Starting phenix.real_space_refine on Sat Mar 7 01:54:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbs_27304/03_2026/8dbs_27304.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbs_27304/03_2026/8dbs_27304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dbs_27304/03_2026/8dbs_27304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbs_27304/03_2026/8dbs_27304.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbs_27304/03_2026/8dbs_27304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbs_27304/03_2026/8dbs_27304.cif" } resolution = 3.5 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 179 5.16 5 C 23302 2.51 5 N 6263 2.21 5 O 6913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.04s 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: 36678 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3826 Classifications: {'peptide': 508} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 489} Chain: "B" Number of atoms: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3877 Classifications: {'peptide': 513} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3849 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 18, 'TRANS': 491} Chain: "D" 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: "F" 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: "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: "H" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} 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: "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: "X" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1200 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} 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: "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: "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: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.16, per 1000 atoms: 0.22 Number of scatterers: 36678 At special positions: 0 Unit cell: (185.588, 215.8, 134.875, 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 179 16.00 P 16 15.00 Mg 5 11.99 O 6913 8.00 N 6263 7.00 C 23302 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: 3.27 Conformation dependent library (CDL) restraints added in 1.6 seconds 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8746 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 27 sheets defined 61.4% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 removed outlier: 3.625A pdb=" N ILE A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' 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 233 through 253 removed outlier: 3.740A pdb=" N LEU A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.829A pdb=" N ALA A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.560A pdb=" N ALA A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.547A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 333 through 336 Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.821A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.551A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 408 removed outlier: 3.612A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 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: 3.943A pdb=" N ASP A 478 " --> pdb=" O TYR A 474 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 493 through 510 Processing helix chain 'B' and resid 3 through 19 removed outlier: 4.227A pdb=" N GLU B 7 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU B 10 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.679A 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 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 252 Proline residue: B 239 - end of helix removed outlier: 3.971A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.592A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (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 Processing helix chain 'B' and resid 305 through 314 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.781A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 408 removed outlier: 4.853A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 479 through 490 removed outlier: 3.501A pdb=" N MET B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 511 Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.534A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.689A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 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 253 Proline residue: C 239 - end of helix removed outlier: 4.199A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 305 through 313 Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.798A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 404 removed outlier: 4.240A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.948A pdb=" N GLN C 408 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA C 410 " --> pdb=" O SER C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 432 removed outlier: 3.593A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 432 " --> pdb=" O THR C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 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: 3.600A pdb=" N MET C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 509 removed outlier: 3.630A pdb=" N LYS C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 509 " --> pdb=" O ASP C 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 115 through 119 removed outlier: 3.582A pdb=" N LEU D 119 " --> pdb=" O TYR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 154 through 167 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 233 removed outlier: 3.571A pdb=" N ARG D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 256 removed outlier: 4.023A pdb=" N THR D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 281 removed outlier: 3.635A pdb=" N LEU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG D 281 " --> pdb=" O VAL D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 302 Processing helix chain 'D' and resid 305 through 313 removed outlier: 4.408A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) 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 378 removed outlier: 4.243A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 382 Processing helix chain 'D' and resid 383 through 400 Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 419 through 433 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.982A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.685A pdb=" N LEU E 119 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 137 Processing helix chain 'E' and resid 154 through 171 removed outlier: 4.309A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU E 169 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 196 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: 3.523A pdb=" N ARG E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR E 222 " --> pdb=" O ARG E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 256 removed outlier: 3.796A pdb=" N THR E 248 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 280 Processing helix chain 'E' and resid 299 through 302 Processing helix chain 'E' and resid 305 through 312 removed outlier: 3.625A pdb=" N THR E 311 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE E 312 " --> pdb=" O PRO E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 322 through 327 Processing helix chain 'E' and resid 345 through 378 removed outlier: 7.441A pdb=" N GLN E 351 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N GLU E 352 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N HIS E 353 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 382 Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.552A pdb=" N ARG E 398 " --> pdb=" O ARG E 394 " (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 433 through 436 Processing helix chain 'E' and resid 440 through 444 Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 451 through 459 Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 130 through 137 Processing helix chain 'F' and resid 154 through 169 Processing helix chain 'F' and resid 182 through 196 Processing helix chain 'F' and resid 198 through 200 No H-bonds generated for 'chain 'F' and resid 198 through 200' Processing helix chain 'F' and resid 212 through 233 removed outlier: 3.511A pdb=" N ARG F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 259 Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 270 through 281 removed outlier: 3.601A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG F 281 " --> pdb=" O VAL F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 313 removed outlier: 3.776A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 328 removed outlier: 3.606A pdb=" N ALA F 326 " --> pdb=" O SER F 322 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 350 through 378 removed outlier: 3.966A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 382 Processing helix chain 'F' and resid 383 through 400 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 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.702A pdb=" N GLU F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 57 removed outlier: 3.703A pdb=" N MET G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.561A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 129 Processing helix chain 'G' and resid 144 through 161 removed outlier: 3.668A pdb=" N LEU G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 4.664A 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 210 through 283 removed outlier: 3.807A pdb=" N LEU G 214 " --> pdb=" O ASP G 210 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 103 removed outlier: 3.800A pdb=" N ARG H 93 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU H 96 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA H 97 " --> pdb=" O ARG H 93 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 42 removed outlier: 3.915A pdb=" N LEU I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR I 10 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 61 removed outlier: 3.577A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 77 Processing helix chain 'J' and resid 4 through 42 removed outlier: 3.775A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 3.556A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 78 Processing helix chain 'L' and resid 4 through 42 removed outlier: 4.080A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR L 10 " --> pdb=" O MET L 6 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET L 11 " --> pdb=" O ASP L 7 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 removed outlier: 3.805A 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: 3.637A pdb=" N MET M 11 " --> pdb=" O ASP M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 61 removed outlier: 3.603A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 77 removed outlier: 3.514A pdb=" N ILE M 66 " --> pdb=" O ALA M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 42 removed outlier: 4.410A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 61 removed outlier: 3.694A pdb=" N GLY N 58 " --> pdb=" O PHE N 54 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL N 60 " --> pdb=" O VAL N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 77 removed outlier: 3.509A pdb=" N ILE N 66 " --> pdb=" O ALA N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 42 removed outlier: 4.192A pdb=" N LEU O 9 " --> pdb=" O ASN O 5 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 77 removed outlier: 3.785A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA O 62 " --> pdb=" O GLY O 58 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ILE O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) Proline residue: O 64 - end of helix Processing helix chain 'P' and resid 4 through 42 removed outlier: 3.952A pdb=" N LEU P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU P 9 " --> pdb=" O ASN P 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 77 removed outlier: 4.500A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.722A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 Processing helix chain 'Q' and resid 45 through 77 removed outlier: 3.592A pdb=" N THR Q 51 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Proline residue: Q 64 - end of helix Processing helix chain 'R' and resid 5 through 42 removed outlier: 3.807A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 61 removed outlier: 3.622A pdb=" N GLN R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 77 removed outlier: 3.510A pdb=" N ILE R 66 " --> pdb=" O ALA R 62 " (cutoff:3.500A) 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: 3.528A pdb=" N MET S 16 " --> pdb=" O ALA S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.673A pdb=" N GLY S 58 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 3.874A 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 'W' and resid 3 through 21 removed outlier: 3.717A pdb=" N ARG W 8 " --> pdb=" O ILE W 4 " (cutoff:3.500A) Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 23 through 39 removed outlier: 3.505A pdb=" N THR W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 49 Processing helix chain 'W' and resid 52 through 63 removed outlier: 3.648A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 82 removed outlier: 4.224A pdb=" N ASN W 74 " --> pdb=" O GLU W 70 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN W 82 " --> pdb=" O VAL W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 86 removed outlier: 4.603A pdb=" N ASN W 86 " --> pdb=" O GLY W 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 83 through 86' Processing helix chain 'W' and resid 87 through 103 Processing helix chain 'W' and resid 117 through 133 Processing helix chain 'W' and resid 162 through 172 Processing helix chain 'X' and resid 5 through 25 removed outlier: 3.556A pdb=" N GLY X 9 " --> pdb=" O ALA X 5 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA X 11 " --> pdb=" O ILE X 7 " (cutoff:3.500A) Processing helix chain 'X' and resid 30 through 55 Processing helix chain 'X' and resid 55 through 63 removed outlier: 4.345A pdb=" N ALA X 59 " --> pdb=" O ASP X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 124 removed outlier: 3.646A pdb=" N GLN X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL X 74 " --> pdb=" O ALA X 70 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN X 96 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA X 111 " --> pdb=" O ALA X 107 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU X 118 " --> pdb=" O LYS X 114 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 136 removed outlier: 4.384A pdb=" N LYS X 134 " --> pdb=" O ALA X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 146 through 156 Processing helix chain 'Y' and resid 2 through 25 removed outlier: 3.988A pdb=" N THR Y 6 " --> pdb=" O ASN Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 27 through 138 removed outlier: 3.770A pdb=" N ALA Y 31 " --> pdb=" O PRO Y 27 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS Y 35 " --> pdb=" O ALA Y 31 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG Y 36 " --> pdb=" O ALA Y 32 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN Y 73 " --> pdb=" O LYS Y 69 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU Y 95 " --> pdb=" O LYS Y 91 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA Y 103 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE Y 126 " --> pdb=" O LYS Y 122 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU Y 127 " --> pdb=" O GLN Y 123 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS Y 134 " --> pdb=" O ALA Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 154 Processing helix chain 'a' and resid 7 through 16 Processing helix chain 'a' and resid 43 through 65 Processing helix chain 'a' and resid 73 through 94 removed outlier: 4.272A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE a 79 " --> pdb=" O PHE a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 118 removed outlier: 3.690A pdb=" N MET a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) 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 146 through 168 Processing helix chain 'a' and resid 171 through 180 removed outlier: 3.616A pdb=" N GLU a 177 " --> pdb=" O GLY a 173 " (cutoff:3.500A) Processing helix chain 'a' and resid 188 through 229 Proline residue: a 204 - end of helix removed outlier: 3.833A pdb=" N ILE a 221 " --> pdb=" O ALA a 217 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 269 removed outlier: 4.561A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.687A pdb=" N PHE a 244 " --> pdb=" O PRO a 240 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 4.353A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N MET A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASP D 67 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLN D 32 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE D 50 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 109 removed outlier: 6.322A pdb=" N LYS A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE A 259 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE A 194 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ASP A 261 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL A 196 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.446A pdb=" N ILE A 159 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331 removed outlier: 6.413A pdb=" N ILE A 167 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'W' and resid 135 through 140 removed outlier: 13.307A pdb=" N ALA B 25 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY B 92 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN B 27 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR B 91 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N SER B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG B 93 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER B 70 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (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 removed outlier: 6.369A pdb=" N LYS B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE B 259 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 194 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASP B 261 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B 196 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 322 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 329 through 331 removed outlier: 6.393A pdb=" N ILE B 167 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 66 removed outlier: 3.502A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ARG C 93 " --> pdb=" O MET C 52 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR C 91 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASP F 67 " --> pdb=" O GLN F 32 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLN F 32 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA F 28 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP F 27 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLN F 45 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE F 50 " --> pdb=" O GLN F 45 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AB3, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.116A pdb=" N LYS C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE C 259 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE C 194 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ASP C 261 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL C 196 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.499A pdb=" N ILE C 159 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.388A pdb=" N ILE C 167 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.671A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.397A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL D 296 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU D 147 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 125 through 126 removed outlier: 4.770A pdb=" N PHE D 139 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 3 through 9 removed outlier: 6.626A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU E 36 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA E 28 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLN E 32 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASP E 67 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.746A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.160A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLN E 208 " --> pdb=" O MET E 88 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL E 296 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU E 147 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY E 146 " --> pdb=" O VAL E 319 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 125 through 126 removed outlier: 3.874A pdb=" N PHE E 139 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.566A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 87 through 88 removed outlier: 6.003A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLN F 208 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR F 173 " --> pdb=" O ASP F 236 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL F 237 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL F 293 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU F 239 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA F 295 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL F 241 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL F 145 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS F 144 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL F 319 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY F 146 " --> pdb=" O VAL F 319 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 132 through 136 removed outlier: 8.269A pdb=" N VAL G 133 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU G 114 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN G 135 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N MET G 116 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ARG G 74 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N TYR G 168 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY G 76 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL G 170 " --> pdb=" O GLY G 76 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU G 78 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N ASN G 172 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N VAL G 80 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 12.223A pdb=" N PHE G 174 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 206 through 208 removed outlier: 6.038A pdb=" N LEU G 206 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ALA H 44 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLU G 208 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU H 41 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR H 4 " --> pdb=" O VAL H 20 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 206 through 208 removed outlier: 6.038A pdb=" N LEU G 206 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ALA H 44 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLU G 208 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU H 41 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR H 4 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS H 22 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR H 26 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N MET H 49 " --> pdb=" O THR H 26 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'a' and resid 20 through 22 2317 hydrogen bonds defined for protein. 6765 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: 9.24 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6284 1.31 - 1.43: 8700 1.43 - 1.56: 21863 1.56 - 1.68: 26 1.68 - 1.81: 358 Bond restraints: 37231 Sorted by residual: bond pdb=" N VAL a 142 " pdb=" CA VAL a 142 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.50e-03 1.78e+04 1.97e+01 bond pdb=" C PRO A 239 " pdb=" O PRO A 239 " ideal model delta sigma weight residual 1.236 1.183 0.053 1.23e-02 6.61e+03 1.88e+01 bond pdb=" CA SER A 274 " pdb=" CB SER A 274 " ideal model delta sigma weight residual 1.529 1.464 0.065 1.58e-02 4.01e+03 1.68e+01 bond pdb=" CA SER A 155 " pdb=" CB SER A 155 " ideal model delta sigma weight residual 1.533 1.476 0.057 1.58e-02 4.01e+03 1.31e+01 bond pdb=" C PRO A 287 " pdb=" O PRO A 287 " ideal model delta sigma weight residual 1.232 1.190 0.042 1.20e-02 6.94e+03 1.25e+01 ... (remaining 37226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 50139 3.22 - 6.45: 245 6.45 - 9.67: 13 9.67 - 12.89: 1 12.89 - 16.11: 1 Bond angle restraints: 50399 Sorted by residual: angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 123.76 16.11 1.00e+00 1.00e+00 2.60e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 124.91 11.92 1.00e+00 1.00e+00 1.42e+02 angle pdb=" C VAL a 141 " pdb=" N VAL a 142 " pdb=" CA VAL a 142 " ideal model delta sigma weight residual 122.59 115.34 7.25 7.20e-01 1.93e+00 1.01e+02 angle pdb=" N VAL E 406 " pdb=" CA VAL E 406 " pdb=" C VAL E 406 " ideal model delta sigma weight residual 113.20 105.41 7.79 9.60e-01 1.09e+00 6.59e+01 angle pdb=" N TYR A 240 " pdb=" CA TYR A 240 " pdb=" C TYR A 240 " ideal model delta sigma weight residual 113.55 104.05 9.50 1.26e+00 6.30e-01 5.68e+01 ... (remaining 50394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.61: 21729 23.61 - 47.23: 750 47.23 - 70.84: 125 70.84 - 94.46: 25 94.46 - 118.07: 5 Dihedral angle restraints: 22634 sinusoidal: 8960 harmonic: 13674 Sorted by residual: dihedral pdb=" O1B ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PB ADP F 500 " pdb=" PA ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 -178.07 118.07 1 2.00e+01 2.50e-03 3.53e+01 dihedral pdb=" C5' ADP F 500 " pdb=" O5' ADP F 500 " pdb=" PA ADP F 500 " pdb=" O2A ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 50.06 -110.05 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 -165.07 105.07 1 2.00e+01 2.50e-03 3.02e+01 ... (remaining 22631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 5501 0.091 - 0.182: 349 0.182 - 0.273: 20 0.273 - 0.364: 3 0.364 - 0.455: 2 Chirality restraints: 5875 Sorted by residual: chirality pdb=" CA ASP A 262 " pdb=" N ASP A 262 " pdb=" C ASP A 262 " pdb=" CB ASP A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA VAL A 146 " pdb=" N VAL A 146 " pdb=" C VAL A 146 " pdb=" CB VAL A 146 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA GLN A 266 " pdb=" N GLN A 266 " pdb=" C GLN A 266 " pdb=" CB GLN A 266 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 5872 not shown) Planarity restraints: 6501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 236 " 0.049 2.00e-02 2.50e+03 2.76e-02 1.52e+01 pdb=" CG TYR A 236 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR A 236 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 236 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 236 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 236 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 236 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 236 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 266 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.09e+00 pdb=" C GLN A 266 " -0.046 2.00e-02 2.50e+03 pdb=" O GLN A 266 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA A 267 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 234 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" C LEU A 234 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU A 234 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN A 235 " 0.014 2.00e-02 2.50e+03 ... (remaining 6498 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 39 2.31 - 2.96: 17443 2.96 - 3.61: 55050 3.61 - 4.25: 83991 4.25 - 4.90: 143648 Nonbonded interactions: 300171 Sorted by model distance: nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 1.666 2.170 nonbonded pdb=" N THR E 156 " pdb="MG MG E 502 " model vdw 1.786 2.250 nonbonded pdb=" CB THR E 156 " pdb="MG MG E 502 " model vdw 1.836 2.600 nonbonded pdb=" O2A ADP E 501 " pdb="MG MG E 502 " model vdw 1.884 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.918 2.170 ... (remaining 300166 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 410 through 601)) selection = (chain 'B' and (resid 4 through 408 or resid 410 through 511 or resid 600 throug \ h 601)) selection = (chain 'C' and (resid 4 through 408 or resid 410 through 601)) } ncs_group { reference = (chain 'D' and resid 2 through 459) selection = (chain 'E' and resid 2 through 459) selection = (chain 'F' and resid 2 through 459) } 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' and (resid 1 through 80 or resid 83 through 156)) selection = (chain 'Y' and (resid 1 through 80 or resid 83 through 156)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 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: 0.040 Extract box with map and model: 0.490 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 35.340 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 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 : 0.004 0.065 37231 Z= 0.216 Angle : 0.637 16.114 50399 Z= 0.394 Chirality : 0.046 0.455 5875 Planarity : 0.004 0.048 6501 Dihedral : 12.596 118.071 13888 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.53 % Favored : 98.43 % Rotamer: Outliers : 1.94 % Allowed : 5.12 % Favored : 92.93 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.47 % 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: 1.03 (0.12), residues: 4770 helix: 1.28 (0.10), residues: 2516 sheet: 0.57 (0.21), residues: 548 loop : -0.03 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 93 TYR 0.056 0.001 TYR A 236 PHE 0.016 0.001 PHE a 48 TRP 0.009 0.001 TRP G 105 HIS 0.006 0.001 HIS a 185 Details of bonding type rmsd covalent geometry : bond 0.00392 (37231) covalent geometry : angle 0.63721 (50399) hydrogen bonds : bond 0.15332 ( 2297) hydrogen bonds : angle 6.19242 ( 6765) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 617 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4397 (tpt) cc_final: 0.1863 (mtm) REVERT: B 394 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8272 (tmt170) REVERT: C 236 TYR cc_start: 0.9384 (OUTLIER) cc_final: 0.8855 (t80) REVERT: D 226 MET cc_start: 0.8546 (mtt) cc_final: 0.8254 (mtt) REVERT: D 340 THR cc_start: 0.8568 (m) cc_final: 0.8287 (p) REVERT: D 445 MET cc_start: 0.8669 (mmt) cc_final: 0.8426 (mpp) REVERT: E 265 VAL cc_start: 0.9497 (OUTLIER) cc_final: 0.9258 (t) REVERT: F 373 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8874 (mt) REVERT: G 60 LEU cc_start: 0.6306 (tt) cc_final: 0.5303 (mt) REVERT: H 50 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8576 (mp) REVERT: H 54 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8274 (tptm) REVERT: I 11 MET cc_start: 0.7660 (tpp) cc_final: 0.6581 (mpp) REVERT: I 75 MET cc_start: 0.4979 (ttp) cc_final: 0.4774 (ttp) REVERT: J 10 TYR cc_start: 0.6983 (m-80) cc_final: 0.6722 (m-80) REVERT: L 6 MET cc_start: 0.5881 (ttp) cc_final: 0.5548 (ptt) REVERT: L 11 MET cc_start: 0.5056 (tpt) cc_final: 0.4604 (mtm) REVERT: L 16 MET cc_start: 0.7804 (ttm) cc_final: 0.7244 (mtp) REVERT: L 26 ILE cc_start: 0.7600 (mt) cc_final: 0.7306 (mm) REVERT: L 34 LYS cc_start: 0.7043 (mmtm) cc_final: 0.6619 (mmtt) REVERT: M 11 MET cc_start: 0.7848 (tpt) cc_final: 0.7580 (mtm) REVERT: M 68 VAL cc_start: 0.6994 (t) cc_final: 0.6743 (t) REVERT: M 76 PHE cc_start: 0.2853 (m-80) cc_final: 0.2596 (m-10) REVERT: N 16 MET cc_start: 0.6731 (mtp) cc_final: 0.5542 (mmm) REVERT: N 34 LYS cc_start: 0.7516 (mmtm) cc_final: 0.6708 (mmmt) REVERT: N 44 ASP cc_start: 0.7451 (m-30) cc_final: 0.6785 (p0) REVERT: P 11 MET cc_start: 0.6641 (tpp) cc_final: 0.6378 (mmm) REVERT: P 22 ILE cc_start: 0.8161 (mm) cc_final: 0.7891 (mm) REVERT: P 44 ASP cc_start: 0.8456 (m-30) cc_final: 0.8179 (p0) REVERT: P 49 LEU cc_start: 0.8899 (mt) cc_final: 0.8029 (tp) REVERT: P 54 PHE cc_start: 0.6580 (m-10) cc_final: 0.6279 (m-80) REVERT: Q 5 ASN cc_start: 0.2774 (t0) cc_final: 0.2324 (t0) REVERT: Q 37 GLU cc_start: 0.8584 (tp30) cc_final: 0.8384 (pt0) REVERT: Q 76 PHE cc_start: 0.5997 (m-10) cc_final: 0.5377 (t80) REVERT: R 22 ILE cc_start: 0.7844 (mm) cc_final: 0.7609 (mm) REVERT: S 11 MET cc_start: 0.6960 (tpp) cc_final: 0.6318 (mpp) REVERT: S 54 PHE cc_start: 0.6346 (m-80) cc_final: 0.6032 (t80) REVERT: S 73 TYR cc_start: 0.5716 (t80) cc_final: 0.4536 (m-10) REVERT: W 137 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.7837 (tmmm) REVERT: X 136 ILE cc_start: 0.6869 (OUTLIER) cc_final: 0.6648 (tt) REVERT: Y 44 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7775 (pp) REVERT: a 42 ASN cc_start: 0.6810 (OUTLIER) cc_final: 0.5942 (m110) REVERT: a 61 ARG cc_start: 0.6366 (tpt170) cc_final: 0.5363 (mmp-170) REVERT: a 66 LYS cc_start: 0.5292 (mtpt) cc_final: 0.4943 (ttpt) REVERT: a 91 LYS cc_start: 0.9092 (ttpp) cc_final: 0.8870 (ttpp) REVERT: a 118 MET cc_start: 0.7857 (mmp) cc_final: 0.7504 (mtp) REVERT: a 168 MET cc_start: 0.7826 (mmt) cc_final: 0.7101 (mtt) REVERT: a 215 MET cc_start: 0.7763 (mmt) cc_final: 0.6608 (tpt) REVERT: a 266 MET cc_start: 0.7903 (ttm) cc_final: 0.7697 (ptm) outliers start: 74 outliers final: 18 residues processed: 678 average time/residue: 0.2437 time to fit residues: 262.2597 Evaluate side-chains 378 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 351 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain a residue 42 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 30.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN B 333 GLN C 425 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 HIS F 361 GLN G 54 HIS G 131 ASN G 135 GLN G 142 ASN O 52 GLN S 52 GLN W 67 GLN W 73 GLN a 17 ASN a 245 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.079095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.052180 restraints weight = 145185.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.054369 restraints weight = 72030.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.054373 restraints weight = 35454.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.054432 restraints weight = 29238.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.054587 restraints weight = 30985.808| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 37231 Z= 0.267 Angle : 0.683 12.310 50399 Z= 0.357 Chirality : 0.046 0.224 5875 Planarity : 0.005 0.052 6501 Dihedral : 7.578 118.992 5371 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.93 % Favored : 98.05 % Rotamer: Outliers : 2.52 % Allowed : 9.99 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 4770 helix: 1.54 (0.10), residues: 2595 sheet: 0.50 (0.20), residues: 555 loop : -0.12 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG X 117 TYR 0.061 0.002 TYR A 236 PHE 0.023 0.002 PHE I 54 TRP 0.015 0.002 TRP a 235 HIS 0.008 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00603 (37231) covalent geometry : angle 0.68257 (50399) hydrogen bonds : bond 0.05540 ( 2297) hydrogen bonds : angle 4.96575 ( 6765) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 360 time to evaluate : 1.306 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: A 86 MET cc_start: 0.8638 (mtp) cc_final: 0.8303 (mtp) REVERT: B 504 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9320 (mm) REVERT: C 236 TYR cc_start: 0.9588 (OUTLIER) cc_final: 0.8944 (t80) REVERT: C 365 ARG cc_start: 0.7676 (mmp80) cc_final: 0.7438 (mmp80) REVERT: D 445 MET cc_start: 0.8838 (mmt) cc_final: 0.8525 (mpp) REVERT: E 56 MET cc_start: 0.8914 (mmp) cc_final: 0.8600 (mmt) REVERT: G 60 LEU cc_start: 0.6567 (tt) cc_final: 0.5651 (mt) REVERT: G 139 MET cc_start: 0.8057 (mtm) cc_final: 0.7852 (ttm) REVERT: H 24 GLN cc_start: 0.8773 (tp40) cc_final: 0.8510 (mm110) REVERT: H 31 GLU cc_start: 0.7253 (pm20) cc_final: 0.6932 (pm20) REVERT: I 57 MET cc_start: 0.6479 (tmm) cc_final: 0.6170 (tpp) REVERT: J 6 MET cc_start: 0.6763 (mtp) cc_final: 0.6013 (ppp) REVERT: L 11 MET cc_start: 0.4919 (tpt) cc_final: 0.4638 (mtm) REVERT: M 11 MET cc_start: 0.7865 (tpt) cc_final: 0.7630 (mtm) REVERT: M 17 MET cc_start: 0.6640 (tpt) cc_final: 0.6278 (tpt) REVERT: M 53 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.5701 (t80) REVERT: N 16 MET cc_start: 0.6834 (mtp) cc_final: 0.5805 (mmm) REVERT: O 11 MET cc_start: 0.2327 (tpp) cc_final: 0.0459 (ttt) REVERT: O 16 MET cc_start: 0.3554 (ttp) cc_final: 0.3323 (ptm) REVERT: O 28 ILE cc_start: 0.8126 (tt) cc_final: 0.7735 (pt) REVERT: O 53 PHE cc_start: 0.6904 (t80) cc_final: 0.6053 (t80) REVERT: O 74 VAL cc_start: 0.4214 (t) cc_final: 0.3817 (m) REVERT: P 22 ILE cc_start: 0.8268 (mm) cc_final: 0.7931 (mm) REVERT: P 35 PHE cc_start: 0.7785 (t80) cc_final: 0.7424 (t80) REVERT: P 49 LEU cc_start: 0.9098 (mt) cc_final: 0.8766 (mt) REVERT: Q 65 MET cc_start: 0.5041 (OUTLIER) cc_final: 0.4837 (ptm) REVERT: Q 76 PHE cc_start: 0.5813 (m-10) cc_final: 0.5065 (t80) REVERT: S 11 MET cc_start: 0.6795 (tpp) cc_final: 0.6411 (mpp) REVERT: S 35 PHE cc_start: 0.4773 (t80) cc_final: 0.4373 (t80) REVERT: S 73 TYR cc_start: 0.5832 (t80) cc_final: 0.4463 (m-10) REVERT: W 137 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7645 (tmmm) REVERT: W 157 MET cc_start: 0.7958 (mmm) cc_final: 0.7668 (mmm) REVERT: X 98 ARG cc_start: 0.9139 (ttp80) cc_final: 0.8682 (ttp80) REVERT: X 145 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7747 (p0) REVERT: Y 44 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7867 (pp) REVERT: a 61 ARG cc_start: 0.6354 (tpt170) cc_final: 0.5218 (mmp-170) REVERT: a 66 LYS cc_start: 0.5118 (mtpt) cc_final: 0.4780 (ttpt) REVERT: a 168 MET cc_start: 0.7656 (mmt) cc_final: 0.7155 (mtt) REVERT: a 215 MET cc_start: 0.7774 (mmt) cc_final: 0.6531 (tpt) REVERT: a 216 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8598 (t80) REVERT: a 266 MET cc_start: 0.8028 (ttm) cc_final: 0.7686 (ptm) outliers start: 96 outliers final: 56 residues processed: 434 average time/residue: 0.2221 time to fit residues: 158.1112 Evaluate side-chains 391 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 327 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain M residue 53 PHE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain Q residue 65 MET Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain X residue 30 MET Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 216 TYR Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 184 optimal weight: 0.9980 chunk 356 optimal weight: 8.9990 chunk 436 optimal weight: 7.9990 chunk 373 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 350 optimal weight: 8.9990 chunk 389 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 386 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN C 484 GLN F 243 ASN G 131 ASN G 135 GLN H 75 ASN L 42 GLN Q 5 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.079661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.052936 restraints weight = 144439.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.054630 restraints weight = 72623.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.054877 restraints weight = 37657.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.055080 restraints weight = 39034.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.055059 restraints weight = 33754.234| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 37231 Z= 0.163 Angle : 0.580 8.513 50399 Z= 0.303 Chirality : 0.042 0.198 5875 Planarity : 0.004 0.055 6501 Dihedral : 7.139 121.141 5359 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.66 % Favored : 98.32 % Rotamer: Outliers : 2.37 % Allowed : 10.49 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.45 (0.12), residues: 4770 helix: 1.77 (0.10), residues: 2597 sheet: 0.49 (0.20), residues: 544 loop : -0.11 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 83 TYR 0.038 0.001 TYR A 236 PHE 0.027 0.001 PHE P 54 TRP 0.017 0.001 TRP a 235 HIS 0.005 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00357 (37231) covalent geometry : angle 0.57981 (50399) hydrogen bonds : bond 0.04916 ( 2297) hydrogen bonds : angle 4.63712 ( 6765) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 352 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8696 (mtp) cc_final: 0.8399 (mtp) REVERT: B 504 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9317 (mm) REVERT: C 236 TYR cc_start: 0.9573 (OUTLIER) cc_final: 0.8948 (t80) REVERT: D 445 MET cc_start: 0.8854 (mmt) cc_final: 0.8500 (mpp) REVERT: E 136 MET cc_start: 0.8828 (mmm) cc_final: 0.8626 (mmm) REVERT: G 23 MET cc_start: 0.7760 (mtt) cc_final: 0.7555 (mtt) REVERT: G 60 LEU cc_start: 0.6545 (tt) cc_final: 0.5743 (mt) REVERT: H 24 GLN cc_start: 0.8747 (tp40) cc_final: 0.8484 (mm110) REVERT: H 49 MET cc_start: 0.7554 (mmt) cc_final: 0.7351 (mmm) REVERT: H 78 VAL cc_start: 0.8745 (t) cc_final: 0.8514 (m) REVERT: H 96 GLU cc_start: 0.8517 (mp0) cc_final: 0.8224 (pp20) REVERT: I 11 MET cc_start: 0.7561 (tpt) cc_final: 0.6485 (mmm) REVERT: L 11 MET cc_start: 0.4688 (tpt) cc_final: 0.4346 (mtm) REVERT: M 11 MET cc_start: 0.7899 (tpt) cc_final: 0.7595 (mtp) REVERT: M 17 MET cc_start: 0.6485 (tpt) cc_final: 0.6043 (tpt) REVERT: N 16 MET cc_start: 0.6862 (mtp) cc_final: 0.6119 (mmm) REVERT: N 54 PHE cc_start: 0.7408 (m-80) cc_final: 0.7127 (m-80) REVERT: O 11 MET cc_start: 0.2443 (tpp) cc_final: 0.0902 (ttt) REVERT: O 28 ILE cc_start: 0.8006 (tt) cc_final: 0.7610 (pt) REVERT: O 53 PHE cc_start: 0.6917 (t80) cc_final: 0.6131 (t80) REVERT: P 11 MET cc_start: 0.6252 (mmm) cc_final: 0.5520 (mmp) REVERT: P 35 PHE cc_start: 0.7782 (t80) cc_final: 0.7437 (t80) REVERT: P 49 LEU cc_start: 0.9032 (mt) cc_final: 0.8777 (mt) REVERT: P 54 PHE cc_start: 0.6596 (m-80) cc_final: 0.6210 (m-80) REVERT: P 65 MET cc_start: 0.8065 (mtp) cc_final: 0.7792 (mmp) REVERT: Q 65 MET cc_start: 0.5015 (ptm) cc_final: 0.4814 (ptm) REVERT: Q 75 MET cc_start: 0.7401 (mtm) cc_final: 0.7107 (mmm) REVERT: Q 76 PHE cc_start: 0.5837 (m-10) cc_final: 0.4869 (t80) REVERT: R 16 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.5130 (ttm) REVERT: R 17 MET cc_start: 0.7897 (tpp) cc_final: 0.7670 (tpp) REVERT: S 11 MET cc_start: 0.6950 (tpp) cc_final: 0.6320 (mpp) REVERT: S 17 MET cc_start: 0.6714 (mmp) cc_final: 0.6280 (mmp) REVERT: S 73 TYR cc_start: 0.5317 (t80) cc_final: 0.4233 (m-10) REVERT: W 69 ASP cc_start: 0.7840 (m-30) cc_final: 0.7432 (t0) REVERT: W 137 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7627 (tmmm) REVERT: W 157 MET cc_start: 0.8046 (mmm) cc_final: 0.7745 (mmm) REVERT: X 1 MET cc_start: 0.1081 (mmp) cc_final: 0.0853 (ttp) REVERT: X 10 GLN cc_start: 0.4793 (tp40) cc_final: 0.3933 (mt0) REVERT: X 98 ARG cc_start: 0.9114 (ttp80) cc_final: 0.8689 (ttp80) REVERT: X 145 ASN cc_start: 0.8284 (p0) cc_final: 0.7462 (p0) REVERT: Y 44 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7866 (pp) REVERT: a 61 ARG cc_start: 0.6363 (tpt170) cc_final: 0.5244 (mmp-170) REVERT: a 66 LYS cc_start: 0.5069 (mtpt) cc_final: 0.4721 (ttpt) REVERT: a 266 MET cc_start: 0.7877 (ttm) cc_final: 0.7454 (ptm) outliers start: 90 outliers final: 46 residues processed: 420 average time/residue: 0.2167 time to fit residues: 150.7087 Evaluate side-chains 372 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 321 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 243 ASN Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain P residue 6 MET Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain X residue 30 MET Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 170 optimal weight: 10.0000 chunk 408 optimal weight: 30.0000 chunk 459 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 277 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 294 HIS H 5 HIS L 5 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.078953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.052094 restraints weight = 146152.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.053644 restraints weight = 64875.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.054557 restraints weight = 38516.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.055133 restraints weight = 27756.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.055465 restraints weight = 22946.473| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 37231 Z= 0.202 Angle : 0.600 8.778 50399 Z= 0.310 Chirality : 0.043 0.186 5875 Planarity : 0.004 0.069 6501 Dihedral : 7.013 122.803 5356 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 2.63 % Allowed : 11.51 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.45 (0.12), residues: 4770 helix: 1.82 (0.10), residues: 2591 sheet: 0.41 (0.20), residues: 560 loop : -0.17 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 50 TYR 0.024 0.001 TYR A 236 PHE 0.024 0.001 PHE S 35 TRP 0.017 0.001 TRP a 235 HIS 0.005 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00458 (37231) covalent geometry : angle 0.59953 (50399) hydrogen bonds : bond 0.04852 ( 2297) hydrogen bonds : angle 4.56772 ( 6765) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 340 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8683 (mtp) cc_final: 0.8409 (mtp) REVERT: C 48 MET cc_start: 0.7227 (mtt) cc_final: 0.7013 (mtt) REVERT: C 236 TYR cc_start: 0.9582 (OUTLIER) cc_final: 0.8940 (t80) REVERT: D 84 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9349 (mp) REVERT: D 445 MET cc_start: 0.8733 (mmt) cc_final: 0.8511 (mpp) REVERT: H 24 GLN cc_start: 0.8600 (tp40) cc_final: 0.8332 (mm110) REVERT: H 49 MET cc_start: 0.7615 (mmt) cc_final: 0.7342 (mmm) REVERT: H 96 GLU cc_start: 0.8546 (mp0) cc_final: 0.8153 (pp20) REVERT: I 11 MET cc_start: 0.7497 (tpt) cc_final: 0.6543 (mmm) REVERT: I 16 MET cc_start: 0.7488 (tpt) cc_final: 0.7284 (tpt) REVERT: I 50 ARG cc_start: 0.6105 (mtt180) cc_final: 0.5903 (mtt180) REVERT: J 17 MET cc_start: 0.6322 (ptp) cc_final: 0.5971 (ptp) REVERT: J 57 MET cc_start: 0.4715 (tpp) cc_final: 0.4464 (tpp) REVERT: L 11 MET cc_start: 0.4764 (tpt) cc_final: 0.4324 (mtm) REVERT: L 61 ASP cc_start: 0.7472 (m-30) cc_final: 0.6726 (p0) REVERT: L 65 MET cc_start: 0.6321 (mmp) cc_final: 0.6086 (mmp) REVERT: M 11 MET cc_start: 0.8226 (tpt) cc_final: 0.7596 (mtp) REVERT: M 17 MET cc_start: 0.6276 (tpt) cc_final: 0.5787 (tpt) REVERT: N 8 LEU cc_start: 0.4052 (OUTLIER) cc_final: 0.3785 (mp) REVERT: N 16 MET cc_start: 0.6835 (mtp) cc_final: 0.6134 (mmm) REVERT: O 11 MET cc_start: 0.2254 (tpp) cc_final: 0.0656 (ttt) REVERT: O 28 ILE cc_start: 0.7921 (tt) cc_final: 0.7525 (pt) REVERT: O 53 PHE cc_start: 0.6847 (t80) cc_final: 0.6101 (t80) REVERT: P 11 MET cc_start: 0.6300 (mmm) cc_final: 0.5720 (mmt) REVERT: P 35 PHE cc_start: 0.7887 (t80) cc_final: 0.7398 (t80) REVERT: P 49 LEU cc_start: 0.8920 (mt) cc_final: 0.8599 (mt) REVERT: P 54 PHE cc_start: 0.6575 (m-80) cc_final: 0.6185 (m-80) REVERT: Q 17 MET cc_start: 0.5659 (mmp) cc_final: 0.5235 (mtp) REVERT: Q 75 MET cc_start: 0.7328 (mtm) cc_final: 0.6980 (mmm) REVERT: Q 76 PHE cc_start: 0.5711 (m-10) cc_final: 0.4830 (t80) REVERT: R 11 MET cc_start: 0.6172 (tpp) cc_final: 0.4829 (mmt) REVERT: R 17 MET cc_start: 0.7707 (tpp) cc_final: 0.7477 (tpp) REVERT: S 11 MET cc_start: 0.6807 (tpp) cc_final: 0.6290 (mpp) REVERT: S 73 TYR cc_start: 0.5199 (t80) cc_final: 0.4151 (m-10) REVERT: W 137 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7891 (tmmm) REVERT: X 1 MET cc_start: 0.1061 (mmp) cc_final: 0.0490 (ttt) REVERT: X 98 ARG cc_start: 0.9276 (ttp80) cc_final: 0.8868 (ttp80) REVERT: X 145 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7125 (p0) REVERT: Y 44 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7842 (pp) REVERT: a 61 ARG cc_start: 0.6276 (tpt170) cc_final: 0.5232 (mmp-170) REVERT: a 66 LYS cc_start: 0.5094 (mtpt) cc_final: 0.4663 (ttpt) REVERT: a 215 MET cc_start: 0.7130 (mmp) cc_final: 0.6305 (tpt) REVERT: a 257 MET cc_start: 0.9125 (ppp) cc_final: 0.8700 (ppp) REVERT: a 266 MET cc_start: 0.7702 (ttm) cc_final: 0.7459 (ptm) outliers start: 100 outliers final: 64 residues processed: 415 average time/residue: 0.2219 time to fit residues: 153.6428 Evaluate side-chains 389 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 319 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 391 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 447 optimal weight: 30.0000 chunk 221 optimal weight: 6.9990 chunk 260 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 300 optimal weight: 6.9990 chunk 467 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.078871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.052111 restraints weight = 145485.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.053638 restraints weight = 64350.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.054571 restraints weight = 38247.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.055152 restraints weight = 27530.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055503 restraints weight = 22683.607| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 37231 Z= 0.182 Angle : 0.581 9.722 50399 Z= 0.300 Chirality : 0.042 0.198 5875 Planarity : 0.004 0.062 6501 Dihedral : 6.843 121.153 5356 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.97 % Favored : 98.01 % Rotamer: Outliers : 2.55 % Allowed : 12.56 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.49 (0.12), residues: 4770 helix: 1.84 (0.10), residues: 2627 sheet: 0.43 (0.21), residues: 558 loop : -0.16 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 83 TYR 0.026 0.001 TYR A 236 PHE 0.028 0.001 PHE N 54 TRP 0.022 0.001 TRP a 235 HIS 0.005 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00407 (37231) covalent geometry : angle 0.58084 (50399) hydrogen bonds : bond 0.04659 ( 2297) hydrogen bonds : angle 4.46664 ( 6765) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 338 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8672 (mtp) cc_final: 0.8402 (mtp) REVERT: C 236 TYR cc_start: 0.9561 (OUTLIER) cc_final: 0.8976 (t80) REVERT: D 84 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9360 (mp) REVERT: D 340 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8391 (p) REVERT: G 105 TRP cc_start: 0.8248 (m100) cc_final: 0.7742 (m100) REVERT: H 24 GLN cc_start: 0.8603 (tp40) cc_final: 0.8325 (mm110) REVERT: H 49 MET cc_start: 0.7558 (mmt) cc_final: 0.7260 (mmm) REVERT: H 70 GLU cc_start: 0.8209 (pm20) cc_final: 0.7802 (pp20) REVERT: I 11 MET cc_start: 0.7784 (tpt) cc_final: 0.6821 (mmm) REVERT: I 16 MET cc_start: 0.7402 (tpt) cc_final: 0.6670 (tpt) REVERT: J 57 MET cc_start: 0.5019 (tpp) cc_final: 0.4814 (tpp) REVERT: L 11 MET cc_start: 0.4963 (tpt) cc_final: 0.4365 (mtm) REVERT: L 61 ASP cc_start: 0.7436 (m-30) cc_final: 0.6686 (p0) REVERT: M 11 MET cc_start: 0.8270 (tpt) cc_final: 0.7686 (mtp) REVERT: M 17 MET cc_start: 0.6333 (tpt) cc_final: 0.5672 (tpt) REVERT: N 16 MET cc_start: 0.6749 (mtp) cc_final: 0.6189 (mmm) REVERT: O 11 MET cc_start: 0.2206 (tpp) cc_final: 0.0468 (ttt) REVERT: O 53 PHE cc_start: 0.6960 (t80) cc_final: 0.6227 (t80) REVERT: P 11 MET cc_start: 0.6429 (mmm) cc_final: 0.5842 (mmt) REVERT: P 35 PHE cc_start: 0.7875 (t80) cc_final: 0.7456 (t80) REVERT: P 49 LEU cc_start: 0.8918 (mt) cc_final: 0.8555 (mt) REVERT: P 54 PHE cc_start: 0.6639 (m-80) cc_final: 0.6206 (m-80) REVERT: P 65 MET cc_start: 0.7944 (mtp) cc_final: 0.7600 (mmt) REVERT: P 76 PHE cc_start: 0.6786 (m-80) cc_final: 0.6518 (m-10) REVERT: Q 17 MET cc_start: 0.6278 (mmp) cc_final: 0.5887 (ptm) REVERT: Q 76 PHE cc_start: 0.5389 (m-10) cc_final: 0.4540 (t80) REVERT: R 6 MET cc_start: 0.8277 (mmm) cc_final: 0.7716 (ptt) REVERT: R 17 MET cc_start: 0.7269 (tpp) cc_final: 0.6780 (tpp) REVERT: S 11 MET cc_start: 0.6852 (tpp) cc_final: 0.6418 (mpp) REVERT: W 69 ASP cc_start: 0.7637 (m-30) cc_final: 0.7387 (t0) REVERT: W 137 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7876 (tmmm) REVERT: X 1 MET cc_start: 0.1199 (mmp) cc_final: 0.0785 (ttt) REVERT: X 86 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8844 (tp) REVERT: X 98 ARG cc_start: 0.9260 (ttp80) cc_final: 0.8871 (ttp80) REVERT: X 145 ASN cc_start: 0.7872 (p0) cc_final: 0.7089 (p0) REVERT: Y 44 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7880 (pp) REVERT: Y 49 ARG cc_start: 0.7090 (tmm160) cc_final: 0.6835 (ptt180) REVERT: Y 129 VAL cc_start: 0.9287 (t) cc_final: 0.9087 (m) REVERT: a 66 LYS cc_start: 0.5215 (mtpt) cc_final: 0.4791 (ttpt) REVERT: a 257 MET cc_start: 0.9073 (ppp) cc_final: 0.8636 (ppp) REVERT: a 266 MET cc_start: 0.7694 (ttm) cc_final: 0.7485 (ptt) outliers start: 97 outliers final: 60 residues processed: 414 average time/residue: 0.2099 time to fit residues: 146.8548 Evaluate side-chains 375 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 309 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 25 VAL Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 216 TYR Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 139 optimal weight: 4.9990 chunk 320 optimal weight: 20.0000 chunk 422 optimal weight: 5.9990 chunk 297 optimal weight: 10.0000 chunk 423 optimal weight: 7.9990 chunk 300 optimal weight: 9.9990 chunk 198 optimal weight: 7.9990 chunk 251 optimal weight: 0.8980 chunk 459 optimal weight: 6.9990 chunk 284 optimal weight: 8.9990 chunk 420 optimal weight: 0.0370 overall best weight: 3.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 ASN B 27 ASN D 343 GLN G 59 ASN ** L 5 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 = 0.3669 r_free = 0.3669 target = 0.078194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.051609 restraints weight = 144818.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.053115 restraints weight = 65570.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.054036 restraints weight = 39271.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.054611 restraints weight = 28315.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054933 restraints weight = 23380.615| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 37231 Z= 0.207 Angle : 0.612 14.983 50399 Z= 0.312 Chirality : 0.043 0.215 5875 Planarity : 0.004 0.063 6501 Dihedral : 6.813 118.383 5356 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.16 % Favored : 97.82 % Rotamer: Outliers : 2.73 % Allowed : 13.43 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.43 (0.12), residues: 4770 helix: 1.80 (0.10), residues: 2624 sheet: 0.36 (0.20), residues: 574 loop : -0.20 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 85 TYR 0.029 0.001 TYR A 236 PHE 0.022 0.001 PHE a 56 TRP 0.028 0.001 TRP a 241 HIS 0.005 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00469 (37231) covalent geometry : angle 0.61177 (50399) hydrogen bonds : bond 0.04749 ( 2297) hydrogen bonds : angle 4.50381 ( 6765) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 318 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8651 (mtp) cc_final: 0.8381 (mtp) REVERT: A 439 MET cc_start: 0.7768 (ptm) cc_final: 0.7465 (ptm) REVERT: C 236 TYR cc_start: 0.9540 (OUTLIER) cc_final: 0.8944 (t80) REVERT: C 409 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.8255 (p90) REVERT: D 84 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9349 (mp) REVERT: D 340 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8401 (p) REVERT: E 379 MET cc_start: 0.7590 (tmm) cc_final: 0.7338 (tmm) REVERT: E 434 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8353 (mp0) REVERT: H 24 GLN cc_start: 0.8603 (tp40) cc_final: 0.8301 (mm110) REVERT: H 70 GLU cc_start: 0.8263 (pm20) cc_final: 0.7676 (pm20) REVERT: I 11 MET cc_start: 0.7725 (tpt) cc_final: 0.6679 (mmm) REVERT: J 17 MET cc_start: 0.6738 (ptp) cc_final: 0.6449 (ptp) REVERT: J 57 MET cc_start: 0.5048 (tpp) cc_final: 0.4806 (tpp) REVERT: L 28 ILE cc_start: 0.7925 (mm) cc_final: 0.7667 (pt) REVERT: L 57 MET cc_start: 0.6159 (ppp) cc_final: 0.5449 (ptm) REVERT: L 61 ASP cc_start: 0.7550 (m-30) cc_final: 0.6980 (p0) REVERT: M 11 MET cc_start: 0.8163 (tpt) cc_final: 0.7567 (mtp) REVERT: N 16 MET cc_start: 0.6660 (mtp) cc_final: 0.6251 (tpp) REVERT: O 53 PHE cc_start: 0.7009 (t80) cc_final: 0.6329 (t80) REVERT: P 11 MET cc_start: 0.6170 (mmm) cc_final: 0.5943 (mmm) REVERT: P 35 PHE cc_start: 0.7920 (t80) cc_final: 0.7379 (t80) REVERT: P 49 LEU cc_start: 0.9128 (mt) cc_final: 0.8781 (mt) REVERT: P 54 PHE cc_start: 0.6705 (m-80) cc_final: 0.6168 (m-80) REVERT: P 65 MET cc_start: 0.8011 (mtp) cc_final: 0.7693 (mmt) REVERT: Q 17 MET cc_start: 0.6200 (mmp) cc_final: 0.5641 (mtp) REVERT: Q 76 PHE cc_start: 0.5518 (m-10) cc_final: 0.4655 (t80) REVERT: R 7 ASP cc_start: 0.5225 (OUTLIER) cc_final: 0.4884 (p0) REVERT: R 11 MET cc_start: 0.6638 (tpp) cc_final: 0.5505 (mmt) REVERT: R 17 MET cc_start: 0.7247 (tpp) cc_final: 0.6731 (tpp) REVERT: S 11 MET cc_start: 0.6708 (tpp) cc_final: 0.6261 (mpp) REVERT: W 69 ASP cc_start: 0.7610 (m-30) cc_final: 0.7343 (t0) REVERT: W 137 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7806 (tmmm) REVERT: X 1 MET cc_start: 0.1092 (mmp) cc_final: 0.0752 (ttt) REVERT: X 86 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8855 (tp) REVERT: X 98 ARG cc_start: 0.9272 (ttp80) cc_final: 0.8881 (ttp80) REVERT: X 145 ASN cc_start: 0.7932 (p0) cc_final: 0.7185 (p0) REVERT: Y 44 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7817 (pp) REVERT: a 66 LYS cc_start: 0.5242 (mtpt) cc_final: 0.4826 (ttpt) REVERT: a 210 ARG cc_start: 0.8578 (ptp-170) cc_final: 0.8171 (ptt180) REVERT: a 257 MET cc_start: 0.9066 (ppp) cc_final: 0.8697 (ppp) REVERT: a 266 MET cc_start: 0.7680 (ttm) cc_final: 0.7472 (ptt) outliers start: 104 outliers final: 72 residues processed: 398 average time/residue: 0.2076 time to fit residues: 140.1997 Evaluate side-chains 389 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 308 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain R residue 7 ASP Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain X residue 30 MET Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 216 TYR Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 358 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 377 optimal weight: 8.9990 chunk 184 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 314 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 367 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 386 optimal weight: 10.0000 chunk 468 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN E 43 GLN L 5 ASN X 10 GLN a 95 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.077400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.050978 restraints weight = 144499.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.052426 restraints weight = 65492.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.053322 restraints weight = 39500.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.053889 restraints weight = 28772.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.054241 restraints weight = 23698.702| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 37231 Z= 0.240 Angle : 0.634 11.566 50399 Z= 0.325 Chirality : 0.044 0.207 5875 Planarity : 0.004 0.064 6501 Dihedral : 6.870 115.166 5356 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.43 % Favored : 97.55 % Rotamer: Outliers : 3.26 % Allowed : 13.38 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.35 (0.12), residues: 4770 helix: 1.78 (0.10), residues: 2618 sheet: 0.30 (0.21), residues: 540 loop : -0.29 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 49 TYR 0.036 0.002 TYR A 236 PHE 0.022 0.002 PHE I 53 TRP 0.025 0.001 TRP a 235 HIS 0.006 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00548 (37231) covalent geometry : angle 0.63359 (50399) hydrogen bonds : bond 0.04866 ( 2297) hydrogen bonds : angle 4.54549 ( 6765) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 321 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.8635 (t80) REVERT: C 236 TYR cc_start: 0.9549 (OUTLIER) cc_final: 0.8903 (t80) REVERT: C 409 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8324 (p90) REVERT: D 84 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9355 (mp) REVERT: D 340 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8427 (p) REVERT: E 56 MET cc_start: 0.8997 (mmp) cc_final: 0.8727 (mmt) REVERT: E 379 MET cc_start: 0.7630 (tmm) cc_final: 0.7314 (tmm) REVERT: E 434 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: H 24 GLN cc_start: 0.8487 (tp40) cc_final: 0.8181 (mm110) REVERT: H 31 GLU cc_start: 0.7806 (pm20) cc_final: 0.7385 (pm20) REVERT: H 70 GLU cc_start: 0.8286 (pm20) cc_final: 0.7621 (pm20) REVERT: I 11 MET cc_start: 0.7917 (tpt) cc_final: 0.7180 (mmm) REVERT: J 57 MET cc_start: 0.4865 (tpp) cc_final: 0.4597 (tpp) REVERT: L 57 MET cc_start: 0.6180 (ppp) cc_final: 0.5545 (ptm) REVERT: L 61 ASP cc_start: 0.7603 (m-30) cc_final: 0.7024 (p0) REVERT: M 11 MET cc_start: 0.8020 (tpt) cc_final: 0.7456 (mtm) REVERT: N 16 MET cc_start: 0.6543 (mtp) cc_final: 0.6077 (tpp) REVERT: O 11 MET cc_start: 0.1711 (OUTLIER) cc_final: -0.0261 (ttt) REVERT: O 19 LEU cc_start: 0.8447 (tp) cc_final: 0.8020 (mt) REVERT: O 41 ARG cc_start: 0.6653 (mmm160) cc_final: 0.6195 (ttp80) REVERT: P 35 PHE cc_start: 0.7988 (t80) cc_final: 0.7432 (t80) REVERT: P 49 LEU cc_start: 0.8984 (mt) cc_final: 0.8733 (mt) REVERT: P 54 PHE cc_start: 0.6732 (m-80) cc_final: 0.6185 (m-80) REVERT: P 57 MET cc_start: 0.6195 (tmm) cc_final: 0.5929 (tpp) REVERT: P 65 MET cc_start: 0.7932 (mtp) cc_final: 0.7720 (mmt) REVERT: P 76 PHE cc_start: 0.7427 (m-10) cc_final: 0.7077 (m-10) REVERT: Q 17 MET cc_start: 0.6271 (mmp) cc_final: 0.5576 (mtp) REVERT: Q 76 PHE cc_start: 0.5263 (m-10) cc_final: 0.4548 (t80) REVERT: R 6 MET cc_start: 0.8233 (mmm) cc_final: 0.7787 (ptm) REVERT: R 16 MET cc_start: 0.6925 (tpt) cc_final: 0.5442 (ttm) REVERT: R 17 MET cc_start: 0.6999 (tpp) cc_final: 0.6284 (tpp) REVERT: S 11 MET cc_start: 0.6648 (tpp) cc_final: 0.6329 (mpp) REVERT: S 17 MET cc_start: 0.6751 (mmp) cc_final: 0.6204 (mmp) REVERT: W 69 ASP cc_start: 0.7657 (m-30) cc_final: 0.7414 (t0) REVERT: W 137 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7842 (tmmm) REVERT: X 10 GLN cc_start: 0.4408 (tp-100) cc_final: 0.3323 (mp10) REVERT: X 86 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8993 (tp) REVERT: X 98 ARG cc_start: 0.9302 (ttp80) cc_final: 0.8891 (ttp80) REVERT: X 145 ASN cc_start: 0.7798 (p0) cc_final: 0.7142 (p0) REVERT: Y 44 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7893 (pp) REVERT: a 210 ARG cc_start: 0.8562 (ptp-170) cc_final: 0.8161 (ptt180) REVERT: a 266 MET cc_start: 0.7713 (ttm) cc_final: 0.7454 (ptm) outliers start: 124 outliers final: 83 residues processed: 419 average time/residue: 0.2017 time to fit residues: 143.1301 Evaluate side-chains 398 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 305 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 371 LYS Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain X residue 30 MET Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 129 ILE Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 335 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 343 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 chunk 176 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 385 optimal weight: 7.9990 chunk 411 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 384 optimal weight: 9.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 382 GLN F 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.078049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.051735 restraints weight = 143713.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.053160 restraints weight = 65185.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.054062 restraints weight = 39294.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.054643 restraints weight = 28464.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.054969 restraints weight = 23478.148| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 37231 Z= 0.167 Angle : 0.595 11.728 50399 Z= 0.303 Chirality : 0.042 0.178 5875 Planarity : 0.004 0.102 6501 Dihedral : 6.664 110.951 5354 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.42 % Allowed : 14.66 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.43 (0.12), residues: 4770 helix: 1.84 (0.10), residues: 2628 sheet: 0.34 (0.21), residues: 561 loop : -0.26 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 49 TYR 0.032 0.001 TYR A 236 PHE 0.033 0.001 PHE R 54 TRP 0.025 0.001 TRP a 235 HIS 0.004 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00373 (37231) covalent geometry : angle 0.59517 (50399) hydrogen bonds : bond 0.04556 ( 2297) hydrogen bonds : angle 4.40892 ( 6765) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 323 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8661 (mtp) cc_final: 0.8401 (mtt) REVERT: C 236 TYR cc_start: 0.9515 (OUTLIER) cc_final: 0.8869 (t80) REVERT: C 409 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8270 (p90) REVERT: D 84 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9332 (mp) REVERT: D 340 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8403 (p) REVERT: E 379 MET cc_start: 0.7602 (tmm) cc_final: 0.7291 (tmm) REVERT: E 431 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7925 (ppp) REVERT: E 434 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8380 (mp0) REVERT: H 31 GLU cc_start: 0.7803 (pm20) cc_final: 0.7432 (pm20) REVERT: H 70 GLU cc_start: 0.8300 (pm20) cc_final: 0.7636 (pm20) REVERT: I 11 MET cc_start: 0.7750 (tpt) cc_final: 0.7110 (mmm) REVERT: I 16 MET cc_start: 0.7511 (tpt) cc_final: 0.6273 (tpt) REVERT: J 57 MET cc_start: 0.4971 (tpp) cc_final: 0.4712 (tpp) REVERT: L 16 MET cc_start: 0.8466 (ttm) cc_final: 0.8197 (ptp) REVERT: L 57 MET cc_start: 0.6104 (ppp) cc_final: 0.5511 (ptm) REVERT: L 61 ASP cc_start: 0.7657 (m-30) cc_final: 0.7047 (p0) REVERT: M 11 MET cc_start: 0.8024 (tpt) cc_final: 0.7396 (mtp) REVERT: M 76 PHE cc_start: 0.3501 (m-10) cc_final: 0.2108 (t80) REVERT: N 16 MET cc_start: 0.6711 (mtp) cc_final: 0.6359 (tpp) REVERT: O 11 MET cc_start: 0.2119 (OUTLIER) cc_final: 0.0321 (ttt) REVERT: O 19 LEU cc_start: 0.8350 (tp) cc_final: 0.7933 (mt) REVERT: P 35 PHE cc_start: 0.7881 (t80) cc_final: 0.7286 (t80) REVERT: P 41 ARG cc_start: 0.6625 (ttt90) cc_final: 0.6412 (ttp-110) REVERT: P 49 LEU cc_start: 0.9035 (mt) cc_final: 0.8771 (mt) REVERT: P 54 PHE cc_start: 0.6723 (m-80) cc_final: 0.6105 (m-80) REVERT: P 76 PHE cc_start: 0.7662 (m-10) cc_final: 0.7153 (m-10) REVERT: Q 17 MET cc_start: 0.5994 (mmp) cc_final: 0.5660 (ptp) REVERT: Q 76 PHE cc_start: 0.5330 (m-10) cc_final: 0.4494 (t80) REVERT: R 6 MET cc_start: 0.8317 (mmm) cc_final: 0.7943 (ptt) REVERT: R 16 MET cc_start: 0.7075 (tpt) cc_final: 0.6206 (ttm) REVERT: R 17 MET cc_start: 0.7057 (tpp) cc_final: 0.6408 (tpp) REVERT: R 35 PHE cc_start: 0.8152 (t80) cc_final: 0.7697 (t80) REVERT: S 17 MET cc_start: 0.6970 (mmp) cc_final: 0.5878 (tmm) REVERT: W 137 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8263 (tmmm) REVERT: X 98 ARG cc_start: 0.9273 (ttp80) cc_final: 0.8860 (ttp80) REVERT: X 136 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6680 (tt) REVERT: X 145 ASN cc_start: 0.7746 (p0) cc_final: 0.7137 (p0) REVERT: Y 44 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7962 (pp) REVERT: Y 46 SER cc_start: 0.5710 (t) cc_final: 0.4792 (p) REVERT: Y 49 ARG cc_start: 0.7370 (ptt180) cc_final: 0.6325 (ppt170) REVERT: a 46 MET cc_start: 0.0659 (mmm) cc_final: 0.0447 (mmm) REVERT: a 210 ARG cc_start: 0.8600 (ptp-170) cc_final: 0.8205 (ptt180) REVERT: a 257 MET cc_start: 0.8859 (ppp) cc_final: 0.8454 (ppp) REVERT: a 266 MET cc_start: 0.7795 (ttm) cc_final: 0.7537 (ptt) outliers start: 92 outliers final: 66 residues processed: 394 average time/residue: 0.2128 time to fit residues: 142.4837 Evaluate side-chains 383 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 307 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 216 TYR Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 267 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 278 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 284 optimal weight: 4.9990 chunk 233 optimal weight: 7.9990 chunk 328 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 19 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.077715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.051449 restraints weight = 144105.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.052919 restraints weight = 65003.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.053825 restraints weight = 39080.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.054389 restraints weight = 28448.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.054612 restraints weight = 23459.551| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 37231 Z= 0.189 Angle : 0.615 13.859 50399 Z= 0.312 Chirality : 0.043 0.232 5875 Planarity : 0.004 0.078 6501 Dihedral : 6.637 109.649 5352 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.55 % Allowed : 14.85 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.39 (0.12), residues: 4770 helix: 1.81 (0.10), residues: 2622 sheet: 0.29 (0.21), residues: 577 loop : -0.28 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 49 TYR 0.040 0.001 TYR A 236 PHE 0.027 0.002 PHE R 54 TRP 0.026 0.001 TRP a 235 HIS 0.005 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00429 (37231) covalent geometry : angle 0.61491 (50399) hydrogen bonds : bond 0.04582 ( 2297) hydrogen bonds : angle 4.43608 ( 6765) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 316 time to evaluate : 1.379 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: C 236 TYR cc_start: 0.9570 (OUTLIER) cc_final: 0.8909 (t80) REVERT: C 409 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8269 (p90) REVERT: D 84 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9393 (mp) REVERT: D 340 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8338 (p) REVERT: E 431 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7954 (ppp) REVERT: E 434 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8384 (mp0) REVERT: H 31 GLU cc_start: 0.7893 (pm20) cc_final: 0.7511 (pm20) REVERT: H 70 GLU cc_start: 0.8342 (pm20) cc_final: 0.7628 (pm20) REVERT: H 93 ARG cc_start: 0.7411 (tmm-80) cc_final: 0.6095 (tpm170) REVERT: I 11 MET cc_start: 0.7769 (tpt) cc_final: 0.7254 (mmm) REVERT: I 16 MET cc_start: 0.7483 (tpt) cc_final: 0.6293 (tpt) REVERT: L 28 ILE cc_start: 0.7625 (pt) cc_final: 0.7380 (mm) REVERT: L 57 MET cc_start: 0.6195 (ppp) cc_final: 0.5674 (ptm) REVERT: L 61 ASP cc_start: 0.7569 (m-30) cc_final: 0.6834 (p0) REVERT: M 11 MET cc_start: 0.8038 (tpt) cc_final: 0.7339 (mtp) REVERT: M 76 PHE cc_start: 0.3732 (m-10) cc_final: 0.2393 (t80) REVERT: N 16 MET cc_start: 0.6734 (mtp) cc_final: 0.6297 (tpp) REVERT: O 11 MET cc_start: 0.2076 (OUTLIER) cc_final: -0.0239 (ttt) REVERT: P 6 MET cc_start: 0.2820 (mpp) cc_final: 0.2592 (mpp) REVERT: P 35 PHE cc_start: 0.7890 (t80) cc_final: 0.7254 (t80) REVERT: P 49 LEU cc_start: 0.9027 (mt) cc_final: 0.8767 (mt) REVERT: P 54 PHE cc_start: 0.6798 (m-80) cc_final: 0.6198 (m-80) REVERT: P 57 MET cc_start: 0.6033 (tmm) cc_final: 0.5820 (tpp) REVERT: P 76 PHE cc_start: 0.7749 (m-80) cc_final: 0.7346 (m-10) REVERT: Q 17 MET cc_start: 0.6257 (mmp) cc_final: 0.5863 (ptp) REVERT: Q 76 PHE cc_start: 0.5287 (m-10) cc_final: 0.4469 (t80) REVERT: R 11 MET cc_start: 0.6799 (tpp) cc_final: 0.5767 (mmt) REVERT: R 16 MET cc_start: 0.7174 (tpt) cc_final: 0.6396 (ttp) REVERT: R 17 MET cc_start: 0.6968 (tpp) cc_final: 0.6399 (tpp) REVERT: R 35 PHE cc_start: 0.8226 (t80) cc_final: 0.7703 (t80) REVERT: S 17 MET cc_start: 0.6933 (mmp) cc_final: 0.5804 (tmm) REVERT: W 69 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7031 (t0) REVERT: W 128 MET cc_start: 0.9197 (mmm) cc_final: 0.8991 (mmm) REVERT: W 137 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7953 (tmmm) REVERT: X 86 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8917 (tp) REVERT: X 98 ARG cc_start: 0.9265 (ttp80) cc_final: 0.8849 (ttp80) REVERT: X 136 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6645 (tt) REVERT: X 145 ASN cc_start: 0.7807 (p0) cc_final: 0.7289 (p0) REVERT: Y 44 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8020 (pp) REVERT: Y 46 SER cc_start: 0.5768 (t) cc_final: 0.4815 (p) REVERT: Y 49 ARG cc_start: 0.7266 (ptt180) cc_final: 0.6259 (ppt170) REVERT: a 210 ARG cc_start: 0.8488 (ptp-170) cc_final: 0.8223 (ptt180) REVERT: a 257 MET cc_start: 0.8875 (ppp) cc_final: 0.8425 (ppp) REVERT: a 266 MET cc_start: 0.7767 (ttm) cc_final: 0.7443 (ptm) outliers start: 97 outliers final: 76 residues processed: 391 average time/residue: 0.2079 time to fit residues: 138.2685 Evaluate side-chains 396 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 308 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain J residue 73 TYR Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain W residue 69 ASP Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain X residue 30 MET Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 216 TYR Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 392 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 373 optimal weight: 5.9990 chunk 454 optimal weight: 10.0000 chunk 267 optimal weight: 6.9990 chunk 310 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 277 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 348 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN F 19 GLN N 42 GLN W 73 GLN Y 51 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.078002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.051926 restraints weight = 144476.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.053336 restraints weight = 66999.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.054225 restraints weight = 40968.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.054793 restraints weight = 29981.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.055101 restraints weight = 24713.481| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 37231 Z= 0.163 Angle : 0.613 13.360 50399 Z= 0.310 Chirality : 0.042 0.244 5875 Planarity : 0.004 0.065 6501 Dihedral : 6.541 108.360 5352 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.39 % Allowed : 15.19 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.44 (0.12), residues: 4770 helix: 1.84 (0.10), residues: 2626 sheet: 0.43 (0.21), residues: 553 loop : -0.29 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 49 TYR 0.045 0.001 TYR A 236 PHE 0.023 0.001 PHE R 54 TRP 0.025 0.001 TRP a 235 HIS 0.009 0.001 HIS Y 51 Details of bonding type rmsd covalent geometry : bond 0.00367 (37231) covalent geometry : angle 0.61321 (50399) hydrogen bonds : bond 0.04442 ( 2297) hydrogen bonds : angle 4.39583 ( 6765) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 314 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 236 TYR cc_start: 0.9523 (OUTLIER) cc_final: 0.8857 (t80) REVERT: C 409 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8200 (p90) REVERT: D 84 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9341 (mp) REVERT: D 340 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8377 (p) REVERT: E 56 MET cc_start: 0.9181 (mmp) cc_final: 0.8724 (mmt) REVERT: E 379 MET cc_start: 0.7562 (tmm) cc_final: 0.7243 (tmm) REVERT: E 431 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7949 (ppp) REVERT: H 70 GLU cc_start: 0.8122 (pm20) cc_final: 0.7548 (pm20) REVERT: H 93 ARG cc_start: 0.7421 (tmm-80) cc_final: 0.6026 (tpm170) REVERT: I 11 MET cc_start: 0.7751 (tpt) cc_final: 0.7371 (mmm) REVERT: I 16 MET cc_start: 0.7487 (tpt) cc_final: 0.6239 (tpt) REVERT: L 28 ILE cc_start: 0.7613 (pt) cc_final: 0.7389 (mm) REVERT: L 57 MET cc_start: 0.6352 (ppp) cc_final: 0.5836 (ptm) REVERT: L 61 ASP cc_start: 0.7460 (m-30) cc_final: 0.6808 (p0) REVERT: M 11 MET cc_start: 0.7971 (tpt) cc_final: 0.7265 (mtp) REVERT: M 76 PHE cc_start: 0.3798 (m-10) cc_final: 0.2444 (t80) REVERT: N 16 MET cc_start: 0.6762 (mtp) cc_final: 0.6261 (mmm) REVERT: O 11 MET cc_start: 0.2479 (OUTLIER) cc_final: 0.0715 (ttt) REVERT: P 6 MET cc_start: 0.2981 (mpp) cc_final: 0.2728 (mpp) REVERT: P 35 PHE cc_start: 0.7880 (t80) cc_final: 0.7227 (t80) REVERT: P 49 LEU cc_start: 0.8998 (mt) cc_final: 0.8732 (mt) REVERT: P 54 PHE cc_start: 0.6918 (m-80) cc_final: 0.6301 (m-80) REVERT: P 76 PHE cc_start: 0.7763 (m-80) cc_final: 0.7239 (m-10) REVERT: Q 17 MET cc_start: 0.6406 (mmp) cc_final: 0.5936 (ptp) REVERT: Q 76 PHE cc_start: 0.5065 (m-10) cc_final: 0.4239 (t80) REVERT: R 6 MET cc_start: 0.8287 (mmm) cc_final: 0.7985 (ptt) REVERT: R 11 MET cc_start: 0.6454 (tpp) cc_final: 0.5439 (mmt) REVERT: R 16 MET cc_start: 0.7444 (tpt) cc_final: 0.6529 (ttp) REVERT: R 17 MET cc_start: 0.6895 (tpp) cc_final: 0.6310 (tpp) REVERT: R 35 PHE cc_start: 0.8196 (t80) cc_final: 0.7772 (t80) REVERT: S 17 MET cc_start: 0.6866 (mmp) cc_final: 0.5748 (tmm) REVERT: W 137 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.7997 (tmmm) REVERT: X 10 GLN cc_start: 0.4765 (tp-100) cc_final: 0.3746 (mp10) REVERT: X 86 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8917 (tp) REVERT: X 98 ARG cc_start: 0.9293 (ttp80) cc_final: 0.8892 (ttp80) REVERT: X 136 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6677 (tt) REVERT: Y 44 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7995 (pp) REVERT: Y 49 ARG cc_start: 0.7237 (ptt180) cc_final: 0.6905 (ptt-90) REVERT: a 168 MET cc_start: 0.7550 (mmt) cc_final: 0.6987 (mtt) REVERT: a 210 ARG cc_start: 0.8506 (ptp-170) cc_final: 0.8198 (ptt180) REVERT: a 257 MET cc_start: 0.8931 (ppp) cc_final: 0.8492 (ppp) REVERT: a 266 MET cc_start: 0.7762 (ttm) cc_final: 0.7466 (ptt) outliers start: 91 outliers final: 69 residues processed: 383 average time/residue: 0.2133 time to fit residues: 139.3703 Evaluate side-chains 382 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 303 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain N residue 6 MET Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain X residue 30 MET Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 216 TYR Chi-restraints excluded: chain a residue 237 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 239 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 466 optimal weight: 2.9990 chunk 416 optimal weight: 3.9990 chunk 374 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 320 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN D 191 HIS F 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.077251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.051408 restraints weight = 144140.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.053507 restraints weight = 70123.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.053605 restraints weight = 34428.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.053642 restraints weight = 27805.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.053804 restraints weight = 30982.630| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 37231 Z= 0.216 Angle : 0.645 13.113 50399 Z= 0.327 Chirality : 0.043 0.242 5875 Planarity : 0.004 0.099 6501 Dihedral : 6.611 105.992 5352 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.29 % Allowed : 15.40 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.33 (0.12), residues: 4770 helix: 1.77 (0.10), residues: 2620 sheet: 0.26 (0.21), residues: 569 loop : -0.33 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG S 50 TYR 0.048 0.001 TYR A 236 PHE 0.024 0.002 PHE R 53 TRP 0.025 0.001 TRP a 235 HIS 0.006 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00494 (37231) covalent geometry : angle 0.64521 (50399) hydrogen bonds : bond 0.04628 ( 2297) hydrogen bonds : angle 4.49215 ( 6765) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7805.76 seconds wall clock time: 134 minutes 50.08 seconds (8090.08 seconds total)