Starting phenix.real_space_refine on Mon Aug 25 20:17:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bym_45038/08_2025/9bym_45038.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bym_45038/08_2025/9bym_45038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bym_45038/08_2025/9bym_45038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bym_45038/08_2025/9bym_45038.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bym_45038/08_2025/9bym_45038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bym_45038/08_2025/9bym_45038.map" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.027 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 4 5.21 5 S 103 5.16 5 C 18955 2.51 5 N 5117 2.21 5 O 5681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29873 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3728 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain: "C" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3689 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 466} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3560 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3532 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "F" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3532 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "J" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 399 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 51} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2112 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 973 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "I" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Chain: "K" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "L" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "Q" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "R" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3728 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.99, per 1000 atoms: 0.23 Number of scatterers: 29873 At special positions: 0 Unit cell: (127.33, 131.61, 211.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 13 15.00 Mg 4 11.99 O 5681 8.00 N 5117 7.00 C 18955 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7104 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 24 sheets defined 55.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.579A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 192 removed outlier: 3.574A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 3.619A pdb=" N TYR A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.558A pdb=" N GLN A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 295 through 296 No H-bonds generated for 'chain 'A' and resid 295 through 296' Processing helix chain 'A' and resid 297 through 307 removed outlier: 3.854A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.771A pdb=" N ALA A 377 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 405 removed outlier: 4.017A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 459 through 476 removed outlier: 4.354A pdb=" N LYS A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.561A pdb=" N LEU A 480 " --> pdb=" O HIS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 removed outlier: 4.212A pdb=" N GLU A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 239 through 259 Proline residue: C 247 - end of helix removed outlier: 3.895A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.513A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 295 through 296 No H-bonds generated for 'chain 'C' and resid 295 through 296' Processing helix chain 'C' and resid 297 through 308 removed outlier: 3.988A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 330 through 333 Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 380 through 401 removed outlier: 3.845A pdb=" N VAL C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 429 removed outlier: 3.648A pdb=" N LEU C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 460 through 476 Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 490 through 509 removed outlier: 4.536A pdb=" N GLU C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 175 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 233 through 245 Processing helix chain 'D' and resid 260 through 269 removed outlier: 3.727A pdb=" N THR D 264 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY D 267 " --> pdb=" O PHE D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 275 Processing helix chain 'D' and resid 287 through 298 removed outlier: 4.021A pdb=" N ARG D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 298 " --> pdb=" O MET D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 318 Processing helix chain 'D' and resid 321 through 329 removed outlier: 3.547A pdb=" N THR D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA D 329 " --> pdb=" O ALA D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 345 Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'D' and resid 366 through 394 removed outlier: 3.920A pdb=" N ASP D 388 " --> pdb=" O LYS D 384 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE D 389 " --> pdb=" O SER D 385 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 398 removed outlier: 3.513A pdb=" N LEU D 398 " --> pdb=" O MET D 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 395 through 398' Processing helix chain 'D' and resid 399 through 417 removed outlier: 3.706A pdb=" N SER D 417 " --> pdb=" O GLN D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 428 Processing helix chain 'D' and resid 435 through 449 Processing helix chain 'D' and resid 455 through 460 Processing helix chain 'D' and resid 464 through 478 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 178 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 227 through 248 removed outlier: 4.430A pdb=" N ALA E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU E 236 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE E 245 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 275 removed outlier: 3.600A pdb=" N PHE E 263 " --> pdb=" O ASN E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 283 removed outlier: 3.533A pdb=" N TYR E 283 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 297 removed outlier: 4.042A pdb=" N ARG E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 318 Processing helix chain 'E' and resid 321 through 330 removed outlier: 3.819A pdb=" N HIS E 330 " --> pdb=" O THR E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 345 Processing helix chain 'E' and resid 361 through 366 Processing helix chain 'E' and resid 366 through 393 removed outlier: 3.635A pdb=" N TYR E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP E 388 " --> pdb=" O LYS E 384 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE E 389 " --> pdb=" O SER E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 417 removed outlier: 4.108A pdb=" N SER E 417 " --> pdb=" O GLN E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 428 Processing helix chain 'E' and resid 435 through 449 Processing helix chain 'E' and resid 455 through 460 Processing helix chain 'E' and resid 464 through 475 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 124 through 128 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 175 Processing helix chain 'F' and resid 191 through 206 removed outlier: 3.731A pdb=" N GLY F 195 " --> pdb=" O ARG F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 233 through 248 removed outlier: 3.635A pdb=" N PHE F 245 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 274 removed outlier: 3.583A pdb=" N THR F 264 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F 272 " --> pdb=" O SER F 268 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU F 273 " --> pdb=" O GLU F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 298 removed outlier: 3.753A pdb=" N ARG F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE F 298 " --> pdb=" O MET F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 318 Processing helix chain 'F' and resid 321 through 328 removed outlier: 3.526A pdb=" N PHE F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 331 No H-bonds generated for 'chain 'F' and resid 329 through 331' Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'F' and resid 366 through 394 removed outlier: 4.639A pdb=" N ASP F 388 " --> pdb=" O LYS F 384 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE F 389 " --> pdb=" O SER F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 398 Processing helix chain 'F' and resid 399 through 417 removed outlier: 3.674A pdb=" N SER F 417 " --> pdb=" O GLN F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 422 No H-bonds generated for 'chain 'F' and resid 420 through 422' Processing helix chain 'F' and resid 423 through 428 Processing helix chain 'F' and resid 435 through 449 Processing helix chain 'F' and resid 455 through 460 Processing helix chain 'F' and resid 464 through 475 Processing helix chain 'J' and resid 13 through 19 removed outlier: 3.980A pdb=" N GLY J 19 " --> pdb=" O VAL J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 55 Processing helix chain 'G' and resid 2 through 55 removed outlier: 3.608A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 3.786A pdb=" N VAL G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR G 44 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 96 removed outlier: 3.568A pdb=" N VAL G 85 " --> pdb=" O ILE G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 118 removed outlier: 4.217A pdb=" N ARG G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 152 removed outlier: 3.814A pdb=" N GLY G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 186 Processing helix chain 'G' and resid 187 through 193 removed outlier: 4.206A pdb=" N ILE G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 272 Processing helix chain 'H' and resid 104 through 122 removed outlier: 4.245A pdb=" N LEU H 120 " --> pdb=" O GLN H 116 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 145 Processing helix chain 'I' and resid 10 through 26 Processing helix chain 'I' and resid 30 through 38 removed outlier: 3.888A pdb=" N ALA I 34 " --> pdb=" O PHE I 30 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER I 38 " --> pdb=" O ALA I 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 16 removed outlier: 3.712A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 39 Processing helix chain 'K' and resid 42 through 73 Processing helix chain 'L' and resid 3 through 39 removed outlier: 3.957A pdb=" N VAL L 16 " --> pdb=" O GLY L 12 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL L 18 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA L 19 " --> pdb=" O THR L 15 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY L 20 " --> pdb=" O VAL L 16 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 73 removed outlier: 3.553A pdb=" N GLY L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 17 through 39 removed outlier: 3.570A pdb=" N SER N 21 " --> pdb=" O GLY N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 73 removed outlier: 4.468A pdb=" N SER N 48 " --> pdb=" O GLN N 44 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 21 removed outlier: 4.264A pdb=" N GLY O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA O 11 " --> pdb=" O LYS O 7 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL O 16 " --> pdb=" O GLY O 12 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA O 19 " --> pdb=" O THR O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 39 Processing helix chain 'O' and resid 42 through 73 removed outlier: 3.800A pdb=" N SER O 48 " --> pdb=" O GLN O 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 16 removed outlier: 3.663A pdb=" N VAL P 16 " --> pdb=" O GLY P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 39 removed outlier: 3.732A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE P 29 " --> pdb=" O ILE P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 73 removed outlier: 3.925A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 39 removed outlier: 3.526A pdb=" N VAL Q 16 " --> pdb=" O GLY Q 12 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL Q 18 " --> pdb=" O ALA Q 14 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA Q 19 " --> pdb=" O THR Q 15 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY Q 20 " --> pdb=" O VAL Q 16 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 73 Processing helix chain 'R' and resid 3 through 17 removed outlier: 3.876A pdb=" N PHE R 8 " --> pdb=" O THR R 4 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE R 9 " --> pdb=" O ALA R 5 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 39 removed outlier: 4.240A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY R 26 " --> pdb=" O GLY R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 73 removed outlier: 3.931A pdb=" N VAL R 67 " --> pdb=" O PHE R 63 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA R 68 " --> pdb=" O CYS R 64 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 19 removed outlier: 3.606A pdb=" N VAL M 16 " --> pdb=" O GLY M 12 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 39 removed outlier: 4.009A pdb=" N GLY M 24 " --> pdb=" O GLY M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 73 removed outlier: 3.629A pdb=" N MET M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 239 through 260 Proline residue: B 247 - end of helix removed outlier: 4.001A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 295 through 296 No H-bonds generated for 'chain 'B' and resid 295 through 296' Processing helix chain 'B' and resid 297 through 308 removed outlier: 3.918A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.521A pdb=" N GLN B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.530A pdb=" N VAL B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 removed outlier: 3.873A pdb=" N GLN B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 429 Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 460 through 475 Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.536A pdb=" N LEU B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 509 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 35 removed outlier: 6.698A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 43 current: chain 'A' and resid 60 through 66 removed outlier: 5.779A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 71 through 75 current: chain 'D' and resid 22 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 22 through 27 current: chain 'D' and resid 48 through 56 removed outlier: 6.594A pdb=" N ARG D 61 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N HIS D 54 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR D 59 " --> pdb=" O HIS D 54 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 64 current: chain 'E' and resid 22 through 26 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 22 through 26 current: chain 'E' and resid 48 through 54 removed outlier: 6.861A pdb=" N ARG E 61 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N HIS E 54 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR E 59 " --> pdb=" O HIS E 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.474A pdb=" N VAL A 108 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N ILE A 230 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 206 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.705A pdb=" N ILE A 327 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 349 Processing sheet with id=AA6, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.766A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 43 current: chain 'C' and resid 60 through 66 removed outlier: 5.803A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 75 current: chain 'F' and resid 22 through 27 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 22 through 27 current: chain 'F' and resid 48 through 54 removed outlier: 6.680A pdb=" N ARG F 61 " --> pdb=" O ALA F 52 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N HIS F 54 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR F 59 " --> pdb=" O HIS F 54 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 59 through 64 current: chain 'B' and resid 38 through 43 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 43 current: chain 'B' and resid 60 through 66 removed outlier: 6.302A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.924A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.524A pdb=" N VAL C 108 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N ILE C 230 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR C 200 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ILE C 267 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE C 202 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASP C 269 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 204 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 326 through 328 removed outlier: 6.375A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU C 352 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE C 168 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 85 through 88 removed outlier: 4.061A pdb=" N GLN D 114 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 96 through 97 removed outlier: 6.607A pdb=" N SER D 183 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL D 220 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE D 185 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLY D 222 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLY D 187 " --> pdb=" O GLY D 222 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL D 184 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ASP D 258 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA D 186 " --> pdb=" O ASP D 258 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL D 253 " --> pdb=" O THR D 307 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL D 309 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU D 255 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ALA D 311 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE D 257 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N TYR D 313 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS D 153 " --> pdb=" O ALA D 333 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N THR D 335 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY D 155 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU D 337 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE D 157 " --> pdb=" O LEU D 337 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 85 through 88 removed outlier: 4.088A pdb=" N GLN E 114 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 96 through 97 removed outlier: 6.981A pdb=" N SER E 183 " --> pdb=" O ALA E 218 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N VAL E 220 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE E 185 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLY E 222 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY E 187 " --> pdb=" O GLY E 222 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL E 184 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASP E 258 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ALA E 186 " --> pdb=" O ASP E 258 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS E 153 " --> pdb=" O ALA E 333 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR E 335 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLY E 155 " --> pdb=" O THR E 335 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.404A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 85 through 88 removed outlier: 4.158A pdb=" N GLN F 114 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 96 through 97 removed outlier: 6.299A pdb=" N MET F 97 " --> pdb=" O TYR F 221 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER F 183 " --> pdb=" O ALA F 218 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL F 220 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE F 185 " --> pdb=" O VAL F 220 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLY F 222 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY F 187 " --> pdb=" O GLY F 222 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL F 253 " --> pdb=" O THR F 307 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL F 309 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU F 255 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ALA F 311 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE F 257 " --> pdb=" O ALA F 311 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N TYR F 313 " --> pdb=" O ILE F 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.355A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 102 through 106 removed outlier: 3.652A pdb=" N GLY G 70 " --> pdb=" O VAL G 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 126 through 129 removed outlier: 3.523A pdb=" N THR G 127 " --> pdb=" O VAL I 45 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 16 through 21 removed outlier: 4.083A pdb=" N MET H 16 " --> pdb=" O VAL H 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 46 through 47 current: chain 'H' and resid 72 through 77 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 72 through 77 current: chain 'H' and resid 89 through 94 Processing sheet with id=AC3, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.625A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.556A pdb=" N VAL B 108 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N THR B 235 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N ILE B 230 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N CYS B 201 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL B 232 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N TYR B 203 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALA B 234 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA B 205 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.524A pdb=" N ILE B 159 " --> pdb=" O MET B 146 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.746A pdb=" N ILE B 327 " --> pdb=" O ILE B 167 " (cutoff:3.500A) 1612 hydrogen bonds defined for protein. 4674 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: 4.78 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9933 1.34 - 1.46: 4188 1.46 - 1.57: 15994 1.57 - 1.69: 19 1.69 - 1.81: 190 Bond restraints: 30324 Sorted by residual: bond pdb=" C GLY N 20 " pdb=" N SER N 21 " ideal model delta sigma weight residual 1.334 1.415 -0.080 1.27e-02 6.20e+03 4.02e+01 bond pdb=" C SER N 21 " pdb=" N GLY N 22 " ideal model delta sigma weight residual 1.334 1.276 0.058 1.23e-02 6.61e+03 2.21e+01 bond pdb=" C LEU F 398 " pdb=" N SER F 399 " ideal model delta sigma weight residual 1.330 1.378 -0.048 1.31e-02 5.83e+03 1.36e+01 bond pdb=" N ILE A 266 " pdb=" CA ILE A 266 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.14e-02 7.69e+03 9.05e+00 bond pdb=" N ILE D 257 " pdb=" CA ILE D 257 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.14e-02 7.69e+03 8.76e+00 ... (remaining 30319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 40076 1.54 - 3.08: 790 3.08 - 4.62: 117 4.62 - 6.17: 28 6.17 - 7.71: 4 Bond angle restraints: 41015 Sorted by residual: angle pdb=" CA GLY N 20 " pdb=" C GLY N 20 " pdb=" N SER N 21 " ideal model delta sigma weight residual 117.04 111.18 5.86 9.90e-01 1.02e+00 3.51e+01 angle pdb=" O GLY N 20 " pdb=" C GLY N 20 " pdb=" N SER N 21 " ideal model delta sigma weight residual 122.19 127.77 -5.58 9.60e-01 1.09e+00 3.38e+01 angle pdb=" N LEU A 271 " pdb=" CA LEU A 271 " pdb=" C LEU A 271 " ideal model delta sigma weight residual 112.54 107.50 5.04 1.22e+00 6.72e-01 1.70e+01 angle pdb=" N LEU C 271 " pdb=" CA LEU C 271 " pdb=" C LEU C 271 " ideal model delta sigma weight residual 112.38 107.47 4.91 1.22e+00 6.72e-01 1.62e+01 angle pdb=" N LEU B 271 " pdb=" CA LEU B 271 " pdb=" C LEU B 271 " ideal model delta sigma weight residual 111.71 107.21 4.50 1.15e+00 7.56e-01 1.53e+01 ... (remaining 41010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 17942 35.45 - 70.90: 371 70.90 - 106.35: 12 106.35 - 141.80: 2 141.80 - 177.25: 2 Dihedral angle restraints: 18329 sinusoidal: 7182 harmonic: 11147 Sorted by residual: dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 117.25 -177.25 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2' ADP D 501 " pdb=" C1' ADP D 501 " pdb=" N9 ADP D 501 " pdb=" C4 ADP D 501 " ideal model delta sinusoidal sigma weight residual 91.55 -94.84 -173.62 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 69.62 -129.63 1 2.00e+01 2.50e-03 3.93e+01 ... (remaining 18326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3909 0.050 - 0.100: 689 0.100 - 0.150: 165 0.150 - 0.200: 18 0.200 - 0.250: 5 Chirality restraints: 4786 Sorted by residual: chirality pdb=" CA ILE D 257 " pdb=" N ILE D 257 " pdb=" C ILE D 257 " pdb=" CB ILE D 257 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE F 257 " pdb=" N ILE F 257 " pdb=" C ILE F 257 " pdb=" CB ILE F 257 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA LEU R 32 " pdb=" N LEU R 32 " pdb=" C LEU R 32 " pdb=" CB LEU R 32 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 4783 not shown) Planarity restraints: 5279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 390 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C ILE F 390 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE F 390 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA F 391 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 362 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C PRO E 362 " -0.034 2.00e-02 2.50e+03 pdb=" O PRO E 362 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN E 363 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 472 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C VAL C 472 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL C 472 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE C 473 " -0.011 2.00e-02 2.50e+03 ... (remaining 5276 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 115 2.47 - 3.08: 22807 3.08 - 3.69: 48917 3.69 - 4.29: 74132 4.29 - 4.90: 119458 Nonbonded interactions: 265429 Sorted by model distance: nonbonded pdb=" O2G ATP A 601 " pdb="MG MG A 602 " model vdw 1.868 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 602 " model vdw 2.024 2.170 nonbonded pdb=" O2B ATP C 601 " pdb="MG MG C 602 " model vdw 2.098 2.170 nonbonded pdb=" O1B ADP F 501 " pdb="MG MG F 502 " model vdw 2.137 2.170 nonbonded pdb=" OG1 THR D 165 " pdb="MG MG D 502 " model vdw 2.186 2.170 ... (remaining 265424 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 26 and (name N or name CA or name C or name O or name CB \ )) or resid 27 through 407 or resid 409 through 601)) selection = (chain 'B' and ((resid 26 and (name N or name CA or name C or name O or name CB \ )) or resid 27 through 407 or resid 409 through 601)) selection = (chain 'C' and resid 26 through 601) } ncs_group { reference = (chain 'D' and resid 10 through 476) selection = chain 'E' selection = (chain 'F' and resid 10 through 476) } ncs_group { reference = (chain 'K' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'L' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'M' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 73)) selection = (chain 'N' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 65 or (resid 66 and (name N or name C \ A or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'O' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 73)) selection = (chain 'P' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'Q' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'R' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 65 or (resid 66 and (name N or name \ CA or name C or name O or name CB )) or resid 67 through 73)) } 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=0.75 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: 12.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.510 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 30324 Z= 0.193 Angle : 0.556 7.707 41015 Z= 0.334 Chirality : 0.042 0.250 4786 Planarity : 0.004 0.049 5279 Dihedral : 13.189 177.251 11225 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.23 % Favored : 97.70 % Rotamer: Outliers : 4.81 % Allowed : 6.39 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.13), residues: 3909 helix: 1.56 (0.12), residues: 1892 sheet: -1.06 (0.22), residues: 470 loop : -0.28 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 38 TYR 0.020 0.001 TYR I 14 PHE 0.017 0.001 PHE H 28 TRP 0.007 0.002 TRP I 4 HIS 0.004 0.001 HIS D 369 Details of bonding type rmsd covalent geometry : bond 0.00334 (30324) covalent geometry : angle 0.55615 (41015) hydrogen bonds : bond 0.14852 ( 1612) hydrogen bonds : angle 6.40583 ( 4674) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 743 time to evaluate : 1.057 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 336 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8344 (t) REVERT: G 125 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7188 (pt) REVERT: H 84 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7868 (p) REVERT: H 131 ILE cc_start: 0.8189 (mm) cc_final: 0.7666 (tp) REVERT: H 133 ILE cc_start: 0.8373 (mm) cc_final: 0.7648 (mm) REVERT: H 135 ILE cc_start: 0.7875 (pt) cc_final: 0.7402 (pt) REVERT: L 56 LEU cc_start: 0.7305 (mm) cc_final: 0.6609 (mm) REVERT: L 62 LEU cc_start: 0.8154 (tp) cc_final: 0.7751 (mt) REVERT: L 73 PHE cc_start: 0.6039 (m-80) cc_final: 0.5778 (m-80) REVERT: O 49 TYR cc_start: 0.5612 (m-80) cc_final: 0.5350 (m-80) REVERT: O 65 LEU cc_start: 0.8582 (tp) cc_final: 0.8093 (tp) REVERT: P 7 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8040 (mmmt) REVERT: Q 54 PHE cc_start: 0.7724 (t80) cc_final: 0.7387 (t80) REVERT: Q 63 PHE cc_start: 0.7426 (t80) cc_final: 0.7018 (t80) REVERT: R 67 VAL cc_start: 0.8521 (t) cc_final: 0.8278 (t) REVERT: M 8 PHE cc_start: 0.7562 (m-10) cc_final: 0.7361 (m-10) REVERT: M 56 LEU cc_start: 0.7113 (tp) cc_final: 0.6587 (tp) REVERT: M 62 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6538 (mm) outliers start: 149 outliers final: 29 residues processed: 848 average time/residue: 0.1899 time to fit residues: 249.5351 Evaluate side-chains 513 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 480 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain Q residue 45 GLN Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain B residue 73 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS A 302 HIS A 476 HIS C 46 ASN C 186 GLN C 302 HIS C 341 ASN C 441 GLN C 471 HIS C 477 GLN D 330 HIS D 453 HIS D 479 HIS E 377 GLN F 259 ASN F 295 GLN F 330 HIS F 381 GLN G 66 HIS ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN O 45 GLN Q 45 GLN B 65 ASN B 70 ASN B 208 GLN B 302 HIS ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.061500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.049252 restraints weight = 110403.375| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.61 r_work: 0.2886 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 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 : 0.007 0.061 30324 Z= 0.313 Angle : 0.676 12.929 41015 Z= 0.355 Chirality : 0.046 0.246 4786 Planarity : 0.005 0.049 5279 Dihedral : 8.445 170.231 4413 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.07 % Favored : 96.88 % Rotamer: Outliers : 3.90 % Allowed : 12.84 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.13), residues: 3909 helix: 1.50 (0.12), residues: 1910 sheet: -1.08 (0.21), residues: 525 loop : -0.14 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 32 TYR 0.020 0.002 TYR G 193 PHE 0.021 0.002 PHE Q 47 TRP 0.016 0.004 TRP I 4 HIS 0.007 0.002 HIS E 369 Details of bonding type rmsd covalent geometry : bond 0.00708 (30324) covalent geometry : angle 0.67598 (41015) hydrogen bonds : bond 0.05460 ( 1612) hydrogen bonds : angle 5.33663 ( 4674) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 512 time to evaluate : 1.284 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ASP cc_start: 0.9064 (t0) cc_final: 0.8774 (t0) REVERT: C 479 LEU cc_start: 0.9350 (tp) cc_final: 0.8982 (tp) REVERT: D 294 MET cc_start: 0.8798 (tmm) cc_final: 0.8232 (tmm) REVERT: D 474 LYS cc_start: 0.8588 (tttm) cc_final: 0.8328 (tptp) REVERT: E 65 MET cc_start: 0.9044 (mmt) cc_final: 0.8503 (mmm) REVERT: E 128 MET cc_start: 0.9093 (mmp) cc_final: 0.8700 (mmt) REVERT: E 353 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8807 (mp) REVERT: E 381 GLN cc_start: 0.9128 (tp40) cc_final: 0.8781 (tp40) REVERT: F 165 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8967 (m) REVERT: J 40 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7766 (pp20) REVERT: H 18 PHE cc_start: 0.8554 (t80) cc_final: 0.8032 (t80) REVERT: H 35 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8500 (tm-30) REVERT: H 72 THR cc_start: 0.8962 (p) cc_final: 0.8431 (t) REVERT: H 76 PHE cc_start: 0.9054 (t80) cc_final: 0.8810 (t80) REVERT: H 111 ASN cc_start: 0.9088 (m-40) cc_final: 0.8756 (m-40) REVERT: H 131 ILE cc_start: 0.9502 (mm) cc_final: 0.9275 (tp) REVERT: I 43 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8116 (ttpp) REVERT: K 54 PHE cc_start: 0.9257 (t80) cc_final: 0.8985 (t80) REVERT: K 71 ILE cc_start: 0.8213 (tp) cc_final: 0.7935 (tp) REVERT: L 56 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7894 (mt) REVERT: L 60 MET cc_start: 0.8353 (mmm) cc_final: 0.8078 (mtm) REVERT: L 73 PHE cc_start: 0.6121 (m-80) cc_final: 0.5641 (m-80) REVERT: N 44 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8097 (tp40) REVERT: O 49 TYR cc_start: 0.8347 (m-80) cc_final: 0.7507 (m-80) REVERT: O 71 ILE cc_start: 0.8668 (mm) cc_final: 0.8383 (mt) REVERT: P 7 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7715 (mmmt) REVERT: P 29 PHE cc_start: 0.8486 (m-80) cc_final: 0.8272 (m-80) REVERT: P 60 MET cc_start: 0.9161 (ttm) cc_final: 0.8673 (ttm) REVERT: P 62 LEU cc_start: 0.8840 (mt) cc_final: 0.8593 (mm) REVERT: Q 54 PHE cc_start: 0.8240 (t80) cc_final: 0.8015 (t80) REVERT: Q 63 PHE cc_start: 0.8107 (t80) cc_final: 0.7884 (t80) REVERT: R 49 TYR cc_start: 0.8088 (m-80) cc_final: 0.7809 (m-80) REVERT: R 69 PHE cc_start: 0.8307 (t80) cc_final: 0.7951 (t80) REVERT: M 3 ASP cc_start: 0.8238 (p0) cc_final: 0.7990 (p0) REVERT: M 7 LYS cc_start: 0.6851 (mmtt) cc_final: 0.5931 (mttp) REVERT: M 21 SER cc_start: 0.8926 (m) cc_final: 0.8641 (p) REVERT: M 62 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8721 (mm) REVERT: B 253 MET cc_start: 0.9150 (mtt) cc_final: 0.8860 (mtp) outliers start: 121 outliers final: 68 residues processed: 587 average time/residue: 0.1695 time to fit residues: 159.3443 Evaluate side-chains 529 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 456 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 363 ASN Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 3 TYR Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 64 CYS Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 64 CYS Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 462 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 182 optimal weight: 0.2980 chunk 96 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 342 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 241 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 247 optimal weight: 10.0000 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 413 GLN F 179 HIS ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 HIS ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN B 475 GLN B 476 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.062889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.050533 restraints weight = 109675.315| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.72 r_work: 0.2945 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 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 0.057 30324 Z= 0.146 Angle : 0.572 15.010 41015 Z= 0.295 Chirality : 0.043 0.274 4786 Planarity : 0.004 0.042 5279 Dihedral : 7.742 166.635 4393 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.49 % Rotamer: Outliers : 3.71 % Allowed : 13.74 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.13), residues: 3909 helix: 1.64 (0.12), residues: 1915 sheet: -0.95 (0.22), residues: 490 loop : -0.08 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 39 TYR 0.020 0.001 TYR Q 49 PHE 0.018 0.002 PHE N 69 TRP 0.023 0.005 TRP I 4 HIS 0.004 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00318 (30324) covalent geometry : angle 0.57235 (41015) hydrogen bonds : bond 0.04687 ( 1612) hydrogen bonds : angle 4.92520 ( 4674) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 489 time to evaluate : 1.185 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 ARG cc_start: 0.8550 (ptm-80) cc_final: 0.8305 (mtm110) REVERT: C 479 LEU cc_start: 0.9345 (tp) cc_final: 0.9139 (tp) REVERT: D 294 MET cc_start: 0.8829 (tmm) cc_final: 0.8277 (tmm) REVERT: D 395 MET cc_start: 0.8268 (tpp) cc_final: 0.7995 (tpp) REVERT: D 474 LYS cc_start: 0.8618 (tttm) cc_final: 0.8347 (tptp) REVERT: E 65 MET cc_start: 0.9014 (mmt) cc_final: 0.8427 (mmm) REVERT: E 145 LEU cc_start: 0.9243 (mp) cc_final: 0.8577 (mt) REVERT: E 321 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8129 (t0) REVERT: E 347 TYR cc_start: 0.8440 (m-80) cc_final: 0.8045 (m-80) REVERT: E 381 GLN cc_start: 0.9078 (tp40) cc_final: 0.8762 (mm110) REVERT: F 165 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8963 (m) REVERT: F 224 MET cc_start: 0.9203 (ptp) cc_final: 0.8991 (ptp) REVERT: F 396 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8952 (p0) REVERT: J 26 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: G 23 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8771 (mtp) REVERT: G 124 PHE cc_start: 0.9024 (m-80) cc_final: 0.8740 (m-80) REVERT: G 129 LYS cc_start: 0.9385 (mmtp) cc_final: 0.8911 (mmtt) REVERT: H 18 PHE cc_start: 0.8491 (t80) cc_final: 0.7906 (t80) REVERT: H 35 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8602 (tm-30) REVERT: H 74 LYS cc_start: 0.9068 (mttm) cc_final: 0.8750 (mmtt) REVERT: H 128 ARG cc_start: 0.9129 (tpp80) cc_final: 0.8836 (tpp80) REVERT: H 131 ILE cc_start: 0.9500 (mm) cc_final: 0.9270 (tp) REVERT: K 54 PHE cc_start: 0.9241 (t80) cc_final: 0.8921 (t80) REVERT: L 8 PHE cc_start: 0.8101 (m-10) cc_final: 0.7752 (m-10) REVERT: N 44 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8429 (tp-100) REVERT: O 18 VAL cc_start: 0.6747 (OUTLIER) cc_final: 0.6543 (p) REVERT: O 49 TYR cc_start: 0.8402 (m-80) cc_final: 0.8045 (m-80) REVERT: O 71 ILE cc_start: 0.8685 (mm) cc_final: 0.8419 (mt) REVERT: P 7 LYS cc_start: 0.8379 (mtpt) cc_final: 0.7918 (mmmt) REVERT: P 60 MET cc_start: 0.9082 (ttm) cc_final: 0.8576 (ttm) REVERT: P 62 LEU cc_start: 0.8867 (mt) cc_final: 0.8661 (mm) REVERT: Q 54 PHE cc_start: 0.8242 (t80) cc_final: 0.7886 (t80) REVERT: R 49 TYR cc_start: 0.8084 (m-80) cc_final: 0.7848 (m-80) REVERT: R 66 MET cc_start: 0.8327 (tmm) cc_final: 0.7548 (tmm) REVERT: R 69 PHE cc_start: 0.8192 (t80) cc_final: 0.7825 (t80) REVERT: R 70 LEU cc_start: 0.8994 (tt) cc_final: 0.8682 (mm) REVERT: M 21 SER cc_start: 0.8645 (m) cc_final: 0.8432 (t) REVERT: M 58 GLU cc_start: 0.8857 (tp30) cc_final: 0.8340 (tp30) REVERT: M 62 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8253 (mm) REVERT: M 64 CYS cc_start: 0.9239 (t) cc_final: 0.8890 (t) REVERT: M 65 LEU cc_start: 0.8826 (tp) cc_final: 0.8520 (mm) REVERT: M 69 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8195 (t80) REVERT: B 410 LEU cc_start: 0.8953 (mm) cc_final: 0.8741 (mm) REVERT: B 475 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8348 (mp10) REVERT: B 499 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8555 (tm-30) outliers start: 115 outliers final: 66 residues processed: 561 average time/residue: 0.1764 time to fit residues: 157.6778 Evaluate side-chains 523 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 447 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 101 LYS Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 3 TYR Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 54 PHE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 64 CYS Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 64 CYS Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 475 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 130 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 296 optimal weight: 3.9990 chunk 325 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 245 optimal weight: 0.5980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN C 476 HIS D 363 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 GLN H 138 ASN I 41 ASN Q 44 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.061123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.048821 restraints weight = 109781.045| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.60 r_work: 0.2882 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 30324 Z= 0.266 Angle : 0.622 12.521 41015 Z= 0.323 Chirality : 0.045 0.309 4786 Planarity : 0.004 0.047 5279 Dihedral : 7.600 167.261 4392 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.15 % Favored : 96.80 % Rotamer: Outliers : 4.61 % Allowed : 13.77 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.13), residues: 3909 helix: 1.51 (0.12), residues: 1911 sheet: -0.87 (0.22), residues: 482 loop : -0.08 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 35 TYR 0.018 0.002 TYR G 52 PHE 0.034 0.002 PHE C 403 TRP 0.024 0.005 TRP I 4 HIS 0.006 0.001 HIS E 369 Details of bonding type rmsd covalent geometry : bond 0.00601 (30324) covalent geometry : angle 0.62230 (41015) hydrogen bonds : bond 0.04822 ( 1612) hydrogen bonds : angle 4.97658 ( 4674) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 462 time to evaluate : 1.075 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: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8470 (ttm) REVERT: A 439 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8569 (mp0) REVERT: C 136 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8908 (mt) REVERT: C 146 MET cc_start: 0.9062 (tmm) cc_final: 0.8463 (tmm) REVERT: D 294 MET cc_start: 0.8874 (tmm) cc_final: 0.8331 (tmm) REVERT: D 395 MET cc_start: 0.8379 (tpp) cc_final: 0.8131 (tpp) REVERT: E 65 MET cc_start: 0.9044 (mmt) cc_final: 0.8524 (mmm) REVERT: E 128 MET cc_start: 0.8996 (mmm) cc_final: 0.8673 (mmt) REVERT: E 145 LEU cc_start: 0.9314 (mp) cc_final: 0.8953 (mt) REVERT: E 321 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8007 (t0) REVERT: E 347 TYR cc_start: 0.8522 (m-80) cc_final: 0.8093 (m-80) REVERT: F 165 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8923 (m) REVERT: F 390 ILE cc_start: 0.9352 (mt) cc_final: 0.9115 (mt) REVERT: J 26 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: J 30 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8369 (mt-10) REVERT: G 147 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8714 (mm-30) REVERT: H 18 PHE cc_start: 0.8490 (t80) cc_final: 0.7841 (t80) REVERT: H 35 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8698 (tm-30) REVERT: H 40 THR cc_start: 0.9468 (OUTLIER) cc_final: 0.9153 (p) REVERT: H 59 ARG cc_start: 0.8959 (ttp-110) cc_final: 0.8681 (ttm110) REVERT: H 74 LYS cc_start: 0.9161 (mttm) cc_final: 0.8770 (mmtt) REVERT: H 91 GLN cc_start: 0.8656 (mp-120) cc_final: 0.7818 (mp10) REVERT: H 133 ILE cc_start: 0.9273 (mm) cc_final: 0.9006 (mm) REVERT: K 28 VAL cc_start: 0.9326 (t) cc_final: 0.9045 (m) REVERT: K 38 ARG cc_start: 0.7159 (tpt90) cc_final: 0.6929 (tpt90) REVERT: K 71 ILE cc_start: 0.8301 (tp) cc_final: 0.7964 (tp) REVERT: L 7 LYS cc_start: 0.7095 (tmtt) cc_final: 0.6625 (tmtt) REVERT: L 47 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8195 (m-10) REVERT: L 66 MET cc_start: 0.8687 (mmm) cc_final: 0.8353 (mmt) REVERT: N 44 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8338 (tm-30) REVERT: O 18 VAL cc_start: 0.6789 (OUTLIER) cc_final: 0.6332 (p) REVERT: O 45 GLN cc_start: 0.8805 (mt0) cc_final: 0.8207 (mt0) REVERT: O 49 TYR cc_start: 0.8420 (m-10) cc_final: 0.8096 (m-80) REVERT: O 71 ILE cc_start: 0.8721 (mm) cc_final: 0.8457 (mt) REVERT: P 7 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7932 (mmmt) REVERT: P 60 MET cc_start: 0.9049 (ttm) cc_final: 0.8454 (ttt) REVERT: P 62 LEU cc_start: 0.8808 (mt) cc_final: 0.8576 (mm) REVERT: Q 54 PHE cc_start: 0.8198 (t80) cc_final: 0.7952 (t80) REVERT: R 69 PHE cc_start: 0.8416 (t80) cc_final: 0.8076 (t80) REVERT: M 21 SER cc_start: 0.8697 (m) cc_final: 0.8409 (p) REVERT: M 58 GLU cc_start: 0.8911 (tp30) cc_final: 0.8245 (pt0) REVERT: M 69 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8296 (t80) REVERT: B 393 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8542 (mp0) REVERT: B 410 LEU cc_start: 0.8846 (mm) cc_final: 0.8619 (mm) REVERT: B 439 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8821 (mp0) outliers start: 143 outliers final: 87 residues processed: 557 average time/residue: 0.1696 time to fit residues: 152.5118 Evaluate side-chains 541 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 442 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 101 LYS Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 16 GLN Chi-restraints excluded: chain I residue 36 LYS Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 54 PHE Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 64 CYS Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 462 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 188 optimal weight: 0.9990 chunk 356 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 273 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 432 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 GLN H 56 GLN B 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.061244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.048859 restraints weight = 110065.752| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.61 r_work: 0.2883 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30324 Z= 0.234 Angle : 0.612 12.719 41015 Z= 0.317 Chirality : 0.044 0.297 4786 Planarity : 0.004 0.045 5279 Dihedral : 7.392 166.459 4387 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.02 % Favored : 96.93 % Rotamer: Outliers : 4.10 % Allowed : 15.26 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.13), residues: 3909 helix: 1.47 (0.12), residues: 1911 sheet: -0.84 (0.22), residues: 481 loop : -0.12 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 59 TYR 0.016 0.002 TYR C 244 PHE 0.032 0.002 PHE C 403 TRP 0.031 0.007 TRP I 4 HIS 0.005 0.001 HIS E 369 Details of bonding type rmsd covalent geometry : bond 0.00530 (30324) covalent geometry : angle 0.61214 (41015) hydrogen bonds : bond 0.04649 ( 1612) hydrogen bonds : angle 4.90711 ( 4674) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 456 time to evaluate : 1.018 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: symmetry clash revert: symmetry clash REVERT: A 439 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8582 (mp0) REVERT: A 457 GLU cc_start: 0.7010 (tm-30) cc_final: 0.6691 (tm-30) REVERT: C 146 MET cc_start: 0.9075 (tmm) cc_final: 0.8524 (tmm) REVERT: D 294 MET cc_start: 0.8862 (tmm) cc_final: 0.8304 (tmm) REVERT: D 395 MET cc_start: 0.8364 (tpp) cc_final: 0.8105 (tpp) REVERT: D 434 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.9140 (t) REVERT: E 65 MET cc_start: 0.9067 (mmt) cc_final: 0.8642 (mmt) REVERT: E 128 MET cc_start: 0.8998 (mmm) cc_final: 0.8724 (mmt) REVERT: E 145 LEU cc_start: 0.9308 (mp) cc_final: 0.9004 (mt) REVERT: E 202 MET cc_start: 0.9022 (mtt) cc_final: 0.8800 (mtt) REVERT: E 321 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8350 (m-30) REVERT: F 165 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8878 (m) REVERT: F 343 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8322 (mp0) REVERT: F 390 ILE cc_start: 0.9270 (mt) cc_final: 0.9028 (mt) REVERT: F 396 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8825 (p0) REVERT: J 26 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: J 30 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8417 (mt-10) REVERT: J 40 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7804 (pp20) REVERT: G 110 ASP cc_start: 0.9095 (t0) cc_final: 0.8883 (m-30) REVERT: G 124 PHE cc_start: 0.9033 (m-80) cc_final: 0.8768 (m-80) REVERT: G 147 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8780 (mm-30) REVERT: H 18 PHE cc_start: 0.8570 (t80) cc_final: 0.7889 (t80) REVERT: H 32 ASN cc_start: 0.7563 (p0) cc_final: 0.6865 (p0) REVERT: H 40 THR cc_start: 0.9502 (OUTLIER) cc_final: 0.9085 (p) REVERT: H 59 ARG cc_start: 0.9005 (ttp-110) cc_final: 0.8642 (ttp-110) REVERT: H 68 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7595 (mt-10) REVERT: H 74 LYS cc_start: 0.9171 (mttm) cc_final: 0.8817 (mmtt) REVERT: H 91 GLN cc_start: 0.8650 (mp-120) cc_final: 0.7848 (mp10) REVERT: H 133 ILE cc_start: 0.9425 (mm) cc_final: 0.8584 (mm) REVERT: K 28 VAL cc_start: 0.9288 (t) cc_final: 0.9041 (m) REVERT: L 8 PHE cc_start: 0.8049 (m-10) cc_final: 0.7599 (m-10) REVERT: L 39 ASN cc_start: 0.9467 (t0) cc_final: 0.9204 (t0) REVERT: L 47 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: L 66 MET cc_start: 0.8592 (mmm) cc_final: 0.8267 (mmt) REVERT: N 44 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8464 (tm-30) REVERT: N 65 LEU cc_start: 0.8533 (pp) cc_final: 0.8268 (mm) REVERT: O 18 VAL cc_start: 0.6835 (OUTLIER) cc_final: 0.6377 (p) REVERT: O 49 TYR cc_start: 0.8430 (m-10) cc_final: 0.8064 (m-80) REVERT: O 71 ILE cc_start: 0.8711 (mm) cc_final: 0.8458 (mt) REVERT: P 60 MET cc_start: 0.9025 (ttm) cc_final: 0.8458 (ttt) REVERT: Q 54 PHE cc_start: 0.8194 (t80) cc_final: 0.7888 (t80) REVERT: Q 63 PHE cc_start: 0.8322 (t80) cc_final: 0.8035 (t80) REVERT: R 7 LYS cc_start: 0.8082 (mttm) cc_final: 0.7683 (mmtt) REVERT: R 69 PHE cc_start: 0.8444 (t80) cc_final: 0.8077 (t80) REVERT: R 70 LEU cc_start: 0.8953 (tt) cc_final: 0.8671 (mt) REVERT: M 58 GLU cc_start: 0.8962 (tp30) cc_final: 0.8236 (pt0) REVERT: M 69 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8370 (t80) REVERT: B 393 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8556 (mp0) REVERT: B 439 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8823 (mp0) outliers start: 127 outliers final: 89 residues processed: 540 average time/residue: 0.1787 time to fit residues: 154.3552 Evaluate side-chains 539 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 438 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 101 LYS Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 36 LYS Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 54 PHE Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 64 CYS Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 483 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 42 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 332 optimal weight: 10.0000 chunk 252 optimal weight: 0.2980 chunk 134 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 381 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 GLN B 65 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.062492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.049994 restraints weight = 108747.948| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.65 r_work: 0.2908 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30324 Z= 0.138 Angle : 0.572 13.049 41015 Z= 0.291 Chirality : 0.042 0.268 4786 Planarity : 0.003 0.044 5279 Dihedral : 7.174 165.045 4385 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 3.52 % Allowed : 16.84 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.14), residues: 3909 helix: 1.58 (0.12), residues: 1912 sheet: -0.73 (0.23), residues: 481 loop : -0.06 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 38 TYR 0.023 0.001 TYR I 3 PHE 0.020 0.001 PHE Q 47 TRP 0.027 0.006 TRP I 4 HIS 0.004 0.001 HIS E 369 Details of bonding type rmsd covalent geometry : bond 0.00305 (30324) covalent geometry : angle 0.57156 (41015) hydrogen bonds : bond 0.04343 ( 1612) hydrogen bonds : angle 4.74258 ( 4674) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 468 time to evaluate : 1.030 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8649 (ttm) REVERT: A 439 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8578 (mp0) REVERT: C 146 MET cc_start: 0.9086 (tmm) cc_final: 0.8516 (tmm) REVERT: D 294 MET cc_start: 0.8838 (tmm) cc_final: 0.8228 (tmm) REVERT: E 65 MET cc_start: 0.9083 (mmt) cc_final: 0.8660 (mmt) REVERT: E 128 MET cc_start: 0.8954 (mmm) cc_final: 0.8470 (mmm) REVERT: E 202 MET cc_start: 0.8956 (mtt) cc_final: 0.8716 (mtt) REVERT: E 321 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8385 (m-30) REVERT: F 165 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8848 (m) REVERT: F 343 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8266 (mp0) REVERT: F 396 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8923 (p0) REVERT: J 16 ARG cc_start: 0.8592 (tpp80) cc_final: 0.8354 (tpt-90) REVERT: J 26 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: J 40 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7711 (pp20) REVERT: G 56 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8723 (m-30) REVERT: G 124 PHE cc_start: 0.9013 (m-80) cc_final: 0.8683 (m-80) REVERT: G 147 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8765 (mm-30) REVERT: G 232 MET cc_start: 0.8593 (mmp) cc_final: 0.8306 (mmp) REVERT: H 18 PHE cc_start: 0.8534 (t80) cc_final: 0.7887 (t80) REVERT: H 32 ASN cc_start: 0.7560 (p0) cc_final: 0.6854 (p0) REVERT: H 68 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7982 (mt-10) REVERT: H 91 GLN cc_start: 0.8614 (mp-120) cc_final: 0.7779 (mp10) REVERT: H 133 ILE cc_start: 0.9466 (mm) cc_final: 0.9020 (mm) REVERT: K 67 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8831 (p) REVERT: K 71 ILE cc_start: 0.8289 (tp) cc_final: 0.7956 (tp) REVERT: L 39 ASN cc_start: 0.9477 (t0) cc_final: 0.9168 (t0) REVERT: L 47 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.8102 (m-10) REVERT: L 66 MET cc_start: 0.8657 (mmm) cc_final: 0.8366 (mmt) REVERT: N 44 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8324 (tm-30) REVERT: N 65 LEU cc_start: 0.8484 (pp) cc_final: 0.8233 (mm) REVERT: O 18 VAL cc_start: 0.6757 (OUTLIER) cc_final: 0.6325 (p) REVERT: O 49 TYR cc_start: 0.8416 (m-10) cc_final: 0.8058 (m-80) REVERT: O 71 ILE cc_start: 0.8703 (mm) cc_final: 0.8449 (mt) REVERT: P 29 PHE cc_start: 0.8511 (m-80) cc_final: 0.8214 (m-80) REVERT: P 60 MET cc_start: 0.9001 (ttm) cc_final: 0.8458 (ttt) REVERT: Q 36 TYR cc_start: 0.8840 (t80) cc_final: 0.8636 (t80) REVERT: Q 54 PHE cc_start: 0.8168 (t80) cc_final: 0.7865 (t80) REVERT: R 7 LYS cc_start: 0.8091 (mttm) cc_final: 0.7811 (mttt) REVERT: R 69 PHE cc_start: 0.8405 (t80) cc_final: 0.8039 (t80) REVERT: R 70 LEU cc_start: 0.8959 (tt) cc_final: 0.8666 (mt) REVERT: M 58 GLU cc_start: 0.8970 (tp30) cc_final: 0.8123 (pt0) REVERT: M 69 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.8297 (t80) REVERT: B 253 MET cc_start: 0.9063 (mtp) cc_final: 0.8842 (mtt) outliers start: 109 outliers final: 78 residues processed: 536 average time/residue: 0.1743 time to fit residues: 149.1311 Evaluate side-chains 537 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 447 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 36 LYS Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 54 PHE Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 64 CYS Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 483 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 215 optimal weight: 3.9990 chunk 356 optimal weight: 3.9990 chunk 282 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 290 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 310 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 HIS ** E 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.047880 restraints weight = 110570.074| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.61 r_work: 0.2853 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 30324 Z= 0.335 Angle : 0.689 14.866 41015 Z= 0.353 Chirality : 0.047 0.282 4786 Planarity : 0.005 0.064 5279 Dihedral : 7.416 167.449 4385 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.67 % Rotamer: Outliers : 4.13 % Allowed : 16.74 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.14), residues: 3909 helix: 1.40 (0.12), residues: 1914 sheet: -0.74 (0.22), residues: 500 loop : -0.18 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 38 TYR 0.019 0.002 TYR C 244 PHE 0.032 0.002 PHE L 63 TRP 0.021 0.004 TRP I 4 HIS 0.007 0.001 HIS E 369 Details of bonding type rmsd covalent geometry : bond 0.00757 (30324) covalent geometry : angle 0.68857 (41015) hydrogen bonds : bond 0.04821 ( 1612) hydrogen bonds : angle 4.97201 ( 4674) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 459 time to evaluate : 0.760 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: A 439 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8629 (mp0) REVERT: C 146 MET cc_start: 0.9103 (tmm) cc_final: 0.8601 (tmm) REVERT: D 294 MET cc_start: 0.8896 (tmm) cc_final: 0.8342 (tmm) REVERT: D 395 MET cc_start: 0.8393 (mmm) cc_final: 0.7814 (tpp) REVERT: E 65 MET cc_start: 0.9107 (mmt) cc_final: 0.8629 (mmt) REVERT: E 128 MET cc_start: 0.9059 (mmm) cc_final: 0.8596 (mmm) REVERT: E 321 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8380 (m-30) REVERT: F 165 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.9017 (t) REVERT: F 294 MET cc_start: 0.8855 (tmm) cc_final: 0.8650 (ttp) REVERT: F 343 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8300 (mp0) REVERT: F 396 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8721 (p0) REVERT: J 26 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: J 30 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8426 (mt-10) REVERT: J 40 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7719 (pp20) REVERT: G 56 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8744 (m-30) REVERT: G 110 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8538 (m-30) REVERT: G 124 PHE cc_start: 0.9026 (m-80) cc_final: 0.8598 (m-80) REVERT: G 147 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8726 (mm-30) REVERT: G 232 MET cc_start: 0.8594 (mmp) cc_final: 0.8299 (mmp) REVERT: H 18 PHE cc_start: 0.8521 (t80) cc_final: 0.7849 (t80) REVERT: H 32 ASN cc_start: 0.7725 (p0) cc_final: 0.7184 (p0) REVERT: H 68 GLU cc_start: 0.8625 (mt-10) cc_final: 0.7730 (mt-10) REVERT: H 74 LYS cc_start: 0.9230 (mttm) cc_final: 0.8922 (mmtt) REVERT: H 91 GLN cc_start: 0.8612 (mp-120) cc_final: 0.8276 (mp10) REVERT: H 128 ARG cc_start: 0.8957 (tpp80) cc_final: 0.8716 (tpp80) REVERT: K 45 GLN cc_start: 0.8984 (mp10) cc_final: 0.8768 (mp10) REVERT: K 71 ILE cc_start: 0.8193 (tp) cc_final: 0.7847 (tp) REVERT: L 38 ARG cc_start: 0.9327 (ttt180) cc_final: 0.9011 (ttt180) REVERT: L 39 ASN cc_start: 0.9424 (t0) cc_final: 0.9164 (t0) REVERT: L 47 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.8064 (m-10) REVERT: N 44 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8300 (tm-30) REVERT: O 36 TYR cc_start: 0.8965 (t80) cc_final: 0.8764 (t80) REVERT: O 45 GLN cc_start: 0.8829 (mt0) cc_final: 0.7939 (mt0) REVERT: O 49 TYR cc_start: 0.8360 (m-10) cc_final: 0.8089 (m-80) REVERT: O 62 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8664 (mm) REVERT: O 71 ILE cc_start: 0.8773 (mm) cc_final: 0.8436 (mt) REVERT: P 60 MET cc_start: 0.9041 (ttm) cc_final: 0.8520 (ttt) REVERT: Q 54 PHE cc_start: 0.8394 (t80) cc_final: 0.8154 (t80) REVERT: Q 63 PHE cc_start: 0.8345 (t80) cc_final: 0.7784 (t80) REVERT: R 7 LYS cc_start: 0.8064 (mttm) cc_final: 0.7834 (mttt) REVERT: R 69 PHE cc_start: 0.8436 (t80) cc_final: 0.8078 (t80) REVERT: M 58 GLU cc_start: 0.8972 (tp30) cc_final: 0.8139 (pt0) REVERT: M 69 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8409 (t80) REVERT: B 321 LEU cc_start: 0.8846 (tp) cc_final: 0.8564 (tt) REVERT: B 439 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8886 (mp0) outliers start: 128 outliers final: 97 residues processed: 539 average time/residue: 0.1812 time to fit residues: 156.5469 Evaluate side-chains 545 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 436 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 41 SER Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 64 CYS Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 483 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 351 optimal weight: 0.0470 chunk 240 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 250 optimal weight: 0.9980 chunk 381 optimal weight: 3.9990 chunk 345 optimal weight: 0.9990 chunk 284 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 246 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 GLN I 16 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.062318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.049834 restraints weight = 109004.683| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.64 r_work: 0.2908 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30324 Z= 0.140 Angle : 0.610 13.338 41015 Z= 0.310 Chirality : 0.044 0.291 4786 Planarity : 0.004 0.050 5279 Dihedral : 7.152 165.336 4384 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 3.39 % Allowed : 17.90 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.14), residues: 3909 helix: 1.52 (0.12), residues: 1910 sheet: -0.61 (0.23), residues: 477 loop : -0.12 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 59 TYR 0.019 0.001 TYR I 11 PHE 0.029 0.002 PHE C 403 TRP 0.031 0.006 TRP I 4 HIS 0.004 0.001 HIS E 369 Details of bonding type rmsd covalent geometry : bond 0.00313 (30324) covalent geometry : angle 0.60993 (41015) hydrogen bonds : bond 0.04310 ( 1612) hydrogen bonds : angle 4.76512 ( 4674) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 451 time to evaluate : 0.716 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: A 52 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8603 (ttm) REVERT: A 439 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8590 (mp0) REVERT: C 146 MET cc_start: 0.9072 (tmm) cc_final: 0.8546 (tmm) REVERT: D 294 MET cc_start: 0.8847 (tmm) cc_final: 0.8248 (tmm) REVERT: D 395 MET cc_start: 0.8277 (mmm) cc_final: 0.7632 (tpp) REVERT: E 128 MET cc_start: 0.8952 (mmm) cc_final: 0.8455 (mmm) REVERT: E 202 MET cc_start: 0.9054 (mtt) cc_final: 0.8748 (mtt) REVERT: E 321 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8386 (m-30) REVERT: F 343 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8253 (mp0) REVERT: F 395 MET cc_start: 0.8557 (mmm) cc_final: 0.8157 (mmm) REVERT: J 16 ARG cc_start: 0.8618 (tpp80) cc_final: 0.8411 (tpt-90) REVERT: J 26 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: J 39 ARG cc_start: 0.8624 (ttp-110) cc_final: 0.8227 (ptm160) REVERT: J 40 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7859 (pp20) REVERT: G 56 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8671 (m-30) REVERT: G 110 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8559 (m-30) REVERT: G 124 PHE cc_start: 0.9006 (m-80) cc_final: 0.8639 (m-80) REVERT: G 125 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8547 (pp) REVERT: G 147 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8721 (mm-30) REVERT: G 232 MET cc_start: 0.8587 (mmp) cc_final: 0.8282 (mmp) REVERT: G 234 ASN cc_start: 0.8833 (m-40) cc_final: 0.8628 (m110) REVERT: H 18 PHE cc_start: 0.8513 (t80) cc_final: 0.7868 (t80) REVERT: H 32 ASN cc_start: 0.7672 (p0) cc_final: 0.7156 (p0) REVERT: H 68 GLU cc_start: 0.8505 (mt-10) cc_final: 0.7530 (mt-10) REVERT: H 74 LYS cc_start: 0.9211 (mttm) cc_final: 0.8950 (mmtt) REVERT: H 91 GLN cc_start: 0.8589 (mp-120) cc_final: 0.7791 (mp10) REVERT: I 3 TYR cc_start: 0.5730 (p90) cc_final: 0.5467 (p90) REVERT: K 45 GLN cc_start: 0.8971 (mp10) cc_final: 0.8748 (mp10) REVERT: L 39 ASN cc_start: 0.9279 (t0) cc_final: 0.8939 (t0) REVERT: L 47 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7865 (m-10) REVERT: N 44 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8324 (tm-30) REVERT: O 18 VAL cc_start: 0.6890 (OUTLIER) cc_final: 0.6445 (p) REVERT: O 36 TYR cc_start: 0.8874 (t80) cc_final: 0.8632 (t80) REVERT: O 45 GLN cc_start: 0.8789 (mt0) cc_final: 0.7902 (mt0) REVERT: O 71 ILE cc_start: 0.8761 (mm) cc_final: 0.8519 (mt) REVERT: P 60 MET cc_start: 0.8998 (ttm) cc_final: 0.8501 (ttt) REVERT: Q 54 PHE cc_start: 0.8342 (t80) cc_final: 0.8050 (t80) REVERT: Q 63 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7725 (t80) REVERT: R 7 LYS cc_start: 0.8039 (mttm) cc_final: 0.7823 (mttt) REVERT: R 69 PHE cc_start: 0.8365 (t80) cc_final: 0.8020 (t80) REVERT: M 58 GLU cc_start: 0.8933 (tp30) cc_final: 0.8185 (pt0) REVERT: M 69 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8290 (t80) REVERT: B 321 LEU cc_start: 0.8746 (tp) cc_final: 0.8543 (tt) outliers start: 105 outliers final: 72 residues processed: 520 average time/residue: 0.1765 time to fit residues: 146.6558 Evaluate side-chains 522 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 438 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 16 GLN Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 41 SER Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 64 CYS Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 63 PHE Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 483 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 16 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 273 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 268 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 347 optimal weight: 0.0980 chunk 127 optimal weight: 0.5980 chunk 203 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 323 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 GLN B 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.062822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.050321 restraints weight = 108244.591| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.63 r_work: 0.2917 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30324 Z= 0.133 Angle : 0.620 12.816 41015 Z= 0.313 Chirality : 0.043 0.270 4786 Planarity : 0.004 0.097 5279 Dihedral : 6.809 164.293 4377 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.44 % Rotamer: Outliers : 2.94 % Allowed : 18.39 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.14), residues: 3909 helix: 1.54 (0.12), residues: 1914 sheet: -0.58 (0.24), residues: 476 loop : -0.09 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 38 TYR 0.040 0.001 TYR O 49 PHE 0.031 0.001 PHE C 403 TRP 0.035 0.007 TRP I 4 HIS 0.006 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00297 (30324) covalent geometry : angle 0.61960 (41015) hydrogen bonds : bond 0.04206 ( 1612) hydrogen bonds : angle 4.71914 ( 4674) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 452 time to evaluate : 1.066 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 415 GLN cc_start: 0.8052 (mp10) cc_final: 0.7751 (mp10) REVERT: A 439 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8593 (mp0) REVERT: A 457 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6744 (tm-30) REVERT: C 146 MET cc_start: 0.9072 (tmm) cc_final: 0.8510 (tmm) REVERT: C 496 LYS cc_start: 0.9113 (tptp) cc_final: 0.8888 (tptp) REVERT: D 294 MET cc_start: 0.8840 (tmm) cc_final: 0.8208 (tmm) REVERT: D 395 MET cc_start: 0.8210 (mmm) cc_final: 0.7628 (tpp) REVERT: E 128 MET cc_start: 0.8931 (mmm) cc_final: 0.8446 (mmm) REVERT: E 202 MET cc_start: 0.9035 (mtt) cc_final: 0.8779 (mtt) REVERT: E 321 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8382 (m-30) REVERT: F 343 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8228 (mp0) REVERT: F 395 MET cc_start: 0.8273 (mmm) cc_final: 0.7885 (mmm) REVERT: J 16 ARG cc_start: 0.8593 (tpp80) cc_final: 0.8373 (tpt-90) REVERT: J 39 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8208 (ptm160) REVERT: J 40 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7822 (pp20) REVERT: G 56 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8610 (m-30) REVERT: G 110 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8566 (m-30) REVERT: G 124 PHE cc_start: 0.9029 (m-80) cc_final: 0.8729 (m-80) REVERT: G 147 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8746 (mm-30) REVERT: G 232 MET cc_start: 0.8591 (mmp) cc_final: 0.8325 (mmp) REVERT: H 18 PHE cc_start: 0.8525 (t80) cc_final: 0.7892 (t80) REVERT: H 74 LYS cc_start: 0.9153 (mttm) cc_final: 0.8926 (mmtt) REVERT: H 91 GLN cc_start: 0.8679 (mp-120) cc_final: 0.8032 (mp10) REVERT: H 134 ARG cc_start: 0.8733 (tpt-90) cc_final: 0.8193 (tpt-90) REVERT: K 36 TYR cc_start: 0.8398 (t80) cc_final: 0.7468 (t80) REVERT: K 45 GLN cc_start: 0.8922 (mp10) cc_final: 0.8720 (mp10) REVERT: L 39 ASN cc_start: 0.9278 (t0) cc_final: 0.8864 (t0) REVERT: L 47 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7945 (m-10) REVERT: N 27 THR cc_start: 0.9234 (m) cc_final: 0.8999 (p) REVERT: N 44 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8342 (tm-30) REVERT: O 18 VAL cc_start: 0.6980 (OUTLIER) cc_final: 0.6513 (p) REVERT: O 54 PHE cc_start: 0.9349 (t80) cc_final: 0.8619 (t80) REVERT: O 71 ILE cc_start: 0.8784 (mm) cc_final: 0.8445 (mt) REVERT: P 46 LEU cc_start: 0.9119 (mt) cc_final: 0.8879 (mt) REVERT: P 60 MET cc_start: 0.8956 (ttm) cc_final: 0.8536 (ttt) REVERT: Q 54 PHE cc_start: 0.8183 (t80) cc_final: 0.7901 (t80) REVERT: Q 63 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7704 (t80) REVERT: R 69 PHE cc_start: 0.8369 (t80) cc_final: 0.8040 (t80) REVERT: R 70 LEU cc_start: 0.8955 (tt) cc_final: 0.8642 (mt) REVERT: M 58 GLU cc_start: 0.8921 (tp30) cc_final: 0.8159 (pt0) REVERT: M 69 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8268 (t80) REVERT: B 439 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8797 (mp0) outliers start: 91 outliers final: 70 residues processed: 508 average time/residue: 0.1757 time to fit residues: 142.7584 Evaluate side-chains 520 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 440 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 41 SER Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 63 PHE Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 146 optimal weight: 0.0980 chunk 219 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 335 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 255 optimal weight: 10.0000 chunk 209 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 GLN B 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.062067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.049538 restraints weight = 108892.595| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.62 r_work: 0.2897 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30324 Z= 0.184 Angle : 0.650 13.169 41015 Z= 0.328 Chirality : 0.044 0.267 4786 Planarity : 0.004 0.045 5279 Dihedral : 6.754 165.182 4374 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 2.74 % Allowed : 18.84 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.14), residues: 3909 helix: 1.48 (0.12), residues: 1910 sheet: -0.52 (0.24), residues: 474 loop : -0.12 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 34 TYR 0.024 0.001 TYR O 49 PHE 0.029 0.002 PHE C 403 TRP 0.035 0.007 TRP I 4 HIS 0.004 0.001 HIS E 369 Details of bonding type rmsd covalent geometry : bond 0.00417 (30324) covalent geometry : angle 0.64977 (41015) hydrogen bonds : bond 0.04338 ( 1612) hydrogen bonds : angle 4.80267 ( 4674) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 445 time to evaluate : 0.876 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: A 415 GLN cc_start: 0.8079 (mp10) cc_final: 0.7768 (mp10) REVERT: A 439 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8614 (mp0) REVERT: A 457 GLU cc_start: 0.7165 (tm-30) cc_final: 0.6777 (tm-30) REVERT: C 146 MET cc_start: 0.9071 (tmm) cc_final: 0.8527 (tmm) REVERT: C 244 TYR cc_start: 0.9252 (OUTLIER) cc_final: 0.8707 (t80) REVERT: C 496 LYS cc_start: 0.9121 (tptp) cc_final: 0.8910 (tptp) REVERT: D 294 MET cc_start: 0.8859 (tmm) cc_final: 0.8235 (tmm) REVERT: D 395 MET cc_start: 0.8252 (mmm) cc_final: 0.7629 (tpp) REVERT: E 128 MET cc_start: 0.8966 (mmm) cc_final: 0.8591 (mmt) REVERT: E 202 MET cc_start: 0.9029 (mtt) cc_final: 0.8780 (mtt) REVERT: E 321 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8391 (m-30) REVERT: F 343 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8236 (mp0) REVERT: F 395 MET cc_start: 0.8294 (mmm) cc_final: 0.7921 (mmm) REVERT: J 39 ARG cc_start: 0.8624 (ttp-110) cc_final: 0.8216 (ptm160) REVERT: J 40 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7742 (pp20) REVERT: G 56 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8573 (m-30) REVERT: G 110 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8587 (m-30) REVERT: G 124 PHE cc_start: 0.8995 (m-80) cc_final: 0.8660 (m-80) REVERT: G 147 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8733 (mm-30) REVERT: G 232 MET cc_start: 0.8554 (mmp) cc_final: 0.8252 (mmp) REVERT: H 18 PHE cc_start: 0.8492 (t80) cc_final: 0.7932 (t80) REVERT: H 34 ARG cc_start: 0.8150 (mtt90) cc_final: 0.7933 (mtm-85) REVERT: H 91 GLN cc_start: 0.8674 (mp-120) cc_final: 0.8051 (mp10) REVERT: K 36 TYR cc_start: 0.8344 (t80) cc_final: 0.7470 (t80) REVERT: K 65 LEU cc_start: 0.9162 (mm) cc_final: 0.8931 (pp) REVERT: L 39 ASN cc_start: 0.9296 (t0) cc_final: 0.8855 (t0) REVERT: L 47 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: L 66 MET cc_start: 0.8695 (mmm) cc_final: 0.8039 (ppp) REVERT: N 27 THR cc_start: 0.9215 (m) cc_final: 0.8972 (p) REVERT: O 54 PHE cc_start: 0.9345 (t80) cc_final: 0.8662 (t80) REVERT: O 71 ILE cc_start: 0.8786 (mm) cc_final: 0.8463 (mt) REVERT: P 46 LEU cc_start: 0.9097 (mt) cc_final: 0.8805 (mt) REVERT: P 60 MET cc_start: 0.8950 (ttm) cc_final: 0.8500 (ttt) REVERT: Q 36 TYR cc_start: 0.8645 (t80) cc_final: 0.8407 (t80) REVERT: Q 54 PHE cc_start: 0.8178 (t80) cc_final: 0.7798 (t80) REVERT: Q 63 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7695 (t80) REVERT: R 7 LYS cc_start: 0.8112 (mttm) cc_final: 0.7888 (mttt) REVERT: R 69 PHE cc_start: 0.8391 (t80) cc_final: 0.8047 (t80) REVERT: R 70 LEU cc_start: 0.8976 (tt) cc_final: 0.8659 (mp) REVERT: M 58 GLU cc_start: 0.8925 (tp30) cc_final: 0.8173 (pt0) REVERT: M 69 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8257 (t80) REVERT: B 439 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8824 (mp0) outliers start: 85 outliers final: 72 residues processed: 498 average time/residue: 0.1764 time to fit residues: 140.2258 Evaluate side-chains 518 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 437 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 63 PHE Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 368 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 358 optimal weight: 3.9990 chunk 373 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 329 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 GLN O 45 GLN B 65 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.062614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.050091 restraints weight = 108779.571| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.60 r_work: 0.2915 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30324 Z= 0.147 Angle : 0.656 13.473 41015 Z= 0.329 Chirality : 0.044 0.301 4786 Planarity : 0.004 0.044 5279 Dihedral : 6.666 164.821 4374 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.44 % Rotamer: Outliers : 2.81 % Allowed : 19.06 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.14), residues: 3909 helix: 1.45 (0.12), residues: 1915 sheet: -0.51 (0.24), residues: 476 loop : -0.09 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 381 TYR 0.018 0.001 TYR Q 36 PHE 0.022 0.001 PHE K 54 TRP 0.034 0.007 TRP I 4 HIS 0.004 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00329 (30324) covalent geometry : angle 0.65585 (41015) hydrogen bonds : bond 0.04243 ( 1612) hydrogen bonds : angle 4.76420 ( 4674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6761.57 seconds wall clock time: 116 minutes 57.37 seconds (7017.37 seconds total)