Starting phenix.real_space_refine on Sat Mar 7 02:28:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oqs_20168/03_2026/6oqs_20168_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oqs_20168/03_2026/6oqs_20168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6oqs_20168/03_2026/6oqs_20168_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oqs_20168/03_2026/6oqs_20168_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oqs_20168/03_2026/6oqs_20168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oqs_20168/03_2026/6oqs_20168.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 16 5.49 5 Mg 5 5.21 5 S 180 5.16 5 C 23485 2.51 5 N 6317 2.21 5 O 6968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 282 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36971 Number of models: 1 Model: "" Number of chains: 28 Chain: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3871 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3832 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 489} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1034 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 274} Chain: "F" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} 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: "B" 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: "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: "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: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.33, per 1000 atoms: 0.23 Number of scatterers: 36971 At special positions: 0 Unit cell: (176.956, 220.116, 139.191, 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 180 16.00 P 16 15.00 Mg 5 11.99 O 6968 8.00 N 6317 7.00 C 23485 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: 3.22 Conformation dependent library (CDL) restraints added in 1.6 seconds 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8818 Finding SS restraints... Secondary structure from input PDB file: 201 helices and 25 sheets defined 61.7% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'W' and resid 7 through 21 removed outlier: 3.511A pdb=" N HIS W 21 " --> pdb=" O PHE W 17 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 38 Processing helix chain 'W' and resid 40 through 49 removed outlier: 3.581A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER W 48 " --> pdb=" O ALA W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 63 removed outlier: 3.632A pdb=" N GLU W 58 " --> pdb=" O GLU W 54 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 70 through 83 Processing helix chain 'W' and resid 84 through 86 No H-bonds generated for 'chain 'W' and resid 84 through 86' Processing helix chain 'W' and resid 87 through 103 removed outlier: 3.709A pdb=" N GLU W 93 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 132 removed outlier: 3.614A pdb=" N LYS W 130 " --> pdb=" O ALA W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 162 through 172 removed outlier: 3.689A pdb=" N ASP W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.667A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.626A pdb=" N ARG C 139 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 removed outlier: 3.586A pdb=" N MET C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.507A pdb=" N ILE C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 231 through 251 Proline residue: C 239 - end of helix removed outlier: 3.815A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.620A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.552A pdb=" N ALA C 285 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 290 through 299 removed outlier: 3.849A pdb=" N ARG C 296 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 313 Processing helix chain 'C' and resid 333 through 336 Processing helix chain 'C' and resid 339 through 349 removed outlier: 4.007A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 377 through 382 Processing helix chain 'C' and resid 383 through 404 removed outlier: 3.930A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 413 removed outlier: 4.015A pdb=" N GLN C 408 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA C 410 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N SER C 411 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 removed outlier: 4.344A pdb=" N GLN C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 Processing helix chain 'C' and resid 454 through 458 removed outlier: 3.954A pdb=" N ASP C 458 " --> pdb=" O TYR C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 479 Processing helix chain 'C' and resid 479 through 490 removed outlier: 3.631A pdb=" N GLN C 488 " --> pdb=" O GLN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 Processing helix chain 'B' and resid 4 through 18 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.784A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.632A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 216 through 219 removed outlier: 3.845A pdb=" N ALA B 219 " --> pdb=" O GLY B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 231 through 252 removed outlier: 3.516A pdb=" N LEU B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.665A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 276 removed outlier: 3.678A pdb=" N ALA B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.775A pdb=" N HIS B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'B' and resid 333 through 336 Processing helix chain 'B' and resid 339 through 347 removed outlier: 3.571A pdb=" N THR B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.625A pdb=" N ALA B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 392 through 408 removed outlier: 3.678A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 479 through 487 Processing helix chain 'B' and resid 493 through 511 Processing helix chain 'A' and resid 5 through 20 removed outlier: 3.678A pdb=" N SER A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.745A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 252 Proline residue: A 239 - end of helix removed outlier: 3.549A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 removed outlier: 3.614A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.510A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 339 through 349 removed outlier: 3.522A pdb=" N SER A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.526A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 392 through 408 removed outlier: 3.810A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 432 removed outlier: 3.634A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS A 432 " --> pdb=" O THR A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 479 removed outlier: 3.730A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 Processing helix chain 'A' and resid 493 through 510 removed outlier: 3.635A pdb=" N LYS A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 25 removed outlier: 3.654A pdb=" N ALA X 11 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE X 12 " --> pdb=" O LEU X 8 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 136 removed outlier: 3.616A pdb=" N LEU X 29 " --> pdb=" O VAL X 25 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP X 55 " --> pdb=" O HIS X 51 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU X 89 " --> pdb=" O GLN X 85 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA X 111 " --> pdb=" O ALA X 107 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL X 129 " --> pdb=" O ALA X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 146 Processing helix chain 'X' and resid 147 through 156 removed outlier: 3.646A pdb=" N LYS X 151 " --> pdb=" O ASP X 147 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU X 152 " --> pdb=" O ILE X 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 104 Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.645A pdb=" N GLN H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 134 removed outlier: 3.555A pdb=" N LEU H 133 " --> pdb=" O ARG H 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 40 removed outlier: 3.751A pdb=" N MET G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 58 removed outlier: 4.286A pdb=" N ALA G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY G 58 " --> pdb=" O HIS G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 68 Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.515A pdb=" N LEU G 94 " --> pdb=" O LEU G 90 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 129 removed outlier: 3.883A pdb=" N VAL G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 removed outlier: 3.764A pdb=" N LEU G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE G 149 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 198 through 203 removed outlier: 4.280A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 283 removed outlier: 3.654A pdb=" N LEU G 214 " --> pdb=" O ASP G 210 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.515A pdb=" N THR F 83 " --> pdb=" O GLY F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 119 Processing helix chain 'F' and resid 130 through 137 Processing helix chain 'F' and resid 156 through 168 removed outlier: 4.025A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 196 removed outlier: 3.504A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 200 removed outlier: 4.394A pdb=" N ASP F 200 " --> pdb=" O ASN F 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 197 through 200' Processing helix chain 'F' and resid 212 through 233 removed outlier: 3.663A pdb=" N ARG F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET F 226 " --> pdb=" O THR F 222 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 256 removed outlier: 3.854A pdb=" N THR F 248 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY F 251 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA F 256 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 259 No H-bonds generated for 'chain 'F' and resid 257 through 259' Processing helix chain 'F' and resid 270 through 280 removed outlier: 3.750A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 302 Processing helix chain 'F' and resid 305 through 312 Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 322 through 327 Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 350 through 370 Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 379 through 382 Processing helix chain 'F' and resid 384 through 400 removed outlier: 3.648A pdb=" N VAL F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 406 No H-bonds generated for 'chain 'F' and resid 404 through 406' Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 419 through 433 removed outlier: 3.732A pdb=" N ARG F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 448 through 456 Processing helix chain 'F' and resid 457 through 459 No H-bonds generated for 'chain 'F' and resid 457 through 459' Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 130 through 137 Processing helix chain 'E' and resid 154 through 169 Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 196 through 197 No H-bonds generated for 'chain 'E' and resid 196 through 197' Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 212 through 233 removed outlier: 3.558A pdb=" N ARG E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 258 removed outlier: 3.576A pdb=" N GLY E 251 " --> pdb=" O TYR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 280 removed outlier: 3.696A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 302 removed outlier: 3.594A pdb=" N ASP E 301 " --> pdb=" O VAL E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 312 Processing helix chain 'E' and resid 322 through 328 removed outlier: 3.501A pdb=" N ALA E 326 " --> pdb=" O SER E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 350 through 378 removed outlier: 4.301A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 382 Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.793A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 419 through 432 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 448 through 458 removed outlier: 4.060A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 154 through 171 Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 212 through 232 removed outlier: 3.677A pdb=" N ARG D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 258 removed outlier: 3.576A pdb=" N TYR D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 280 Processing helix chain 'D' and resid 299 through 302 Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'D' and resid 322 through 328 Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 350 through 377 removed outlier: 4.402A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 382 Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 419 through 432 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.545A pdb=" N ALA D 452 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 42 removed outlier: 3.774A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 77 removed outlier: 3.946A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'J' and resid 4 through 42 removed outlier: 3.713A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 3.809A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 77 Processing helix chain 'L' and resid 4 through 42 removed outlier: 4.147A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG L 41 " --> pdb=" O GLU L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 removed outlier: 3.573A pdb=" N THR L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 77 Processing helix chain 'M' and resid 4 through 42 removed outlier: 3.512A pdb=" N MET M 11 " --> pdb=" O ASP M 7 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN M 42 " --> pdb=" O GLY M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 61 removed outlier: 3.610A pdb=" N THR M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE M 54 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 77 Processing helix chain 'N' and resid 4 through 42 removed outlier: 4.520A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 61 removed outlier: 3.658A pdb=" N THR N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY N 58 " --> pdb=" O PHE N 54 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL N 60 " --> pdb=" O VAL N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 77 removed outlier: 3.619A pdb=" N MET N 65 " --> pdb=" O ASP N 61 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE N 66 " --> pdb=" O ALA N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 42 removed outlier: 4.004A pdb=" N LEU O 9 " --> pdb=" O ASN O 5 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 removed outlier: 3.799A pdb=" N THR O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP O 61 " --> pdb=" O MET O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 77 Processing helix chain 'P' and resid 4 through 42 removed outlier: 3.866A pdb=" N LEU P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU P 9 " --> pdb=" O ASN P 5 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 77 removed outlier: 3.893A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.860A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 removed outlier: 3.547A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU Q 9 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 77 removed outlier: 3.673A pdb=" N THR Q 51 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE Q 55 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.660A pdb=" N ALA Q 67 " --> pdb=" O ILE Q 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 42 removed outlier: 3.755A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU R 9 " --> pdb=" O ASN R 5 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA R 21 " --> pdb=" O MET R 17 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 77 removed outlier: 3.712A pdb=" N THR R 51 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'S' and resid 5 through 7 No H-bonds generated for 'chain 'S' and resid 5 through 7' Processing helix chain 'S' and resid 8 through 42 removed outlier: 3.577A pdb=" N MET S 16 " --> pdb=" O ALA S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.745A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 78 Processing helix chain 'Y' and resid 2 through 25 removed outlier: 4.024A pdb=" N THR Y 6 " --> pdb=" O ASN Y 2 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 140 removed outlier: 3.840A pdb=" N LEU Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA Y 70 " --> pdb=" O LYS Y 66 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN Y 73 " --> pdb=" O LYS Y 69 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR Y 99 " --> pdb=" O GLU Y 95 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS Y 100 " --> pdb=" O GLN Y 96 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN Y 123 " --> pdb=" O GLU Y 119 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 154 Processing helix chain 'a' and resid 7 through 16 removed outlier: 3.604A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 65 removed outlier: 3.605A pdb=" N MET a 46 " --> pdb=" O ASN a 42 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 94 removed outlier: 3.797A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL a 82 " --> pdb=" O ALA a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 118 Processing helix chain 'a' and resid 119 through 121 No H-bonds generated for 'chain 'a' and resid 119 through 121' Processing helix chain 'a' and resid 124 through 133 Processing helix chain 'a' and resid 142 through 145 Processing helix chain 'a' and resid 146 through 181 removed outlier: 3.827A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS a 169 " --> pdb=" O SER a 165 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN a 181 " --> pdb=" O GLU a 177 " (cutoff:3.500A) Processing helix chain 'a' and resid 188 through 229 removed outlier: 3.995A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS a 203 " --> pdb=" O SER a 199 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.698A pdb=" N LEU a 211 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN a 214 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE a 221 " --> pdb=" O ALA a 217 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE a 222 " --> pdb=" O GLY a 218 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 233 Processing helix chain 'a' and resid 234 through 269 Proline residue: a 240 - end of helix removed outlier: 4.035A pdb=" N PHE a 244 " --> pdb=" O PRO a 240 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR a 250 " --> pdb=" O ILE a 246 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE a 256 " --> pdb=" O GLN a 252 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER a 268 " --> pdb=" O LEU a 264 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'W' and resid 135 through 142 removed outlier: 6.875A pdb=" N ALA W 106 " --> pdb=" O LYS W 137 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ASN W 139 " --> pdb=" O ALA W 106 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL W 108 " --> pdb=" O ASN W 139 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LYS W 141 " --> pdb=" O VAL W 108 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL W 110 " --> pdb=" O LYS W 141 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 35 removed outlier: 13.286A pdb=" N ALA B 25 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLY B 92 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASN B 27 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 91 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASP F 27 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA F 28 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLN F 32 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP F 67 " --> pdb=" O GLN F 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 59 through 67 removed outlier: 4.137A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N MET C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS C 42 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER C 33 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 40 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASP D 67 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLN D 32 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA D 28 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP D 27 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE D 50 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN D 7 " --> pdb=" O ASP D 14 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU D 16 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE D 5 " --> pdb=" O GLU D 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AA5, first strand: chain 'C' and resid 107 through 109 removed outlier: 3.621A pdb=" N ILE C 198 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 329 through 331 removed outlier: 8.046A pdb=" N ILE C 330 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE C 167 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA8, first strand: chain 'B' and resid 107 through 109 Processing sheet with id=AA9, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.427A pdb=" N ILE B 159 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 329 through 331 removed outlier: 6.365A pdb=" N ILE B 167 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 59 through 66 removed outlier: 3.750A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N MET A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP E 67 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN E 32 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AB4, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.473A pdb=" N ALA A 256 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LEU A 327 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE A 258 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE A 329 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR A 260 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N GLU A 331 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 167 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 14 through 16 removed outlier: 6.290A pdb=" N VAL H 8 " --> pdb=" O MET H 15 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL H 25 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N MET H 49 " --> pdb=" O VAL H 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 30 through 34 removed outlier: 6.114A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA H 80 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL H 9 " --> pdb=" O ALA H 80 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE H 68 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA H 44 " --> pdb=" O GLU G 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 132 through 136 removed outlier: 8.201A pdb=" N VAL G 133 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU G 114 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN G 135 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N MET G 116 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL G 75 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ALA G 115 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR G 77 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE G 117 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL G 79 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE G 175 " --> pdb=" O SER G 179 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER G 179 " --> pdb=" O ILE G 175 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 76 through 78 Processing sheet with id=AB9, first strand: chain 'F' and resid 87 through 88 removed outlier: 6.324A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL F 237 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL F 293 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU F 239 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA F 295 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL F 241 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N TYR F 297 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL F 145 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL F 296 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU F 147 " --> pdb=" O VAL F 296 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 125 through 126 removed outlier: 4.619A pdb=" N PHE F 139 " --> pdb=" O LEU F 126 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.840A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.255A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL E 237 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL E 293 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU E 239 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA E 295 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL E 241 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY E 146 " --> pdb=" O VAL E 319 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 125 through 126 removed outlier: 4.423A pdb=" N PHE E 139 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.653A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.299A pdb=" N MET D 88 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLN D 208 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL D 296 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU D 147 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'a' and resid 21 through 22 2269 hydrogen bonds defined for protein. 6570 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.68 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 6331 1.29 - 1.42: 8590 1.42 - 1.55: 22222 1.55 - 1.68: 25 1.68 - 1.81: 360 Bond restraints: 37528 Sorted by residual: bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.54e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.14e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.32e+01 bond pdb=" C ASP B 261 " pdb=" O ASP B 261 " ideal model delta sigma weight residual 1.237 1.162 0.075 1.17e-02 7.31e+03 4.12e+01 ... (remaining 37523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.73: 50651 4.73 - 9.47: 139 9.47 - 14.20: 1 14.20 - 18.94: 1 18.94 - 23.67: 5 Bond angle restraints: 50797 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 116.20 23.67 1.00e+00 1.00e+00 5.60e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 118.09 21.78 1.00e+00 1.00e+00 4.74e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 118.42 21.45 1.00e+00 1.00e+00 4.60e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 116.65 20.18 1.00e+00 1.00e+00 4.07e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.74 20.09 1.00e+00 1.00e+00 4.04e+02 ... (remaining 50792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.54: 22086 30.54 - 61.08: 625 61.08 - 91.62: 78 91.62 - 122.16: 2 122.16 - 152.70: 3 Dihedral angle restraints: 22794 sinusoidal: 9010 harmonic: 13784 Sorted by residual: dihedral pdb=" O1B ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PB ADP D 500 " pdb=" PA ADP D 500 " ideal model delta sinusoidal sigma weight residual 300.00 147.29 152.70 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual 300.00 155.99 144.01 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O2A ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PA ADP D 500 " pdb=" PB ADP D 500 " ideal model delta sinusoidal sigma weight residual -60.00 65.65 -125.65 1 2.00e+01 2.50e-03 3.80e+01 ... (remaining 22791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 5208 0.071 - 0.141: 672 0.141 - 0.212: 32 0.212 - 0.283: 6 0.283 - 0.353: 2 Chirality restraints: 5920 Sorted by residual: chirality pdb=" CA LEU a 178 " pdb=" N LEU a 178 " pdb=" C LEU a 178 " pdb=" CB LEU a 178 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA VAL a 29 " pdb=" N VAL a 29 " pdb=" C VAL a 29 " pdb=" CB VAL a 29 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA ASP B 261 " pdb=" N ASP B 261 " pdb=" C ASP B 261 " pdb=" CB ASP B 261 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 5917 not shown) Planarity restraints: 6550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 100 " 0.023 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C LYS H 100 " -0.081 2.00e-02 2.50e+03 pdb=" O LYS H 100 " 0.030 2.00e-02 2.50e+03 pdb=" N ALA H 101 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 18 " -0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C GLN C 18 " 0.061 2.00e-02 2.50e+03 pdb=" O GLN C 18 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE C 19 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO G 191 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C PRO G 191 " 0.054 2.00e-02 2.50e+03 pdb=" O PRO G 191 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA G 192 " -0.018 2.00e-02 2.50e+03 ... (remaining 6547 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 136 2.46 - 3.07: 26913 3.07 - 3.68: 53879 3.68 - 4.29: 82528 4.29 - 4.90: 140054 Nonbonded interactions: 303510 Sorted by model distance: nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.849 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.854 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.872 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.890 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 1.915 2.170 ... (remaining 303505 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 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 601)) selection = (chain 'B' and (resid 4 through 511 or resid 600 through 601)) selection = (chain 'C' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) } ncs_group { reference = (chain 'D' and resid 2 through 500) selection = (chain 'E' and resid 2 through 500) selection = (chain 'F' and resid 2 through 500) } ncs_group { reference = (chain 'I' and resid 3 through 78) selection = (chain 'J' and resid 3 through 78) selection = (chain 'L' and resid 3 through 78) selection = (chain 'M' and resid 3 through 78) selection = (chain 'N' and resid 3 through 78) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and resid 3 through 78) selection = (chain 'Q' and resid 3 through 78) selection = chain 'R' selection = (chain 'S' and resid 3 through 78) } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 33.360 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 0.008 0.112 37528 Z= 0.389 Angle : 0.846 23.673 50797 Z= 0.551 Chirality : 0.048 0.353 5920 Planarity : 0.004 0.049 6550 Dihedral : 14.506 152.702 13976 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.52 % Favored : 97.46 % Rotamer: Outliers : 1.80 % Allowed : 8.08 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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 are not related in a simple way. whole: -2.20 (0.11), residues: 4807 helix: -1.35 (0.09), residues: 2630 sheet: -0.80 (0.20), residues: 539 loop : -1.55 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 50 TYR 0.020 0.002 TYR B 236 PHE 0.015 0.002 PHE D 312 TRP 0.017 0.001 TRP a 39 HIS 0.008 0.002 HIS a 132 Details of bonding type rmsd covalent geometry : bond 0.00761 (37528) covalent geometry : angle 0.84566 (50797) hydrogen bonds : bond 0.15801 ( 2267) hydrogen bonds : angle 6.86877 ( 6570) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 866 time to evaluate : 1.336 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: W 4 ILE cc_start: 0.9239 (mt) cc_final: 0.8897 (mm) REVERT: W 156 ASP cc_start: 0.7806 (p0) cc_final: 0.7196 (p0) REVERT: C 115 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.9020 (tp) REVERT: C 236 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.8230 (t80) REVERT: B 236 TYR cc_start: 0.9507 (OUTLIER) cc_final: 0.9208 (t80) REVERT: B 295 SER cc_start: 0.9297 (t) cc_final: 0.9029 (p) REVERT: B 429 GLU cc_start: 0.8122 (tp30) cc_final: 0.7918 (tp30) REVERT: A 236 TYR cc_start: 0.9343 (OUTLIER) cc_final: 0.9092 (t80) REVERT: X 16 LEU cc_start: 0.9097 (mt) cc_final: 0.8798 (tt) REVERT: X 85 GLN cc_start: 0.8525 (mt0) cc_final: 0.7939 (mt0) REVERT: X 147 ASP cc_start: 0.8084 (p0) cc_final: 0.7580 (p0) REVERT: H 71 VAL cc_start: 0.9404 (p) cc_final: 0.8962 (m) REVERT: H 72 GLN cc_start: 0.7903 (mt0) cc_final: 0.7587 (pt0) REVERT: H 81 ASP cc_start: 0.8006 (p0) cc_final: 0.7790 (p0) REVERT: E 136 MET cc_start: 0.9103 (mmm) cc_final: 0.8849 (mmm) REVERT: E 323 ARG cc_start: 0.7988 (tpp80) cc_final: 0.7668 (ttm170) REVERT: E 373 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8421 (tt) REVERT: E 438 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7715 (pt) REVERT: D 253 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7742 (mt-10) REVERT: I 31 LEU cc_start: 0.8913 (tp) cc_final: 0.8613 (tp) REVERT: I 63 ILE cc_start: 0.8101 (mm) cc_final: 0.7852 (mt) REVERT: I 68 VAL cc_start: 0.8619 (t) cc_final: 0.8392 (t) REVERT: I 73 TYR cc_start: 0.8816 (t80) cc_final: 0.8496 (t80) REVERT: J 41 ARG cc_start: 0.8306 (ttt-90) cc_final: 0.7939 (tpp80) REVERT: J 42 GLN cc_start: 0.8972 (mt0) cc_final: 0.8626 (tt0) REVERT: L 11 MET cc_start: 0.8280 (tpt) cc_final: 0.7775 (tpp) REVERT: L 41 ARG cc_start: 0.8471 (mtt90) cc_final: 0.8226 (mmt90) REVERT: L 42 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8045 (mt0) REVERT: L 57 MET cc_start: 0.9073 (tmm) cc_final: 0.8769 (tmm) REVERT: L 65 MET cc_start: 0.8702 (mmt) cc_final: 0.8486 (mmt) REVERT: L 73 TYR cc_start: 0.8748 (t80) cc_final: 0.8407 (t80) REVERT: L 78 VAL cc_start: 0.7590 (t) cc_final: 0.7101 (t) REVERT: M 34 LYS cc_start: 0.8348 (mmtm) cc_final: 0.8123 (mmtt) REVERT: M 37 GLU cc_start: 0.8544 (pt0) cc_final: 0.8254 (pt0) REVERT: N 57 MET cc_start: 0.8074 (tmm) cc_final: 0.7582 (tmm) REVERT: N 61 ASP cc_start: 0.8283 (m-30) cc_final: 0.7874 (m-30) REVERT: O 28 ILE cc_start: 0.8656 (mt) cc_final: 0.8288 (mt) REVERT: O 65 MET cc_start: 0.7912 (mmt) cc_final: 0.7684 (mmp) REVERT: O 73 TYR cc_start: 0.7360 (t80) cc_final: 0.6459 (m-10) REVERT: O 74 VAL cc_start: 0.8369 (t) cc_final: 0.7937 (m) REVERT: P 52 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8315 (mm-40) REVERT: P 72 LEU cc_start: 0.7467 (mt) cc_final: 0.7142 (pp) REVERT: P 76 PHE cc_start: 0.6188 (m-80) cc_final: 0.5581 (m-10) REVERT: Q 41 ARG cc_start: 0.8065 (mtp-110) cc_final: 0.7348 (mtp-110) REVERT: Q 42 GLN cc_start: 0.8597 (mt0) cc_final: 0.8115 (mp10) REVERT: Q 51 THR cc_start: 0.9497 (m) cc_final: 0.9282 (p) REVERT: Q 53 PHE cc_start: 0.8845 (t80) cc_final: 0.8573 (t80) REVERT: Q 68 VAL cc_start: 0.9071 (t) cc_final: 0.8854 (t) REVERT: S 63 ILE cc_start: 0.8584 (mm) cc_final: 0.8294 (mt) REVERT: S 66 ILE cc_start: 0.7749 (mm) cc_final: 0.7510 (mt) REVERT: Y 14 PHE cc_start: 0.8800 (t80) cc_final: 0.8256 (t80) REVERT: Y 18 VAL cc_start: 0.8754 (t) cc_final: 0.8518 (p) REVERT: Y 26 TRP cc_start: 0.6604 (t60) cc_final: 0.6011 (t-100) REVERT: Y 33 ILE cc_start: 0.8537 (mt) cc_final: 0.8257 (pt) REVERT: Y 54 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6302 (mm) REVERT: Y 96 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: Y 98 ARG cc_start: 0.7921 (ttt90) cc_final: 0.7399 (ttt180) REVERT: Y 150 ASP cc_start: 0.8413 (m-30) cc_final: 0.8208 (m-30) REVERT: a 20 GLN cc_start: 0.7986 (mt0) cc_final: 0.7783 (mp10) REVERT: a 24 ARG cc_start: 0.5963 (mmt90) cc_final: 0.5520 (mmp-170) REVERT: a 30 ASP cc_start: 0.6384 (p0) cc_final: 0.6089 (p0) REVERT: a 80 GLU cc_start: 0.9072 (pt0) cc_final: 0.8725 (pt0) REVERT: a 117 LEU cc_start: 0.9407 (tp) cc_final: 0.9200 (mt) REVERT: a 140 ARG cc_start: 0.5257 (ptm160) cc_final: 0.5032 (ptm160) REVERT: a 199 SER cc_start: 0.8848 (t) cc_final: 0.8413 (p) REVERT: a 216 TYR cc_start: 0.9094 (t80) cc_final: 0.8220 (t80) REVERT: a 231 TRP cc_start: 0.7354 (p-90) cc_final: 0.6703 (p-90) REVERT: a 232 TRP cc_start: 0.7377 (p-90) cc_final: 0.6874 (p-90) outliers start: 69 outliers final: 28 residues processed: 923 average time/residue: 0.2383 time to fit residues: 350.6613 Evaluate side-chains 642 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 606 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 81 LYS Chi-restraints excluded: chain Y residue 96 GLN Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 165 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 470 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN W 71 ASN C 408 GLN B 14 GLN B 26 HIS B 147 GLN B 186 GLN A 42 HIS A 65 ASN A 344 ASN A 484 GLN X 80 ASN H 5 HIS H 56 HIS G 54 HIS G 274 GLN F 32 GLN F 324 GLN F 353 HIS F 368 GLN D 121 ASN D 279 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 ASN R 5 ASN S 5 ASN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Y 73 GLN a 5 ASN ** a 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 ASN a 116 ASN a 132 HIS a 185 HIS ** a 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.096300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.068261 restraints weight = 83595.773| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.15 r_work: 0.2802 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37528 Z= 0.158 Angle : 0.640 10.682 50797 Z= 0.333 Chirality : 0.044 0.254 5920 Planarity : 0.004 0.050 6550 Dihedral : 7.861 147.471 5398 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.63 % Allowed : 12.59 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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 are not related in a simple way. whole: -0.14 (0.12), residues: 4807 helix: 0.47 (0.10), residues: 2655 sheet: -0.42 (0.21), residues: 544 loop : -0.73 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 394 TYR 0.025 0.001 TYR B 236 PHE 0.040 0.001 PHE I 54 TRP 0.008 0.001 TRP a 111 HIS 0.011 0.001 HIS a 14 Details of bonding type rmsd covalent geometry : bond 0.00347 (37528) covalent geometry : angle 0.64022 (50797) hydrogen bonds : bond 0.05351 ( 2267) hydrogen bonds : angle 4.92817 ( 6570) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 655 time to evaluate : 1.424 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: W 4 ILE cc_start: 0.9298 (mt) cc_final: 0.9063 (mm) REVERT: W 156 ASP cc_start: 0.8262 (p0) cc_final: 0.7649 (p0) REVERT: W 157 MET cc_start: 0.8787 (ttp) cc_final: 0.8549 (ttp) REVERT: C 236 TYR cc_start: 0.9367 (OUTLIER) cc_final: 0.8211 (t80) REVERT: C 343 THR cc_start: 0.9602 (OUTLIER) cc_final: 0.9172 (p) REVERT: B 262 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8446 (m-30) REVERT: B 471 LEU cc_start: 0.8243 (tp) cc_final: 0.7980 (mt) REVERT: B 484 GLN cc_start: 0.8461 (mp10) cc_final: 0.8132 (mp10) REVERT: A 262 ASP cc_start: 0.8436 (m-30) cc_final: 0.8189 (m-30) REVERT: A 460 GLU cc_start: 0.8105 (pm20) cc_final: 0.7871 (pm20) REVERT: H 24 GLN cc_start: 0.8621 (tt0) cc_final: 0.8384 (tt0) REVERT: H 71 VAL cc_start: 0.9572 (OUTLIER) cc_final: 0.9254 (m) REVERT: H 72 GLN cc_start: 0.8621 (mt0) cc_final: 0.8030 (pt0) REVERT: H 81 ASP cc_start: 0.8274 (p0) cc_final: 0.8074 (p0) REVERT: G 70 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8066 (ptt180) REVERT: F 193 MET cc_start: 0.9083 (mmp) cc_final: 0.8850 (mmp) REVERT: E 323 ARG cc_start: 0.8613 (tpp80) cc_final: 0.8389 (ttm170) REVERT: E 438 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7963 (pp) REVERT: D 253 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8134 (mt-10) REVERT: D 445 MET cc_start: 0.9038 (mmt) cc_final: 0.8697 (mmm) REVERT: I 73 TYR cc_start: 0.8736 (t80) cc_final: 0.8527 (t80) REVERT: J 17 MET cc_start: 0.9037 (mtm) cc_final: 0.8786 (mtt) REVERT: J 41 ARG cc_start: 0.8396 (ttt-90) cc_final: 0.8097 (tpp80) REVERT: J 42 GLN cc_start: 0.9074 (mt0) cc_final: 0.8683 (tt0) REVERT: J 48 LEU cc_start: 0.8517 (tp) cc_final: 0.8114 (tp) REVERT: J 52 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8974 (mm-40) REVERT: J 72 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8835 (mm) REVERT: J 76 PHE cc_start: 0.7662 (m-10) cc_final: 0.7408 (m-10) REVERT: L 11 MET cc_start: 0.8322 (tpt) cc_final: 0.7767 (tpp) REVERT: L 37 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8616 (tm-30) REVERT: L 42 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8019 (mt0) REVERT: M 17 MET cc_start: 0.8088 (mtm) cc_final: 0.7851 (ptp) REVERT: M 34 LYS cc_start: 0.8907 (mmtm) cc_final: 0.8600 (mmtt) REVERT: M 37 GLU cc_start: 0.8761 (pt0) cc_final: 0.8550 (pt0) REVERT: M 63 ILE cc_start: 0.8992 (mm) cc_final: 0.8709 (tt) REVERT: N 6 MET cc_start: 0.7823 (tmm) cc_final: 0.7451 (tmm) REVERT: N 16 MET cc_start: 0.7058 (tpt) cc_final: 0.6615 (mmm) REVERT: N 50 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7439 (ttm-80) REVERT: N 57 MET cc_start: 0.8376 (tmm) cc_final: 0.7772 (tmm) REVERT: N 65 MET cc_start: 0.7617 (mmm) cc_final: 0.7149 (mmm) REVERT: O 17 MET cc_start: 0.8237 (ttm) cc_final: 0.8011 (tmm) REVERT: O 61 ASP cc_start: 0.8534 (t70) cc_final: 0.8298 (t70) REVERT: O 73 TYR cc_start: 0.7194 (t80) cc_final: 0.6419 (m-10) REVERT: O 74 VAL cc_start: 0.8376 (t) cc_final: 0.7649 (p) REVERT: P 6 MET cc_start: 0.7368 (ppp) cc_final: 0.6956 (ppp) REVERT: P 11 MET cc_start: 0.8139 (tpp) cc_final: 0.7733 (tpp) REVERT: P 17 MET cc_start: 0.8518 (mtp) cc_final: 0.8126 (mmm) REVERT: P 50 ARG cc_start: 0.9192 (ttp80) cc_final: 0.8990 (ttp80) REVERT: P 52 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8184 (mm-40) REVERT: P 76 PHE cc_start: 0.6121 (m-80) cc_final: 0.5297 (m-10) REVERT: Q 41 ARG cc_start: 0.7950 (mtp-110) cc_final: 0.7372 (mtp-110) REVERT: Q 42 GLN cc_start: 0.8593 (mt0) cc_final: 0.8116 (mp10) REVERT: Q 50 ARG cc_start: 0.8680 (ttp80) cc_final: 0.8405 (ttt180) REVERT: Q 54 PHE cc_start: 0.8995 (m-80) cc_final: 0.8713 (m-80) REVERT: R 6 MET cc_start: 0.7335 (tmm) cc_final: 0.6899 (ppp) REVERT: S 16 MET cc_start: 0.7947 (tpp) cc_final: 0.7581 (tpp) REVERT: S 17 MET cc_start: 0.7591 (mmm) cc_final: 0.7077 (mtt) REVERT: Y 18 VAL cc_start: 0.8825 (t) cc_final: 0.8526 (p) REVERT: Y 54 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6428 (mm) REVERT: Y 96 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8041 (tm-30) REVERT: a 11 TYR cc_start: 0.8103 (t80) cc_final: 0.7554 (t80) REVERT: a 20 GLN cc_start: 0.8206 (mt0) cc_final: 0.7800 (mp10) REVERT: a 24 ARG cc_start: 0.5501 (mmt90) cc_final: 0.5201 (mmp-170) REVERT: a 54 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8353 (pp) REVERT: a 80 GLU cc_start: 0.9069 (pt0) cc_final: 0.8802 (pt0) REVERT: a 176 LYS cc_start: 0.8531 (tptt) cc_final: 0.8164 (tptp) REVERT: a 199 SER cc_start: 0.8750 (t) cc_final: 0.8482 (p) REVERT: a 231 TRP cc_start: 0.7631 (p-90) cc_final: 0.7271 (p-90) REVERT: a 237 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9279 (mm) outliers start: 101 outliers final: 52 residues processed: 714 average time/residue: 0.2183 time to fit residues: 253.6093 Evaluate side-chains 628 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 565 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 70 ARG Chi-restraints excluded: chain G residue 176 ASN Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 96 GLN Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 75 PHE Chi-restraints excluded: chain a residue 131 GLU Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 245 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 389 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 344 optimal weight: 7.9990 chunk 431 optimal weight: 0.5980 chunk 167 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 307 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 511 GLN A 147 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 ASN H 116 GLN F 324 GLN D 121 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 GLN Y 2 ASN Y 96 GLN a 116 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.093892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.065909 restraints weight = 83471.666| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.13 r_work: 0.2760 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 37528 Z= 0.248 Angle : 0.657 8.389 50797 Z= 0.338 Chirality : 0.046 0.220 5920 Planarity : 0.004 0.043 6550 Dihedral : 7.342 124.027 5367 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.01 % Allowed : 13.71 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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 are not related in a simple way. whole: 0.34 (0.12), residues: 4807 helix: 1.01 (0.10), residues: 2626 sheet: -0.37 (0.21), residues: 547 loop : -0.73 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Y 83 TYR 0.025 0.001 TYR B 236 PHE 0.031 0.002 PHE a 113 TRP 0.007 0.001 TRP B 513 HIS 0.011 0.001 HIS H 56 Details of bonding type rmsd covalent geometry : bond 0.00591 (37528) covalent geometry : angle 0.65735 (50797) hydrogen bonds : bond 0.05234 ( 2267) hydrogen bonds : angle 4.76640 ( 6570) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 601 time to evaluate : 1.441 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: W 4 ILE cc_start: 0.9346 (mt) cc_final: 0.9114 (mm) REVERT: W 156 ASP cc_start: 0.8384 (p0) cc_final: 0.7795 (p0) REVERT: W 157 MET cc_start: 0.8916 (ttp) cc_final: 0.8698 (ttp) REVERT: C 236 TYR cc_start: 0.9439 (OUTLIER) cc_final: 0.8472 (t80) REVERT: C 343 THR cc_start: 0.9609 (OUTLIER) cc_final: 0.9215 (p) REVERT: B 419 LYS cc_start: 0.9029 (mttt) cc_final: 0.8789 (pttt) REVERT: B 484 GLN cc_start: 0.8543 (mp10) cc_final: 0.8247 (tm-30) REVERT: X 2 ASN cc_start: 0.7764 (t0) cc_final: 0.7393 (m-40) REVERT: X 85 GLN cc_start: 0.8451 (mt0) cc_final: 0.8094 (mp10) REVERT: H 15 MET cc_start: 0.9258 (mtp) cc_final: 0.9010 (mtt) REVERT: H 28 SER cc_start: 0.8840 (t) cc_final: 0.8541 (t) REVERT: H 49 MET cc_start: 0.8564 (tpp) cc_final: 0.8346 (tpp) REVERT: H 71 VAL cc_start: 0.9658 (OUTLIER) cc_final: 0.9306 (m) REVERT: H 98 LYS cc_start: 0.8972 (mttm) cc_final: 0.8725 (mttt) REVERT: G 70 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8242 (ptt180) REVERT: E 323 ARG cc_start: 0.8558 (tpp80) cc_final: 0.8333 (ttm170) REVERT: E 366 ARG cc_start: 0.8645 (tpt90) cc_final: 0.8432 (tpt90) REVERT: E 438 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8185 (pt) REVERT: D 117 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: D 253 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8229 (mt-10) REVERT: I 53 PHE cc_start: 0.8580 (t80) cc_final: 0.8369 (t80) REVERT: I 54 PHE cc_start: 0.8753 (m-80) cc_final: 0.8413 (m-80) REVERT: J 6 MET cc_start: 0.7916 (ptm) cc_final: 0.6526 (ppp) REVERT: J 52 GLN cc_start: 0.9303 (mm-40) cc_final: 0.8980 (mm-40) REVERT: J 72 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8797 (mm) REVERT: L 11 MET cc_start: 0.8323 (tpt) cc_final: 0.7676 (tpp) REVERT: L 17 MET cc_start: 0.8789 (mmm) cc_final: 0.8498 (mpp) REVERT: L 37 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8612 (tm-30) REVERT: L 73 TYR cc_start: 0.8641 (t80) cc_final: 0.8222 (t80) REVERT: M 16 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7713 (mtm) REVERT: M 57 MET cc_start: 0.8504 (ttp) cc_final: 0.8267 (tmm) REVERT: N 11 MET cc_start: 0.7616 (tpt) cc_final: 0.7377 (tpt) REVERT: N 57 MET cc_start: 0.8235 (tmm) cc_final: 0.7769 (tmm) REVERT: N 65 MET cc_start: 0.7751 (mmm) cc_final: 0.7320 (mmm) REVERT: O 73 TYR cc_start: 0.7274 (t80) cc_final: 0.6520 (m-10) REVERT: O 75 MET cc_start: 0.7391 (mtm) cc_final: 0.7179 (mtt) REVERT: P 6 MET cc_start: 0.7400 (ppp) cc_final: 0.7123 (ppp) REVERT: P 17 MET cc_start: 0.8573 (mtp) cc_final: 0.8119 (mmm) REVERT: P 50 ARG cc_start: 0.9194 (ttp80) cc_final: 0.8930 (ttp80) REVERT: P 57 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6611 (tpt) REVERT: P 76 PHE cc_start: 0.6161 (m-80) cc_final: 0.5794 (m-10) REVERT: Q 41 ARG cc_start: 0.7896 (mtp-110) cc_final: 0.7571 (mtp-110) REVERT: Q 50 ARG cc_start: 0.8594 (ttp80) cc_final: 0.8388 (ttt180) REVERT: S 16 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7545 (tpp) REVERT: S 17 MET cc_start: 0.7701 (mmm) cc_final: 0.7032 (mtt) REVERT: Y 18 VAL cc_start: 0.8798 (t) cc_final: 0.8437 (p) REVERT: Y 54 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6367 (mm) REVERT: a 20 GLN cc_start: 0.8311 (mt0) cc_final: 0.7859 (mp10) REVERT: a 54 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8396 (pp) REVERT: a 56 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7645 (t80) REVERT: a 80 GLU cc_start: 0.9091 (pt0) cc_final: 0.8705 (pt0) REVERT: a 199 SER cc_start: 0.8824 (t) cc_final: 0.8516 (p) REVERT: a 231 TRP cc_start: 0.7678 (p-90) cc_final: 0.6994 (p-90) REVERT: a 234 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7776 (mm-40) outliers start: 154 outliers final: 88 residues processed: 708 average time/residue: 0.2191 time to fit residues: 254.6064 Evaluate side-chains 664 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 563 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 123 LYS Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain G residue 70 ARG Chi-restraints excluded: chain G residue 176 ASN Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 57 MET Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 75 PHE Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 266 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 267 optimal weight: 0.9990 chunk 362 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 331 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 chunk 300 optimal weight: 1.9990 chunk 394 optimal weight: 10.0000 chunk 292 optimal weight: 0.9980 chunk 379 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN B 511 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 ASN H 72 GLN G 64 HIS D 121 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 GLN a 116 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.096059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.068291 restraints weight = 83247.203| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.13 r_work: 0.2791 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37528 Z= 0.139 Angle : 0.588 14.880 50797 Z= 0.299 Chirality : 0.043 0.225 5920 Planarity : 0.004 0.041 6550 Dihedral : 6.870 113.044 5361 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.18 % Allowed : 15.82 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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 are not related in a simple way. whole: 0.82 (0.12), residues: 4807 helix: 1.43 (0.10), residues: 2618 sheet: -0.19 (0.22), residues: 538 loop : -0.55 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 41 TYR 0.028 0.001 TYR B 236 PHE 0.026 0.001 PHE L 53 TRP 0.008 0.001 TRP Y 26 HIS 0.005 0.001 HIS B 479 Details of bonding type rmsd covalent geometry : bond 0.00311 (37528) covalent geometry : angle 0.58775 (50797) hydrogen bonds : bond 0.04540 ( 2267) hydrogen bonds : angle 4.51522 ( 6570) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 607 time to evaluate : 1.370 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: W 4 ILE cc_start: 0.9286 (mt) cc_final: 0.9086 (mm) REVERT: W 156 ASP cc_start: 0.8416 (p0) cc_final: 0.7811 (p0) REVERT: C 70 SER cc_start: 0.8281 (OUTLIER) cc_final: 0.7851 (m) REVERT: C 236 TYR cc_start: 0.9407 (OUTLIER) cc_final: 0.8451 (t80) REVERT: C 343 THR cc_start: 0.9616 (OUTLIER) cc_final: 0.9276 (p) REVERT: B 419 LYS cc_start: 0.9028 (mttt) cc_final: 0.8825 (pttt) REVERT: B 429 GLU cc_start: 0.8278 (tp30) cc_final: 0.8037 (tp30) REVERT: B 484 GLN cc_start: 0.8566 (mp10) cc_final: 0.8275 (tm-30) REVERT: X 85 GLN cc_start: 0.8220 (mt0) cc_final: 0.7874 (mp10) REVERT: H 15 MET cc_start: 0.9224 (mtp) cc_final: 0.8996 (mtt) REVERT: H 71 VAL cc_start: 0.9637 (OUTLIER) cc_final: 0.9301 (m) REVERT: H 72 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8069 (tp40) REVERT: H 113 ASP cc_start: 0.8849 (m-30) cc_final: 0.8587 (m-30) REVERT: G 205 TYR cc_start: 0.9070 (m-80) cc_final: 0.8852 (m-80) REVERT: E 323 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8357 (ttm170) REVERT: E 366 ARG cc_start: 0.8669 (tpt90) cc_final: 0.8457 (tpt90) REVERT: E 438 LEU cc_start: 0.8681 (pp) cc_final: 0.8115 (pt) REVERT: D 117 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8150 (pm20) REVERT: D 253 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8169 (mt-10) REVERT: J 52 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8909 (mm-40) REVERT: J 72 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8653 (mm) REVERT: L 11 MET cc_start: 0.8285 (tpt) cc_final: 0.7626 (tpp) REVERT: L 37 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8628 (tm-30) REVERT: N 11 MET cc_start: 0.7709 (tpt) cc_final: 0.7459 (tpt) REVERT: N 57 MET cc_start: 0.8222 (tmm) cc_final: 0.7794 (tmm) REVERT: N 65 MET cc_start: 0.7681 (mmm) cc_final: 0.7093 (mmm) REVERT: O 73 TYR cc_start: 0.7348 (t80) cc_final: 0.6514 (m-10) REVERT: P 6 MET cc_start: 0.7339 (ppp) cc_final: 0.7106 (ppp) REVERT: P 17 MET cc_start: 0.8525 (mtp) cc_final: 0.8079 (mmm) REVERT: P 50 ARG cc_start: 0.9182 (ttp80) cc_final: 0.8921 (ttp80) REVERT: P 57 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.6759 (tpt) REVERT: P 76 PHE cc_start: 0.6144 (m-80) cc_final: 0.5686 (m-10) REVERT: Q 42 GLN cc_start: 0.8585 (mt0) cc_final: 0.7991 (mp10) REVERT: R 10 TYR cc_start: 0.7423 (m-10) cc_final: 0.6845 (m-10) REVERT: S 16 MET cc_start: 0.7909 (tpp) cc_final: 0.7686 (tpp) REVERT: S 17 MET cc_start: 0.7645 (mmm) cc_final: 0.7003 (mtt) REVERT: Y 18 VAL cc_start: 0.8673 (t) cc_final: 0.8351 (p) REVERT: Y 19 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7592 (pp) REVERT: Y 26 TRP cc_start: 0.6176 (t60) cc_final: 0.5775 (t60) REVERT: Y 30 MET cc_start: 0.8024 (ppp) cc_final: 0.7765 (mtp) REVERT: Y 54 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6287 (mm) REVERT: a 11 TYR cc_start: 0.7599 (t80) cc_final: 0.7130 (t80) REVERT: a 20 GLN cc_start: 0.8264 (mt0) cc_final: 0.7841 (mp10) REVERT: a 54 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8325 (pp) REVERT: a 56 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7663 (t80) REVERT: a 80 GLU cc_start: 0.9030 (pt0) cc_final: 0.8799 (pt0) REVERT: a 124 ASP cc_start: 0.8067 (t0) cc_final: 0.7660 (m-30) REVERT: a 176 LYS cc_start: 0.8436 (tptm) cc_final: 0.8140 (tptp) REVERT: a 199 SER cc_start: 0.8777 (t) cc_final: 0.8517 (p) REVERT: a 231 TRP cc_start: 0.7705 (p-90) cc_final: 0.7106 (p-90) REVERT: a 232 TRP cc_start: 0.7621 (p-90) cc_final: 0.7110 (p-90) REVERT: a 234 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7916 (mm-40) REVERT: a 244 PHE cc_start: 0.8793 (t80) cc_final: 0.8482 (m-10) outliers start: 122 outliers final: 75 residues processed: 687 average time/residue: 0.2159 time to fit residues: 243.0026 Evaluate side-chains 658 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 572 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 73 TYR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 57 MET Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 75 PHE Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 131 GLU Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 237 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 404 optimal weight: 10.0000 chunk 445 optimal weight: 9.9990 chunk 374 optimal weight: 5.9990 chunk 443 optimal weight: 3.9990 chunk 278 optimal weight: 6.9990 chunk 324 optimal weight: 4.9990 chunk 320 optimal weight: 0.5980 chunk 263 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 362 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN X 2 ASN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 GLN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.094314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.066094 restraints weight = 82180.830| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.12 r_work: 0.2775 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37528 Z= 0.178 Angle : 0.600 12.022 50797 Z= 0.305 Chirality : 0.043 0.210 5920 Planarity : 0.004 0.041 6550 Dihedral : 6.762 110.865 5359 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.60 % Allowed : 16.01 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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 are not related in a simple way. whole: 0.98 (0.12), residues: 4807 helix: 1.57 (0.10), residues: 2620 sheet: -0.08 (0.22), residues: 518 loop : -0.53 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 50 TYR 0.024 0.001 TYR B 236 PHE 0.030 0.001 PHE E 189 TRP 0.006 0.001 TRP W 27 HIS 0.005 0.001 HIS a 185 Details of bonding type rmsd covalent geometry : bond 0.00419 (37528) covalent geometry : angle 0.60045 (50797) hydrogen bonds : bond 0.04561 ( 2267) hydrogen bonds : angle 4.48065 ( 6570) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 575 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 156 ASP cc_start: 0.8445 (p0) cc_final: 0.7850 (p0) REVERT: C 70 SER cc_start: 0.8227 (OUTLIER) cc_final: 0.7785 (m) REVERT: C 343 THR cc_start: 0.9591 (OUTLIER) cc_final: 0.9245 (p) REVERT: B 429 GLU cc_start: 0.8290 (tp30) cc_final: 0.8042 (tp30) REVERT: B 484 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8307 (tm-30) REVERT: B 511 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.5620 (mp10) REVERT: A 86 MET cc_start: 0.9290 (mtt) cc_final: 0.9074 (mtp) REVERT: X 85 GLN cc_start: 0.8217 (mt0) cc_final: 0.7872 (mp10) REVERT: H 15 MET cc_start: 0.9251 (mtp) cc_final: 0.9016 (mtt) REVERT: H 71 VAL cc_start: 0.9597 (OUTLIER) cc_final: 0.9259 (m) REVERT: H 113 ASP cc_start: 0.8822 (m-30) cc_final: 0.8580 (m-30) REVERT: G 70 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8371 (ptt180) REVERT: E 323 ARG cc_start: 0.8576 (tpp80) cc_final: 0.8335 (ttm170) REVERT: E 366 ARG cc_start: 0.8682 (tpt90) cc_final: 0.8477 (tpt90) REVERT: E 438 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8154 (pt) REVERT: D 117 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8097 (pm20) REVERT: D 253 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8226 (mt-10) REVERT: D 345 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8575 (p0) REVERT: I 50 ARG cc_start: 0.8698 (mtm110) cc_final: 0.8293 (mtm110) REVERT: J 52 GLN cc_start: 0.9245 (mm-40) cc_final: 0.8970 (mm-40) REVERT: J 59 LEU cc_start: 0.9064 (mm) cc_final: 0.8769 (tt) REVERT: J 72 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8740 (mm) REVERT: L 11 MET cc_start: 0.8214 (tpt) cc_final: 0.7614 (tpt) REVERT: L 37 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8665 (tm-30) REVERT: N 11 MET cc_start: 0.7729 (tpt) cc_final: 0.7528 (tpt) REVERT: N 57 MET cc_start: 0.8192 (tmm) cc_final: 0.7766 (tmm) REVERT: N 65 MET cc_start: 0.7620 (mmm) cc_final: 0.7083 (mmm) REVERT: O 73 TYR cc_start: 0.7336 (t80) cc_final: 0.6483 (m-10) REVERT: P 6 MET cc_start: 0.7378 (ppp) cc_final: 0.7141 (ppp) REVERT: P 50 ARG cc_start: 0.9089 (ttp80) cc_final: 0.8853 (ttp80) REVERT: P 76 PHE cc_start: 0.6206 (m-80) cc_final: 0.5918 (m-10) REVERT: Q 42 GLN cc_start: 0.8539 (mt0) cc_final: 0.7984 (mp10) REVERT: S 16 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7599 (tpp) REVERT: S 17 MET cc_start: 0.7676 (mmm) cc_final: 0.6997 (mtt) REVERT: Y 18 VAL cc_start: 0.8734 (t) cc_final: 0.8379 (p) REVERT: Y 19 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7495 (pp) REVERT: Y 26 TRP cc_start: 0.6257 (t60) cc_final: 0.5936 (t60) REVERT: Y 54 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6117 (mm) REVERT: a 11 TYR cc_start: 0.7558 (t80) cc_final: 0.7055 (t80) REVERT: a 20 GLN cc_start: 0.8321 (mt0) cc_final: 0.7905 (mp10) REVERT: a 54 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8336 (pp) REVERT: a 56 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7660 (t80) REVERT: a 80 GLU cc_start: 0.9062 (pt0) cc_final: 0.8803 (pt0) REVERT: a 124 ASP cc_start: 0.8157 (t0) cc_final: 0.7859 (m-30) REVERT: a 199 SER cc_start: 0.8861 (t) cc_final: 0.8578 (p) REVERT: a 231 TRP cc_start: 0.7715 (p-90) cc_final: 0.7205 (p-90) REVERT: a 234 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7952 (mm-40) REVERT: a 244 PHE cc_start: 0.8778 (t80) cc_final: 0.8479 (m-10) outliers start: 138 outliers final: 94 residues processed: 667 average time/residue: 0.2195 time to fit residues: 240.6386 Evaluate side-chains 664 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 555 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain G residue 70 ARG Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 73 TYR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 75 PHE Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 266 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 326 optimal weight: 6.9990 chunk 395 optimal weight: 1.9990 chunk 425 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 416 optimal weight: 0.8980 chunk 422 optimal weight: 6.9990 chunk 225 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 456 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN C 294 HIS B 511 GLN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN D 121 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN M 52 GLN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 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 = 0.3471 r_free = 0.3471 target = 0.096307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.068536 restraints weight = 83101.423| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.20 r_work: 0.2797 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37528 Z= 0.129 Angle : 0.575 10.866 50797 Z= 0.291 Chirality : 0.042 0.217 5920 Planarity : 0.004 0.048 6550 Dihedral : 6.563 107.362 5359 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.57 % Allowed : 16.21 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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 are not related in a simple way. whole: 1.16 (0.12), residues: 4807 helix: 1.75 (0.10), residues: 2610 sheet: 0.01 (0.22), residues: 519 loop : -0.49 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 41 TYR 0.022 0.001 TYR B 236 PHE 0.030 0.001 PHE Q 53 TRP 0.007 0.001 TRP X 26 HIS 0.005 0.001 HIS a 185 Details of bonding type rmsd covalent geometry : bond 0.00286 (37528) covalent geometry : angle 0.57513 (50797) hydrogen bonds : bond 0.04276 ( 2267) hydrogen bonds : angle 4.37363 ( 6570) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 585 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: W 156 ASP cc_start: 0.8473 (p0) cc_final: 0.7882 (p0) REVERT: C 70 SER cc_start: 0.8170 (OUTLIER) cc_final: 0.7732 (m) REVERT: C 343 THR cc_start: 0.9574 (OUTLIER) cc_final: 0.9276 (p) REVERT: B 429 GLU cc_start: 0.8271 (tp30) cc_final: 0.8029 (tp30) REVERT: B 484 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8308 (tm-30) REVERT: A 76 MET cc_start: 0.9222 (mtp) cc_final: 0.8923 (mtp) REVERT: A 343 THR cc_start: 0.9448 (OUTLIER) cc_final: 0.9192 (p) REVERT: X 1 MET cc_start: 0.8084 (tmm) cc_final: 0.7431 (tmm) REVERT: X 85 GLN cc_start: 0.8257 (mt0) cc_final: 0.7940 (mp10) REVERT: H 15 MET cc_start: 0.9266 (mtp) cc_final: 0.9035 (mtt) REVERT: H 58 HIS cc_start: 0.8206 (m90) cc_final: 0.7639 (m90) REVERT: H 71 VAL cc_start: 0.9560 (OUTLIER) cc_final: 0.9239 (m) REVERT: G 116 MET cc_start: 0.9173 (mmm) cc_final: 0.8863 (mmm) REVERT: E 275 MET cc_start: 0.9539 (tpp) cc_final: 0.9255 (tpt) REVERT: E 323 ARG cc_start: 0.8672 (tpp80) cc_final: 0.8399 (ttm170) REVERT: E 438 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8122 (pt) REVERT: D 117 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8111 (pm20) REVERT: D 253 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8187 (mt-10) REVERT: J 52 GLN cc_start: 0.9274 (mm-40) cc_final: 0.9005 (mm-40) REVERT: J 59 LEU cc_start: 0.9088 (mm) cc_final: 0.8788 (tt) REVERT: J 72 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8805 (mm) REVERT: J 76 PHE cc_start: 0.8084 (m-80) cc_final: 0.7852 (m-80) REVERT: L 11 MET cc_start: 0.8014 (tpt) cc_final: 0.7403 (tpt) REVERT: M 57 MET cc_start: 0.8304 (tmm) cc_final: 0.7877 (tmm) REVERT: N 10 TYR cc_start: 0.6956 (m-80) cc_final: 0.6640 (m-80) REVERT: N 16 MET cc_start: 0.7479 (mmm) cc_final: 0.7022 (mmm) REVERT: N 57 MET cc_start: 0.8177 (tmm) cc_final: 0.7765 (tmm) REVERT: N 65 MET cc_start: 0.7598 (mmm) cc_final: 0.7075 (mmm) REVERT: O 73 TYR cc_start: 0.7304 (t80) cc_final: 0.6483 (m-10) REVERT: P 6 MET cc_start: 0.7392 (ppp) cc_final: 0.7158 (ppp) REVERT: P 50 ARG cc_start: 0.9032 (ttp80) cc_final: 0.8760 (ttp80) REVERT: P 54 PHE cc_start: 0.7915 (m-10) cc_final: 0.7646 (m-80) REVERT: P 76 PHE cc_start: 0.6247 (m-80) cc_final: 0.5943 (m-10) REVERT: Q 42 GLN cc_start: 0.8588 (mt0) cc_final: 0.8006 (mp10) REVERT: R 16 MET cc_start: 0.8634 (tpp) cc_final: 0.8404 (tpp) REVERT: S 16 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7609 (tpp) REVERT: S 17 MET cc_start: 0.7771 (mmm) cc_final: 0.7119 (mtt) REVERT: S 50 ARG cc_start: 0.8395 (ttp-170) cc_final: 0.7999 (ttp80) REVERT: S 65 MET cc_start: 0.8147 (mmm) cc_final: 0.7946 (mtm) REVERT: Y 18 VAL cc_start: 0.8755 (t) cc_final: 0.8395 (p) REVERT: Y 19 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7452 (pp) REVERT: Y 54 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6251 (mm) REVERT: Y 152 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8524 (pp) REVERT: a 11 TYR cc_start: 0.7579 (t80) cc_final: 0.7120 (t80) REVERT: a 20 GLN cc_start: 0.8307 (mt0) cc_final: 0.7838 (mp10) REVERT: a 54 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8328 (pp) REVERT: a 56 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7664 (t80) REVERT: a 80 GLU cc_start: 0.9055 (pt0) cc_final: 0.8811 (pt0) REVERT: a 124 ASP cc_start: 0.8205 (t0) cc_final: 0.7870 (m-30) REVERT: a 199 SER cc_start: 0.8882 (t) cc_final: 0.8602 (p) REVERT: a 231 TRP cc_start: 0.7594 (p-90) cc_final: 0.7095 (p-90) REVERT: a 232 TRP cc_start: 0.7753 (p-90) cc_final: 0.7205 (p-90) REVERT: a 234 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8069 (mm-40) REVERT: a 244 PHE cc_start: 0.8831 (t80) cc_final: 0.8452 (m-10) outliers start: 137 outliers final: 83 residues processed: 669 average time/residue: 0.2180 time to fit residues: 239.5590 Evaluate side-chains 661 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 564 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 73 TYR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 75 PHE Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 237 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 141 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 435 optimal weight: 5.9990 chunk 376 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 342 optimal weight: 3.9990 chunk 293 optimal weight: 0.9980 chunk 323 optimal weight: 2.9990 chunk 311 optimal weight: 4.9990 chunk 389 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 GLN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN J 3 ASN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 GLN a 116 ASN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.094726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.067051 restraints weight = 83071.808| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.10 r_work: 0.2778 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37528 Z= 0.182 Angle : 0.604 10.029 50797 Z= 0.306 Chirality : 0.043 0.214 5920 Planarity : 0.004 0.054 6550 Dihedral : 6.560 108.436 5356 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.57 % Allowed : 16.81 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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 are not related in a simple way. whole: 1.17 (0.12), residues: 4807 helix: 1.77 (0.10), residues: 2615 sheet: 0.01 (0.22), residues: 518 loop : -0.50 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 50 TYR 0.024 0.001 TYR B 236 PHE 0.024 0.001 PHE E 189 TRP 0.010 0.001 TRP X 26 HIS 0.006 0.001 HIS a 185 Details of bonding type rmsd covalent geometry : bond 0.00430 (37528) covalent geometry : angle 0.60387 (50797) hydrogen bonds : bond 0.04425 ( 2267) hydrogen bonds : angle 4.43313 ( 6570) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 572 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 156 ASP cc_start: 0.8447 (p0) cc_final: 0.7876 (p0) REVERT: C 70 SER cc_start: 0.8212 (OUTLIER) cc_final: 0.7786 (m) REVERT: C 343 THR cc_start: 0.9583 (OUTLIER) cc_final: 0.9252 (p) REVERT: B 429 GLU cc_start: 0.8338 (tp30) cc_final: 0.8065 (tp30) REVERT: B 484 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8321 (tm-30) REVERT: A 343 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.9167 (p) REVERT: A 419 LYS cc_start: 0.8777 (mtmm) cc_final: 0.8559 (mtmm) REVERT: X 85 GLN cc_start: 0.8214 (mt0) cc_final: 0.7909 (mp10) REVERT: H 15 MET cc_start: 0.9273 (mtp) cc_final: 0.9038 (mtt) REVERT: H 28 SER cc_start: 0.8856 (t) cc_final: 0.8557 (t) REVERT: H 58 HIS cc_start: 0.8146 (m90) cc_final: 0.7627 (m90) REVERT: E 275 MET cc_start: 0.9535 (tpp) cc_final: 0.9263 (tpt) REVERT: E 323 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8377 (ttm170) REVERT: D 117 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8086 (pm20) REVERT: D 253 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8237 (mt-10) REVERT: D 345 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8554 (p0) REVERT: I 4 LEU cc_start: -0.1689 (OUTLIER) cc_final: -0.2081 (mt) REVERT: I 50 ARG cc_start: 0.8707 (mtm110) cc_final: 0.8498 (mtm110) REVERT: J 52 GLN cc_start: 0.9266 (mm-40) cc_final: 0.8985 (mm-40) REVERT: J 59 LEU cc_start: 0.9060 (mm) cc_final: 0.8775 (tt) REVERT: J 72 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8771 (mm) REVERT: L 11 MET cc_start: 0.7961 (tpt) cc_final: 0.7347 (tpt) REVERT: L 76 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6180 (m-80) REVERT: M 17 MET cc_start: 0.8186 (mtm) cc_final: 0.7724 (ptm) REVERT: M 57 MET cc_start: 0.8356 (tmm) cc_final: 0.7925 (tmm) REVERT: N 57 MET cc_start: 0.8154 (tmm) cc_final: 0.7757 (tmm) REVERT: N 65 MET cc_start: 0.7614 (mmm) cc_final: 0.7071 (mmm) REVERT: O 73 TYR cc_start: 0.7307 (t80) cc_final: 0.6424 (m-10) REVERT: P 6 MET cc_start: 0.7343 (ppp) cc_final: 0.7110 (ppp) REVERT: P 76 PHE cc_start: 0.6192 (m-80) cc_final: 0.5887 (m-10) REVERT: Q 42 GLN cc_start: 0.8559 (mt0) cc_final: 0.7992 (mp10) REVERT: R 75 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8294 (tpp) REVERT: S 16 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7566 (tpp) REVERT: S 17 MET cc_start: 0.7706 (mmm) cc_final: 0.7006 (mtt) REVERT: S 65 MET cc_start: 0.8114 (mmm) cc_final: 0.7913 (mtm) REVERT: Y 18 VAL cc_start: 0.8803 (t) cc_final: 0.8441 (p) REVERT: Y 19 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7442 (pp) REVERT: Y 54 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6178 (mm) REVERT: Y 152 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8569 (pp) REVERT: a 11 TYR cc_start: 0.7639 (t80) cc_final: 0.7125 (t80) REVERT: a 20 GLN cc_start: 0.8345 (mt0) cc_final: 0.7893 (mp10) REVERT: a 54 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8350 (pp) REVERT: a 56 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7729 (t80) REVERT: a 80 GLU cc_start: 0.9094 (pt0) cc_final: 0.8841 (pt0) REVERT: a 124 ASP cc_start: 0.8141 (t0) cc_final: 0.7768 (m-30) REVERT: a 199 SER cc_start: 0.8846 (t) cc_final: 0.8605 (p) REVERT: a 231 TRP cc_start: 0.7577 (p-90) cc_final: 0.7084 (p-90) REVERT: a 234 GLN cc_start: 0.8310 (mm-40) cc_final: 0.8040 (mm-40) REVERT: a 244 PHE cc_start: 0.8862 (t80) cc_final: 0.8464 (m-10) REVERT: a 255 ILE cc_start: 0.9555 (mt) cc_final: 0.9238 (tt) outliers start: 137 outliers final: 97 residues processed: 659 average time/residue: 0.2144 time to fit residues: 233.7552 Evaluate side-chains 667 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 554 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 14 PHE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 75 PHE Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 237 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 40 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 332 optimal weight: 0.8980 chunk 317 optimal weight: 1.9990 chunk 434 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 351 optimal weight: 3.9990 chunk 330 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN M 3 ASN M 5 ASN M 52 GLN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 116 ASN a 185 HIS ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.096440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.068842 restraints weight = 82662.862| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.11 r_work: 0.2813 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37528 Z= 0.126 Angle : 0.586 10.579 50797 Z= 0.295 Chirality : 0.042 0.232 5920 Planarity : 0.004 0.050 6550 Dihedral : 6.369 106.081 5356 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.28 % Allowed : 17.26 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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 are not related in a simple way. whole: 1.24 (0.12), residues: 4807 helix: 1.84 (0.10), residues: 2604 sheet: 0.07 (0.22), residues: 534 loop : -0.50 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 41 TYR 0.020 0.001 TYR B 236 PHE 0.024 0.001 PHE M 53 TRP 0.010 0.001 TRP X 26 HIS 0.006 0.001 HIS a 185 Details of bonding type rmsd covalent geometry : bond 0.00280 (37528) covalent geometry : angle 0.58572 (50797) hydrogen bonds : bond 0.04150 ( 2267) hydrogen bonds : angle 4.34928 ( 6570) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 589 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 156 ASP cc_start: 0.8413 (p0) cc_final: 0.7870 (p0) REVERT: C 70 SER cc_start: 0.8100 (OUTLIER) cc_final: 0.7683 (m) REVERT: C 343 THR cc_start: 0.9530 (OUTLIER) cc_final: 0.9251 (p) REVERT: B 429 GLU cc_start: 0.8314 (tp30) cc_final: 0.8049 (tp30) REVERT: B 484 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8265 (tm-30) REVERT: B 511 GLN cc_start: 0.6848 (OUTLIER) cc_final: 0.5538 (mp10) REVERT: A 76 MET cc_start: 0.9213 (mtp) cc_final: 0.8935 (mtp) REVERT: A 343 THR cc_start: 0.9448 (OUTLIER) cc_final: 0.9201 (p) REVERT: A 419 LYS cc_start: 0.8718 (mtmm) cc_final: 0.8434 (mtmm) REVERT: X 1 MET cc_start: 0.7770 (tmm) cc_final: 0.7187 (tmm) REVERT: X 85 GLN cc_start: 0.8087 (mt0) cc_final: 0.7770 (mp10) REVERT: H 15 MET cc_start: 0.9300 (mtp) cc_final: 0.9078 (mtt) REVERT: H 28 SER cc_start: 0.8829 (t) cc_final: 0.8542 (t) REVERT: H 58 HIS cc_start: 0.8050 (m90) cc_final: 0.7555 (m90) REVERT: G 116 MET cc_start: 0.9186 (mmm) cc_final: 0.8890 (mmm) REVERT: E 274 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8479 (mt-10) REVERT: E 275 MET cc_start: 0.9515 (tpp) cc_final: 0.9273 (tpt) REVERT: E 323 ARG cc_start: 0.8615 (tpp80) cc_final: 0.8336 (ttm170) REVERT: D 117 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8037 (pm20) REVERT: D 253 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8193 (mt-10) REVERT: D 345 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8526 (p0) REVERT: I 17 MET cc_start: 0.9116 (tpt) cc_final: 0.8623 (tpp) REVERT: I 46 ILE cc_start: 0.8566 (mt) cc_final: 0.8353 (mm) REVERT: J 52 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8966 (mm-40) REVERT: J 59 LEU cc_start: 0.9045 (mm) cc_final: 0.8681 (tt) REVERT: J 72 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8838 (mm) REVERT: L 11 MET cc_start: 0.7966 (tpt) cc_final: 0.7337 (tpt) REVERT: L 76 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6117 (m-80) REVERT: M 17 MET cc_start: 0.8144 (mtm) cc_final: 0.7760 (mmp) REVERT: M 57 MET cc_start: 0.8404 (tmm) cc_final: 0.8011 (tmm) REVERT: N 57 MET cc_start: 0.8169 (tmm) cc_final: 0.7791 (tmm) REVERT: N 65 MET cc_start: 0.7527 (mmm) cc_final: 0.6980 (mmm) REVERT: O 73 TYR cc_start: 0.7278 (t80) cc_final: 0.6422 (m-10) REVERT: P 6 MET cc_start: 0.7343 (ppp) cc_final: 0.7137 (ppp) REVERT: P 7 ASP cc_start: 0.5795 (OUTLIER) cc_final: 0.5507 (p0) REVERT: P 42 GLN cc_start: 0.8432 (mm-40) cc_final: 0.7655 (mp10) REVERT: P 54 PHE cc_start: 0.8162 (m-80) cc_final: 0.7648 (m-80) REVERT: P 76 PHE cc_start: 0.6193 (m-80) cc_final: 0.5864 (m-10) REVERT: Q 42 GLN cc_start: 0.8551 (mt0) cc_final: 0.7955 (mp10) REVERT: R 75 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8232 (tpp) REVERT: Y 36 ARG cc_start: 0.8663 (tpp80) cc_final: 0.8446 (tpp80) REVERT: Y 54 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6242 (mm) REVERT: Y 152 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8558 (pp) REVERT: a 11 TYR cc_start: 0.7617 (t80) cc_final: 0.7101 (t80) REVERT: a 20 GLN cc_start: 0.8320 (mt0) cc_final: 0.7907 (mp10) REVERT: a 42 ASN cc_start: 0.7530 (m-40) cc_final: 0.7257 (m-40) REVERT: a 54 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8365 (pp) REVERT: a 56 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7703 (t80) REVERT: a 80 GLU cc_start: 0.9086 (pt0) cc_final: 0.8729 (pt0) REVERT: a 124 ASP cc_start: 0.8084 (t0) cc_final: 0.7705 (m-30) REVERT: a 185 HIS cc_start: 0.3495 (OUTLIER) cc_final: 0.2927 (m-70) REVERT: a 199 SER cc_start: 0.8878 (t) cc_final: 0.8588 (p) REVERT: a 219 GLU cc_start: 0.8999 (pt0) cc_final: 0.8685 (pt0) REVERT: a 231 TRP cc_start: 0.7505 (p-90) cc_final: 0.6996 (p-90) REVERT: a 234 GLN cc_start: 0.8317 (mm-40) cc_final: 0.7894 (mp10) REVERT: a 244 PHE cc_start: 0.8756 (t80) cc_final: 0.8399 (m-10) REVERT: a 255 ILE cc_start: 0.9545 (mt) cc_final: 0.9264 (tt) outliers start: 126 outliers final: 78 residues processed: 669 average time/residue: 0.2131 time to fit residues: 235.7351 Evaluate side-chains 661 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 567 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 14 PHE Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 52 GLN Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 75 PHE Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 161 ILE Chi-restraints excluded: chain a residue 185 HIS Chi-restraints excluded: chain a residue 237 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 179 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 242 optimal weight: 8.9990 chunk 352 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 349 optimal weight: 0.1980 chunk 219 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 317 optimal weight: 4.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN M 52 GLN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 73 GLN a 116 ASN a 192 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.096009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.068444 restraints weight = 82843.466| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.13 r_work: 0.2807 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37528 Z= 0.142 Angle : 0.606 10.668 50797 Z= 0.303 Chirality : 0.043 0.224 5920 Planarity : 0.004 0.051 6550 Dihedral : 6.318 106.684 5355 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.69 % Allowed : 18.30 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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 are not related in a simple way. whole: 1.26 (0.12), residues: 4807 helix: 1.85 (0.10), residues: 2606 sheet: 0.06 (0.22), residues: 541 loop : -0.48 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG I 50 TYR 0.021 0.001 TYR B 236 PHE 0.034 0.001 PHE M 53 TRP 0.011 0.001 TRP X 26 HIS 0.016 0.001 HIS a 185 Details of bonding type rmsd covalent geometry : bond 0.00327 (37528) covalent geometry : angle 0.60568 (50797) hydrogen bonds : bond 0.04186 ( 2267) hydrogen bonds : angle 4.35624 ( 6570) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 574 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 156 ASP cc_start: 0.8377 (p0) cc_final: 0.7850 (p0) REVERT: C 70 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7733 (m) REVERT: C 343 THR cc_start: 0.9539 (OUTLIER) cc_final: 0.9256 (p) REVERT: B 419 LYS cc_start: 0.8369 (pttm) cc_final: 0.7695 (tptt) REVERT: B 429 GLU cc_start: 0.8293 (tp30) cc_final: 0.8035 (tp30) REVERT: B 511 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.5476 (mp10) REVERT: A 343 THR cc_start: 0.9444 (OUTLIER) cc_final: 0.9171 (p) REVERT: X 1 MET cc_start: 0.7823 (tmm) cc_final: 0.7223 (tmm) REVERT: X 85 GLN cc_start: 0.8083 (mt0) cc_final: 0.7754 (mp10) REVERT: H 15 MET cc_start: 0.9304 (mtp) cc_final: 0.9088 (mtt) REVERT: H 28 SER cc_start: 0.8851 (t) cc_final: 0.8562 (t) REVERT: H 58 HIS cc_start: 0.8136 (m90) cc_final: 0.7585 (m90) REVERT: H 100 LYS cc_start: 0.8517 (mtmm) cc_final: 0.8316 (mtmm) REVERT: G 116 MET cc_start: 0.9189 (mmm) cc_final: 0.8903 (mmm) REVERT: E 274 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8467 (mt-10) REVERT: E 275 MET cc_start: 0.9526 (tpp) cc_final: 0.9261 (tpt) REVERT: E 323 ARG cc_start: 0.8682 (tpp80) cc_final: 0.8405 (ttm170) REVERT: D 117 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8014 (pm20) REVERT: D 198 VAL cc_start: 0.9480 (OUTLIER) cc_final: 0.9276 (p) REVERT: D 253 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8225 (mt-10) REVERT: D 345 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8516 (p0) REVERT: I 46 ILE cc_start: 0.8567 (mt) cc_final: 0.8120 (mm) REVERT: I 50 ARG cc_start: 0.8727 (mtm110) cc_final: 0.8364 (mtm110) REVERT: I 57 MET cc_start: 0.8074 (ppp) cc_final: 0.7669 (tmm) REVERT: J 52 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8987 (mm-40) REVERT: J 59 LEU cc_start: 0.9050 (mm) cc_final: 0.8684 (tt) REVERT: J 72 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8885 (mm) REVERT: L 11 MET cc_start: 0.7912 (tpt) cc_final: 0.7261 (tpp) REVERT: L 76 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6100 (m-80) REVERT: M 17 MET cc_start: 0.8092 (mtm) cc_final: 0.7733 (mmp) REVERT: M 57 MET cc_start: 0.8428 (tmm) cc_final: 0.7965 (tmm) REVERT: N 57 MET cc_start: 0.8139 (tmm) cc_final: 0.7761 (tmm) REVERT: N 65 MET cc_start: 0.7568 (mmm) cc_final: 0.7005 (mmm) REVERT: O 73 TYR cc_start: 0.7286 (t80) cc_final: 0.6431 (m-10) REVERT: P 6 MET cc_start: 0.7320 (ppp) cc_final: 0.7086 (ppp) REVERT: P 7 ASP cc_start: 0.5914 (OUTLIER) cc_final: 0.5588 (p0) REVERT: P 42 GLN cc_start: 0.8392 (mm-40) cc_final: 0.7768 (mp10) REVERT: P 54 PHE cc_start: 0.8228 (m-10) cc_final: 0.7613 (m-80) REVERT: P 76 PHE cc_start: 0.6133 (m-80) cc_final: 0.5784 (m-10) REVERT: Q 42 GLN cc_start: 0.8575 (mt0) cc_final: 0.7970 (mp10) REVERT: R 75 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8169 (tpp) REVERT: S 17 MET cc_start: 0.7616 (mmm) cc_final: 0.7109 (mpp) REVERT: S 37 GLU cc_start: 0.8376 (tt0) cc_final: 0.8157 (tt0) REVERT: Y 18 VAL cc_start: 0.8783 (t) cc_final: 0.8465 (m) REVERT: Y 54 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6247 (mm) REVERT: Y 152 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8571 (pp) REVERT: a 11 TYR cc_start: 0.7650 (t80) cc_final: 0.7152 (t80) REVERT: a 20 GLN cc_start: 0.8378 (mt0) cc_final: 0.7952 (mp10) REVERT: a 42 ASN cc_start: 0.7564 (m-40) cc_final: 0.7287 (m-40) REVERT: a 54 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8369 (pp) REVERT: a 56 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7629 (t80) REVERT: a 75 PHE cc_start: 0.6305 (OUTLIER) cc_final: 0.6103 (p90) REVERT: a 80 GLU cc_start: 0.9100 (pt0) cc_final: 0.8750 (pt0) REVERT: a 124 ASP cc_start: 0.8132 (t0) cc_final: 0.7745 (m-30) REVERT: a 199 SER cc_start: 0.8919 (t) cc_final: 0.8614 (p) REVERT: a 219 GLU cc_start: 0.8991 (pt0) cc_final: 0.8372 (pt0) REVERT: a 231 TRP cc_start: 0.7562 (p-90) cc_final: 0.7052 (p-90) REVERT: a 234 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7869 (mp10) REVERT: a 244 PHE cc_start: 0.8750 (t80) cc_final: 0.8432 (m-10) REVERT: a 255 ILE cc_start: 0.9548 (mt) cc_final: 0.9273 (tt) outliers start: 103 outliers final: 75 residues processed: 642 average time/residue: 0.2130 time to fit residues: 225.8895 Evaluate side-chains 654 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 563 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 14 PHE Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 75 PHE Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 237 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 317 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 289 optimal weight: 0.6980 chunk 281 optimal weight: 1.9990 chunk 258 optimal weight: 0.4980 chunk 191 optimal weight: 0.9980 chunk 395 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 253 optimal weight: 0.9980 chunk 432 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN J 3 ASN M 52 GLN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 GLN a 116 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.096808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.069355 restraints weight = 81891.127| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.14 r_work: 0.2846 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37528 Z= 0.120 Angle : 0.600 11.525 50797 Z= 0.301 Chirality : 0.042 0.238 5920 Planarity : 0.004 0.051 6550 Dihedral : 6.136 105.725 5354 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.24 % Allowed : 19.06 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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 are not related in a simple way. whole: 1.36 (0.12), residues: 4807 helix: 1.91 (0.10), residues: 2611 sheet: 0.12 (0.22), residues: 539 loop : -0.41 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 50 TYR 0.025 0.001 TYR G 44 PHE 0.039 0.001 PHE Q 53 TRP 0.010 0.001 TRP X 26 HIS 0.004 0.001 HIS Y 51 Details of bonding type rmsd covalent geometry : bond 0.00266 (37528) covalent geometry : angle 0.59966 (50797) hydrogen bonds : bond 0.04015 ( 2267) hydrogen bonds : angle 4.31870 ( 6570) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 579 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 156 ASP cc_start: 0.8387 (p0) cc_final: 0.7859 (p0) REVERT: C 70 SER cc_start: 0.8104 (OUTLIER) cc_final: 0.7714 (m) REVERT: B 419 LYS cc_start: 0.8259 (pttm) cc_final: 0.7602 (tptt) REVERT: B 429 GLU cc_start: 0.8283 (tp30) cc_final: 0.8026 (tp30) REVERT: A 343 THR cc_start: 0.9423 (OUTLIER) cc_final: 0.9169 (p) REVERT: A 419 LYS cc_start: 0.8826 (mtmm) cc_final: 0.8620 (mtmm) REVERT: X 1 MET cc_start: 0.7786 (tmm) cc_final: 0.7198 (tmm) REVERT: X 85 GLN cc_start: 0.8001 (mt0) cc_final: 0.7751 (mp10) REVERT: H 51 ARG cc_start: 0.8929 (ttp80) cc_final: 0.8494 (ttm170) REVERT: H 58 HIS cc_start: 0.8022 (m90) cc_final: 0.7499 (m90) REVERT: G 116 MET cc_start: 0.9177 (mmm) cc_final: 0.8901 (mmm) REVERT: E 275 MET cc_start: 0.9507 (tpp) cc_final: 0.9246 (tpt) REVERT: E 323 ARG cc_start: 0.8661 (tpp80) cc_final: 0.8388 (ttm170) REVERT: D 117 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: D 253 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8177 (mt-10) REVERT: D 275 MET cc_start: 0.9278 (tpp) cc_final: 0.9040 (tpp) REVERT: I 41 ARG cc_start: 0.8290 (ttp-170) cc_final: 0.7999 (ttp-170) REVERT: I 46 ILE cc_start: 0.8567 (mt) cc_final: 0.8139 (mm) REVERT: I 50 ARG cc_start: 0.8660 (mtm110) cc_final: 0.8336 (mtm110) REVERT: J 41 ARG cc_start: 0.8219 (ttt-90) cc_final: 0.7958 (ttt-90) REVERT: J 59 LEU cc_start: 0.9080 (mm) cc_final: 0.8712 (tt) REVERT: L 11 MET cc_start: 0.7911 (tpt) cc_final: 0.7491 (mmm) REVERT: L 76 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6065 (m-80) REVERT: M 17 MET cc_start: 0.8112 (mtm) cc_final: 0.7723 (mmp) REVERT: M 57 MET cc_start: 0.8424 (tmm) cc_final: 0.7991 (tmm) REVERT: N 57 MET cc_start: 0.8127 (tmm) cc_final: 0.7758 (tmm) REVERT: N 65 MET cc_start: 0.7531 (mmm) cc_final: 0.6987 (mmm) REVERT: O 73 TYR cc_start: 0.7247 (t80) cc_final: 0.6432 (m-10) REVERT: P 6 MET cc_start: 0.7349 (ppp) cc_final: 0.7138 (ppp) REVERT: P 42 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7632 (mp10) REVERT: P 54 PHE cc_start: 0.8176 (m-10) cc_final: 0.7619 (m-80) REVERT: P 76 PHE cc_start: 0.6229 (m-80) cc_final: 0.5910 (m-10) REVERT: Q 42 GLN cc_start: 0.8555 (mt0) cc_final: 0.7927 (mp10) REVERT: Q 73 TYR cc_start: 0.7977 (t80) cc_final: 0.7741 (t80) REVERT: R 75 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8063 (tpp) REVERT: S 17 MET cc_start: 0.7721 (mmm) cc_final: 0.7270 (mpp) REVERT: Y 18 VAL cc_start: 0.8749 (t) cc_final: 0.8416 (m) REVERT: Y 54 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6320 (mm) REVERT: Y 141 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8058 (p0) REVERT: Y 152 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8570 (pp) REVERT: a 11 TYR cc_start: 0.7623 (t80) cc_final: 0.7115 (t80) REVERT: a 20 GLN cc_start: 0.8363 (mt0) cc_final: 0.7946 (mp10) REVERT: a 42 ASN cc_start: 0.7513 (m-40) cc_final: 0.7239 (m-40) REVERT: a 54 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8351 (pp) REVERT: a 56 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7567 (t80) REVERT: a 80 GLU cc_start: 0.9114 (pt0) cc_final: 0.8877 (pt0) REVERT: a 119 ASP cc_start: 0.8402 (t0) cc_final: 0.8201 (t0) REVERT: a 124 ASP cc_start: 0.8028 (t0) cc_final: 0.7641 (m-30) REVERT: a 199 SER cc_start: 0.8930 (t) cc_final: 0.8602 (p) REVERT: a 219 GLU cc_start: 0.8864 (pt0) cc_final: 0.8263 (pt0) REVERT: a 231 TRP cc_start: 0.7482 (p-90) cc_final: 0.6978 (p-90) REVERT: a 234 GLN cc_start: 0.8318 (mm-40) cc_final: 0.7869 (mp10) REVERT: a 255 ILE cc_start: 0.9519 (mt) cc_final: 0.9287 (tt) outliers start: 86 outliers final: 65 residues processed: 638 average time/residue: 0.2131 time to fit residues: 224.3262 Evaluate side-chains 641 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 566 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain X residue 14 PHE Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 237 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 389 optimal weight: 5.9990 chunk 265 optimal weight: 0.6980 chunk 225 optimal weight: 5.9990 chunk 402 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 238 optimal weight: 0.2980 chunk 422 optimal weight: 0.0040 chunk 303 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS J 3 ASN J 42 GLN M 52 GLN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 116 ASN a 185 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.096726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.069175 restraints weight = 82628.837| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.11 r_work: 0.2830 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37528 Z= 0.133 Angle : 0.609 12.467 50797 Z= 0.305 Chirality : 0.043 0.235 5920 Planarity : 0.004 0.053 6550 Dihedral : 6.045 107.102 5353 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.48 % Allowed : 18.98 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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 are not related in a simple way. whole: 1.40 (0.12), residues: 4807 helix: 1.94 (0.10), residues: 2608 sheet: 0.11 (0.22), residues: 540 loop : -0.38 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 50 TYR 0.020 0.001 TYR B 236 PHE 0.040 0.001 PHE E 189 TRP 0.024 0.001 TRP X 26 HIS 0.008 0.001 HIS a 185 Details of bonding type rmsd covalent geometry : bond 0.00303 (37528) covalent geometry : angle 0.60899 (50797) hydrogen bonds : bond 0.04083 ( 2267) hydrogen bonds : angle 4.32725 ( 6570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11039.46 seconds wall clock time: 188 minutes 25.45 seconds (11305.45 seconds total)