARG B 149 " ideal model delta sigma weight residual 110.44 87.64 22.80 1.68e+00 3.54e-01 1.84e+02 angle pdb=" CA PRO B 10 " pdb=" N PRO B 10 " pdb=" CD PRO B 10 " ideal model delta sigma weight residual 112.00 94.66 17.34 1.40e+00 5.10e-01 1.53e+02 ... (remaining 31473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11847 17.97 - 35.94: 1812 35.94 - 53.91: 643 53.91 - 71.88: 149 71.88 - 89.85: 39 Dihedral angle restraints: 14490 sinusoidal: 6053 harmonic: 8437 Sorted by residual: dihedral pdb=" C LYS d 31 " pdb=" N LYS d 31 " pdb=" CA LYS d 31 " pdb=" CB LYS d 31 " ideal model delta harmonic sigma weight residual -122.60 -93.35 -29.25 0 2.50e+00 1.60e-01 1.37e+02 dihedral pdb=" C ARG B 149 " pdb=" N ARG B 149 " pdb=" CA ARG B 149 " pdb=" CB ARG B 149 " ideal model delta harmonic sigma weight residual -122.60 -100.21 -22.39 0 2.50e+00 1.60e-01 8.02e+01 dihedral pdb=" C SER F 45 " pdb=" N SER F 45 " pdb=" CA SER F 45 " pdb=" CB SER F 45 " ideal model delta harmonic sigma weight residual -122.60 -100.51 -22.09 0 2.50e+00 1.60e-01 7.80e+01 ... (remaining 14487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 3461 0.147 - 0.294: 129 0.294 - 0.440: 11 0.440 - 0.587: 10 0.587 - 0.734: 5 Chirality restraints: 3616 Sorted by residual: chirality pdb=" CA LYS d 31 " pdb=" N LYS d 31 " pdb=" C LYS d 31 " pdb=" CB LYS d 31 " both_signs ideal model delta sigma weight residual False 2.51 3.24 -0.73 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CA THR d 78 " pdb=" N THR d 78 " pdb=" C THR d 78 " pdb=" CB THR d 78 " both_signs ideal model delta sigma weight residual False 2.53 1.80 0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CA GLU D 24 " pdb=" N GLU D 24 " pdb=" C GLU D 24 " pdb=" CB GLU D 24 " both_signs ideal model delta sigma weight residual False 2.51 3.15 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 3613 not shown) Planarity restraints: 4098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 9 " -0.114 5.00e-02 4.00e+02 1.57e-01 3.96e+01 pdb=" N PRO B 10 " 0.271 5.00e-02 4.00e+02 pdb=" CA PRO B 10 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO B 10 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 150 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C GLY B 150 " -0.052 2.00e-02 2.50e+03 pdb=" O GLY B 150 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN B 151 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 404 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.24e+00 pdb=" C ALA C 404 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA C 404 " 0.018 2.00e-02 2.50e+03 pdb=" N MET C 405 " 0.017 2.00e-02 2.50e+03 ... (remaining 4095 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 8 1.99 - 2.72: 989 2.72 - 3.44: 30447 3.44 - 4.17: 48398 4.17 - 4.90: 88516 Nonbonded interactions: 168358 Sorted by model distance: nonbonded pdb=" CD2 LEU b 28 " pdb=" CA PHE b 71 " model vdw 1.262 3.890 nonbonded pdb=" CD2 LEU b 28 " pdb=" CB PHE b 71 " model vdw 1.366 3.860 nonbonded pdb=" OG1 THR b 27 " pdb=" O SER b 72 " model vdw 1.409 2.440 nonbonded pdb=" NE2 GLN E 85 " pdb=" SG CYS e 10 " model vdw 1.438 2.880 nonbonded pdb=" CD GLN E 85 " pdb=" SG CYS e 10 " model vdw 1.667 3.630 ... (remaining 168353 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' and (resid 1 through 134 or resid 137 through 139 or (resid 140 throu \ gh 141 and (name N or name CA or name C or name O or name CB )) or resid 142 thr \ ough 413)) selection = (chain 'B' and (resid 1 through 139 or (resid 140 through 141 and (name N or nam \ e CA or name C or name O or name CB )) or resid 142 through 413)) selection = (chain 'C' and (resid 1 through 134 or resid 137 through 139 or (resid 140 throu \ gh 141 and (name N or name CA or name C or name O or name CB )) or resid 142 thr \ ough 413)) selection = (chain 'D' and (resid 1 through 134 or resid 137 through 139 or (resid 140 throu \ gh 141 and (name N or name CA or name C or name O or name CB )) or resid 142 thr \ ough 413)) selection = (chain 'E' and (resid 1 through 134 or resid 137 through 139 or (resid 140 throu \ gh 141 and (name N or name CA or name C or name O or name CB )) or resid 142 thr \ ough 280 or resid 284 through 413)) selection = (chain 'F' and (resid 1 through 134 or resid 137 through 413)) } ncs_group { reference = (chain 'a' and (resid 5 through 32 or resid 37 through 53 or resid 60 through 72 \ )) selection = (chain 'b' and (resid 5 through 32 or resid 37 through 72)) selection = (chain 'c' and (resid 5 through 53 or resid 60 through 72)) selection = (chain 'd' and (resid 5 through 32 or resid 37 through 53 or resid 60 through 72 \ )) selection = (chain 'e' and (resid 5 through 32 or resid 37 through 53 or resid 60 through 72 \ )) selection = (chain 'f' and (resid 5 through 32 or resid 37 through 53 or resid 60 through 72 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 57.700 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 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 0.131 23363 Z= 0.427 Angle : 1.107 26.273 31478 Z= 0.735 Chirality : 0.074 0.734 3616 Planarity : 0.005 0.157 4098 Dihedral : 19.923 89.850 9014 Min Nonbonded Distance : 1.262 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 7.73 % Allowed : 23.11 % Favored : 69.16 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2881 helix: 0.68 (0.17), residues: 1066 sheet: 0.11 (0.23), residues: 492 loop : -1.96 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 381 HIS 0.005 0.001 HIS F 295 PHE 0.027 0.001 PHE D 398 TYR 0.011 0.001 TYR d 5 ARG 0.007 0.000 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 301 time to evaluate : 2.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6778 (mmtm) REVERT: C 411 ASP cc_start: 0.6225 (OUTLIER) cc_final: 0.6000 (m-30) REVERT: E 186 MET cc_start: 0.4941 (ttp) cc_final: 0.4617 (ttp) outliers start: 195 outliers final: 37 residues processed: 441 average time/residue: 1.3250 time to fit residues: 666.1348 Evaluate side-chains 243 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 204 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 283 LYS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain b residue 12 ASP Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 18 LEU Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 36 LEU Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 71 PHE Chi-restraints excluded: chain b residue 78 THR Chi-restraints excluded: chain d residue 20 CYS Chi-restraints excluded: chain d residue 32 ASP Chi-restraints excluded: chain d residue 71 PHE Chi-restraints excluded: chain d residue 81 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 9.9990 chunk 218 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 225 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS B 151 ASN B 306 ASN B 409 ASN D 198 ASN D 275 ASN D 344 HIS ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN E 151 ASN E 378 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 HIS ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23363 Z= 0.321 Angle : 0.673 10.584 31478 Z= 0.342 Chirality : 0.044 0.178 3616 Planarity : 0.005 0.081 4098 Dihedral : 6.756 104.934 3226 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.11 % Allowed : 27.19 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2881 helix: 1.29 (0.16), residues: 1091 sheet: 0.29 (0.24), residues: 442 loop : -1.82 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 381 HIS 0.007 0.001 HIS e 23 PHE 0.019 0.002 PHE F 133 TYR 0.018 0.001 TYR B 197 ARG 0.007 0.000 ARG c 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 223 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 49 residues processed: 319 average time/residue: 1.1944 time to fit residues: 441.7568 Evaluate side-chains 243 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 194 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain c residue 32 ASP Chi-restraints excluded: chain c residue 52 LEU Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain e residue 67 LYS Chi-restraints excluded: chain e residue 71 PHE Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 18 LEU Chi-restraints excluded: chain b residue 32 ASP Chi-restraints excluded: chain b residue 36 LEU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 78 THR Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain d residue 32 ASP Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 53 VAL Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain d residue 81 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 178 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 chunk 283 optimal weight: 7.9990 chunk 233 optimal weight: 0.0980 chunk 259 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 210 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN C 190 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 HIS F 275 ASN b 9 ASN ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 9 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23363 Z= 0.175 Angle : 0.606 12.919 31478 Z= 0.300 Chirality : 0.043 0.225 3616 Planarity : 0.004 0.054 4098 Dihedral : 4.911 56.571 3182 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.45 % Allowed : 28.26 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.16), residues: 2881 helix: 1.61 (0.16), residues: 1112 sheet: 0.38 (0.23), residues: 466 loop : -1.74 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 381 HIS 0.004 0.001 HIS e 73 PHE 0.016 0.001 PHE B 355 TYR 0.013 0.001 TYR b 5 ARG 0.008 0.000 ARG c 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 210 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 46 residues processed: 274 average time/residue: 1.1850 time to fit residues: 378.4166 Evaluate side-chains 237 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 191 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain c residue 20 CYS Chi-restraints excluded: chain c residue 32 ASP Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain e residue 67 LYS Chi-restraints excluded: chain e residue 71 PHE Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 32 ASP Chi-restraints excluded: chain b residue 36 LEU Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 76 ILE Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain f residue 27 THR Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 71 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 135 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 278 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 249 optimal weight: 20.0000 chunk 75 optimal weight: 0.1980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 9 ASN ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23363 Z= 0.298 Angle : 0.631 11.001 31478 Z= 0.313 Chirality : 0.043 0.169 3616 Planarity : 0.004 0.045 4098 Dihedral : 4.771 57.537 3172 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.04 % Allowed : 27.71 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2881 helix: 1.79 (0.16), residues: 1111 sheet: 0.16 (0.23), residues: 479 loop : -1.63 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 381 HIS 0.007 0.001 HIS C 239 PHE 0.021 0.001 PHE F 133 TYR 0.013 0.001 TYR c 5 ARG 0.005 0.000 ARG E 149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 202 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 147 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.6278 (mmm) outliers start: 102 outliers final: 56 residues processed: 283 average time/residue: 1.1217 time to fit residues: 371.2643 Evaluate side-chains 248 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 191 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 67 LYS Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain b residue 12 ASP Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 32 ASP Chi-restraints excluded: chain b residue 76 ILE Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain f residue 27 THR Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 71 PHE Chi-restraints excluded: chain d residue 80 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 249 optimal weight: 20.0000 chunk 70 optimal weight: 0.5980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS A 275 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 ASN b 9 ASN ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23363 Z= 0.291 Angle : 0.632 10.917 31478 Z= 0.312 Chirality : 0.043 0.213 3616 Planarity : 0.004 0.046 4098 Dihedral : 4.530 51.023 3166 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.77 % Allowed : 28.54 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2881 helix: 1.84 (0.16), residues: 1110 sheet: 0.33 (0.23), residues: 477 loop : -1.68 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 381 HIS 0.005 0.001 HIS A 42 PHE 0.020 0.001 PHE e 71 TYR 0.013 0.001 TYR E 197 ARG 0.008 0.000 ARG e 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 203 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 147 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6246 (mmm) outliers start: 95 outliers final: 63 residues processed: 276 average time/residue: 1.1212 time to fit residues: 362.6982 Evaluate side-chains 255 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 191 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain c residue 32 ASP Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 72 SER Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 67 LYS Chi-restraints excluded: chain e residue 71 PHE Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain b residue 12 ASP Chi-restraints excluded: chain b residue 32 ASP Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain f residue 27 THR Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain d residue 81 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 278 optimal weight: 20.0000 chunk 231 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 146 optimal weight: 0.0770 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 9 ASN ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23363 Z= 0.182 Angle : 0.610 9.892 31478 Z= 0.297 Chirality : 0.042 0.184 3616 Planarity : 0.004 0.046 4098 Dihedral : 4.332 52.109 3164 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.13 % Allowed : 29.25 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2881 helix: 2.04 (0.16), residues: 1115 sheet: 0.45 (0.24), residues: 461 loop : -1.61 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 381 HIS 0.003 0.000 HIS e 73 PHE 0.048 0.001 PHE B 355 TYR 0.013 0.001 TYR E 197 ARG 0.007 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 205 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 156 ASP cc_start: 0.5032 (OUTLIER) cc_final: 0.4621 (p0) REVERT: b 35 LYS cc_start: 0.5043 (mmpt) cc_final: 0.4836 (mmpt) outliers start: 79 outliers final: 52 residues processed: 268 average time/residue: 1.1289 time to fit residues: 353.3091 Evaluate side-chains 241 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 188 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain c residue 32 ASP Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 71 PHE Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain b residue 12 ASP Chi-restraints excluded: chain b residue 32 ASP Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain f residue 27 THR Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 81 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 203 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 277 optimal weight: 50.0000 chunk 173 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 9 ASN ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23363 Z= 0.200 Angle : 0.623 10.612 31478 Z= 0.303 Chirality : 0.042 0.211 3616 Planarity : 0.004 0.046 4098 Dihedral : 4.272 53.121 3163 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.21 % Allowed : 28.97 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 2881 helix: 2.10 (0.16), residues: 1115 sheet: 0.60 (0.24), residues: 449 loop : -1.58 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 381 HIS 0.003 0.001 HIS C 239 PHE 0.019 0.001 PHE e 71 TYR 0.023 0.001 TYR F 197 ARG 0.011 0.000 ARG E 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 197 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 MET cc_start: 0.6046 (mmm) cc_final: 0.5750 (mmp) REVERT: F 156 ASP cc_start: 0.5076 (OUTLIER) cc_final: 0.4679 (p0) outliers start: 81 outliers final: 51 residues processed: 263 average time/residue: 1.1190 time to fit residues: 345.4315 Evaluate side-chains 242 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 190 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 67 LYS Chi-restraints excluded: chain e residue 71 PHE Chi-restraints excluded: chain b residue 12 ASP Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain f residue 27 THR Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 81 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 218 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23363 Z= 0.197 Angle : 0.649 11.450 31478 Z= 0.311 Chirality : 0.042 0.187 3616 Planarity : 0.004 0.045 4098 Dihedral : 4.138 40.203 3160 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.81 % Allowed : 29.81 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2881 helix: 2.13 (0.16), residues: 1115 sheet: 0.63 (0.24), residues: 450 loop : -1.56 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 381 HIS 0.003 0.001 HIS A 42 PHE 0.053 0.001 PHE B 355 TYR 0.029 0.001 TYR E 197 ARG 0.011 0.000 ARG E 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 198 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 156 ASP cc_start: 0.5090 (OUTLIER) cc_final: 0.4698 (p0) outliers start: 71 outliers final: 47 residues processed: 260 average time/residue: 1.1190 time to fit residues: 340.2857 Evaluate side-chains 238 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 190 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain c residue 20 CYS Chi-restraints excluded: chain c residue 23 HIS Chi-restraints excluded: chain c residue 41 SER Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 72 SER Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 71 PHE Chi-restraints excluded: chain b residue 12 ASP Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain f residue 27 THR Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain d residue 28 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 0.0040 chunk 265 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 258 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 112 optimal weight: 0.0970 chunk 203 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 233 optimal weight: 0.0050 chunk 244 optimal weight: 6.9990 chunk 257 optimal weight: 7.9990 overall best weight: 1.6208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23363 Z= 0.223 Angle : 0.680 11.987 31478 Z= 0.325 Chirality : 0.043 0.218 3616 Planarity : 0.004 0.046 4098 Dihedral : 4.164 39.410 3160 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.46 % Allowed : 30.00 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2881 helix: 2.12 (0.16), residues: 1115 sheet: 0.66 (0.24), residues: 448 loop : -1.55 (0.16), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 381 HIS 0.003 0.001 HIS C 239 PHE 0.029 0.001 PHE F 133 TYR 0.029 0.001 TYR E 197 ARG 0.009 0.000 ARG e 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 194 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 156 ASP cc_start: 0.5004 (OUTLIER) cc_final: 0.4593 (p0) outliers start: 62 outliers final: 52 residues processed: 246 average time/residue: 1.2184 time to fit residues: 349.2318 Evaluate side-chains 244 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 191 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain c residue 20 CYS Chi-restraints excluded: chain c residue 41 SER Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 67 LYS Chi-restraints excluded: chain e residue 71 PHE Chi-restraints excluded: chain b residue 12 ASP Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain f residue 27 THR Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 43 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.9980 chunk 273 optimal weight: 0.0470 chunk 166 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 286 optimal weight: 7.9990 chunk 264 optimal weight: 8.9990 chunk 228 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 176 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23363 Z= 0.180 Angle : 0.688 12.558 31478 Z= 0.326 Chirality : 0.043 0.248 3616 Planarity : 0.004 0.046 4098 Dihedral : 4.080 38.696 3159 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.30 % Allowed : 30.20 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2881 helix: 2.16 (0.16), residues: 1117 sheet: 0.69 (0.24), residues: 457 loop : -1.54 (0.16), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 381 HIS 0.002 0.000 HIS D 239 PHE 0.060 0.001 PHE e 71 TYR 0.013 0.001 TYR b 5 ARG 0.009 0.000 ARG e 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 198 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 156 ASP cc_start: 0.4806 (OUTLIER) cc_final: 0.4410 (p0) outliers start: 58 outliers final: 51 residues processed: 248 average time/residue: 1.1705 time to fit residues: 337.4798 Evaluate side-chains 244 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 192 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 355 PHE Chi-restraints excluded: chain c residue 23 HIS Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 64 ARG Chi-restraints excluded: chain c residue 79 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 67 LYS Chi-restraints excluded: chain b residue 12 ASP Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain a residue 13 TYR Chi-restraints excluded: chain f residue 27 THR Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 43 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 0.7980 chunk 243 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 210 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 228 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 234 optimal weight: 0.0270 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.074198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.044703 restraints weight = 85472.942| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 4.46 r_work: 0.2622 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23363 Z= 0.170 Angle : 0.686 12.640 31478 Z= 0.325 Chirality : 0.043 0.180 3616 Planarity : 0.004 0.046 4098 Dihedral : 4.005 37.638 3159 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.86 % Allowed : 30.88 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2881 helix: 2.21 (0.17), residues: 1119 sheet: 0.76 (0.24), residues: 457 loop : -1.48 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 381 HIS 0.002 0.000 HIS e 73 PHE 0.054 0.001 PHE B 355 TYR 0.029 0.001 TYR E 197 ARG 0.009 0.000 ARG e 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7771.10 seconds wall clock time: 136 minutes 59.64 seconds (8219.64 seconds total)