Starting phenix.real_space_refine on Sat Mar 7 02:17:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbu_27307/03_2026/8dbu_27307.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbu_27307/03_2026/8dbu_27307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dbu_27307/03_2026/8dbu_27307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbu_27307/03_2026/8dbu_27307.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dbu_27307/03_2026/8dbu_27307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbu_27307/03_2026/8dbu_27307.map" } resolution = 3.4 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 23452 2.51 5 N 6307 2.21 5 O 6958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 36917 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} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 489} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 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': 1, 'PTRANS': 8, 'TRANS': 274} Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1021 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} 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: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1190 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "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: 8.06, per 1000 atoms: 0.22 Number of scatterers: 36917 At special positions: 0 Unit cell: (181.272, 219.037, 135.954, 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 6958 8.00 N 6307 7.00 C 23452 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: 3.30 Conformation dependent library (CDL) restraints added in 1.4 seconds 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8806 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 23 sheets defined 61.5% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 removed outlier: 3.595A pdb=" N ALA A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.509A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 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 231 through 253 Proline residue: A 239 - end of helix removed outlier: 3.897A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.551A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (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 381 removed outlier: 3.970A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 381 " --> pdb=" O GLY A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 381' Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.570A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 408 removed outlier: 3.581A 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: 3.682A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A 478 " --> pdb=" O TYR A 474 " (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 2 through 19 removed outlier: 3.545A pdb=" N THR B 6 " --> pdb=" O GLN B 2 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 3.835A 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: 3.516A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.616A 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 237 through 251 removed outlier: 3.787A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 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: 4.165A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 408 removed outlier: 5.009A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG B 394 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR B 395 " --> pdb=" O GLY B 391 " (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 462 through 479 removed outlier: 4.477A pdb=" N SER B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 490 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 150 through 157 Processing helix chain 'C' and resid 174 through 186 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 237 through 253 removed outlier: 3.799A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (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 removed outlier: 3.643A pdb=" N HIS C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) 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: 3.698A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 404 removed outlier: 4.304A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.173A pdb=" N GLN C 408 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA C 410 " --> pdb=" O SER C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 432 removed outlier: 3.957A 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: 3.520A pdb=" N MET C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 509 removed outlier: 3.858A pdb=" N LYS C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 154 through 170 removed outlier: 3.833A pdb=" N ILE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) 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: 3.666A pdb=" N ARG D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 256 removed outlier: 3.837A pdb=" N THR D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 280 removed outlier: 3.581A pdb=" N LEU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 302 Processing helix chain 'D' and resid 305 through 313 removed outlier: 4.233A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 327 Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 350 through 378 removed outlier: 4.286A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.796A 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 removed outlier: 3.524A pdb=" N LEU D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 419 through 432 Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.779A 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: 3.690A 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 170 removed outlier: 3.883A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU E 169 " --> pdb=" O ASN E 165 " (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: 3.567A pdb=" N ARG E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 removed outlier: 3.680A pdb=" N THR E 248 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU E 257 " --> pdb=" O GLU E 253 " (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 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: 7.759A pdb=" N GLN E 351 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N GLU E 352 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS E 353 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) removed outlier: 3.912A 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: 3.623A 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 448 through 459 removed outlier: 3.800A pdb=" N VAL E 453 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 removed outlier: 4.448A pdb=" N VAL F 22 " --> pdb=" O GLN F 19 " (cutoff:3.500A) 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: 3.567A pdb=" N ARG F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (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 280 Processing helix chain 'F' and resid 305 through 313 removed outlier: 3.751A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 328 removed outlier: 3.607A 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 377 removed outlier: 4.059A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 382 Processing helix chain 'F' and resid 383 through 400 removed outlier: 3.540A pdb=" N LEU F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 406 No H-bonds generated for 'chain 'F' and resid 404 through 406' Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 419 through 432 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.822A pdb=" N GLU F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 57 removed outlier: 4.079A pdb=" N GLU G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA G 27 " --> pdb=" O MET G 23 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) Proline residue: G 43 - end of helix removed outlier: 3.752A pdb=" N GLY G 53 " --> pdb=" O ARG G 49 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS G 54 " --> pdb=" O LYS G 50 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU G 55 " --> pdb=" O VAL G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 108 removed outlier: 3.837A pdb=" N LYS G 97 " --> pdb=" O ASN G 93 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 129 removed outlier: 3.505A pdb=" N VAL G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 161 removed outlier: 4.462A pdb=" N VAL G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 283 Processing helix chain 'H' and resid 54 through 58 removed outlier: 3.778A pdb=" N HIS H 58 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 108 removed outlier: 3.650A pdb=" N SER H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 134 removed outlier: 3.846A pdb=" N ALA H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU H 132 " --> pdb=" O LEU H 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 42 removed outlier: 3.598A pdb=" N LEU I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 78 removed outlier: 4.254A pdb=" N LEU I 48 " --> pdb=" O ASP I 44 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'J' and resid 4 through 42 removed outlier: 4.031A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 3.582A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 77 removed outlier: 3.870A pdb=" N ILE J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA J 67 " --> pdb=" O ILE J 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 42 removed outlier: 4.092A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR L 10 " --> pdb=" O MET L 6 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET L 11 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS L 34 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 removed outlier: 3.738A pdb=" N THR L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 77 removed outlier: 3.571A pdb=" N ILE L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 42 removed outlier: 3.622A pdb=" N MET M 11 " --> pdb=" O ASP M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 61 removed outlier: 4.157A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 77 removed outlier: 3.501A pdb=" N MET M 65 " --> pdb=" O ASP M 61 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE M 66 " --> pdb=" O ALA M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 42 removed outlier: 4.916A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 77 removed outlier: 3.696A pdb=" N THR N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY N 58 " --> pdb=" O PHE N 54 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE N 63 " --> pdb=" O LEU N 59 " (cutoff:3.500A) Proline residue: N 64 - end of helix Processing helix chain 'O' and resid 5 through 42 removed outlier: 4.016A pdb=" N LEU O 9 " --> pdb=" O ASN O 5 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN O 42 " --> pdb=" O GLY O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 removed outlier: 3.796A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP O 61 " --> pdb=" O MET O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 77 Processing helix chain 'P' and resid 4 through 42 removed outlier: 3.923A pdb=" N LEU P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 77 removed outlier: 3.855A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.674A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 removed outlier: 3.504A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 77 removed outlier: 3.790A pdb=" N THR Q 51 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE Q 55 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.370A 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 4 through 42 removed outlier: 3.677A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA R 21 " --> pdb=" O MET R 17 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 77 removed outlier: 3.940A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'S' and resid 5 through 7 No H-bonds generated for 'chain 'S' and resid 5 through 7' Processing helix chain 'S' and resid 8 through 42 removed outlier: 3.647A pdb=" N MET S 16 " --> pdb=" O ALA S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.710A pdb=" N GLY S 58 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 78 removed outlier: 3.668A pdb=" N MET S 65 " --> pdb=" O ASP S 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 21 Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 23 through 39 removed outlier: 3.550A pdb=" N PHE W 33 " --> pdb=" O ASP W 29 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 48 Processing helix chain 'W' and resid 52 through 64 Processing helix chain 'W' and resid 71 through 82 Processing helix chain 'W' and resid 84 through 86 No H-bonds generated for 'chain 'W' and resid 84 through 86' Processing helix chain 'W' and resid 87 through 92 Processing helix chain 'W' and resid 93 through 103 Processing helix chain 'W' and resid 118 through 132 Processing helix chain 'W' and resid 162 through 171 Processing helix chain 'X' and resid 5 through 24 Processing helix chain 'X' and resid 25 through 47 removed outlier: 3.852A pdb=" N ALA X 47 " --> pdb=" O GLY X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 136 removed outlier: 3.781A pdb=" N LEU X 56 " --> pdb=" O LYS X 52 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 155 removed outlier: 4.139A pdb=" N ILE X 148 " --> pdb=" O ALA X 144 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU X 155 " --> pdb=" O LYS X 151 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 25 removed outlier: 3.739A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 49 removed outlier: 3.768A pdb=" N LEU Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 139 removed outlier: 3.960A pdb=" N ASP Y 53 " --> pdb=" O ARG Y 49 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN Y 73 " --> pdb=" O LYS Y 69 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS Y 114 " --> pdb=" O GLU Y 110 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU Y 119 " --> pdb=" O ARG Y 115 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU Y 120 " --> pdb=" O ALA Y 116 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS Y 134 " --> pdb=" O ALA Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 156 removed outlier: 3.520A pdb=" N ALA Y 154 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) 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: 3.927A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET a 93 " --> pdb=" O SER a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 118 Processing helix chain 'a' and resid 119 through 121 No H-bonds generated for 'chain 'a' and resid 119 through 121' Processing helix chain 'a' and resid 124 through 133 Processing helix chain 'a' and resid 142 through 145 Processing helix chain 'a' and resid 146 through 181 removed outlier: 3.781A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE a 174 " --> pdb=" O GLY a 170 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR a 175 " --> pdb=" O ILE a 171 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN a 181 " --> pdb=" O GLU a 177 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 187 No H-bonds generated for 'chain 'a' and resid 185 through 187' Processing helix chain 'a' and resid 188 through 229 removed outlier: 4.109A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.700A pdb=" N ALA a 217 " --> pdb=" O GLY a 213 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 269 removed outlier: 4.051A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 4.070A 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: 4.385A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG A 93 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER A 54 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR A 91 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP D 67 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLN D 32 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE D 50 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.493A 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: 3.607A pdb=" N ILE A 198 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 256 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LEU A 327 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE A 258 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE A 329 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR A 260 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N GLU A 331 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.341A pdb=" N ILE A 159 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 35 removed outlier: 6.515A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 43 current: chain 'B' and resid 59 through 67 removed outlier: 5.847A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 70 " --> pdb=" O GLU B 67 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 70 through 75 current: chain 'E' and resid 12 through 16 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 12 through 16 current: chain 'E' and resid 36 through 46 removed outlier: 6.640A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 50 through 55 current: chain 'W' and resid 135 through 138 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 135 through 138 current: chain 'W' and resid 157 through 160 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 109 removed outlier: 6.426A pdb=" N LYS B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE B 259 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE B 194 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASP B 261 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 196 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 331 removed outlier: 6.417A pdb=" N ILE B 167 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 66 removed outlier: 4.286A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ARG C 93 " --> pdb=" O MET C 52 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR C 91 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASP F 67 " --> pdb=" O GLN F 32 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN F 32 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA F 28 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLN F 45 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE F 50 " --> pdb=" O GLN F 45 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AB2, first strand: chain 'C' and resid 107 through 109 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 107 through 109 current: chain 'C' and resid 221 through 226 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 221 through 226 current: chain 'C' and resid 322 through 331 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 322 through 331 current: chain 'C' and resid 374 through 375 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.478A pdb=" N ILE C 159 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AB5, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.480A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL D 296 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU D 147 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 125 through 126 removed outlier: 4.745A pdb=" N PHE D 139 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.815A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.188A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLN E 208 " --> pdb=" O MET E 88 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL E 296 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU E 147 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLY E 146 " --> pdb=" O VAL E 319 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 125 through 126 removed outlier: 3.971A pdb=" N PHE E 139 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.658A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 87 through 88 removed outlier: 6.054A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLN F 208 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL F 237 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL F 293 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU F 239 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA F 295 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL F 241 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL F 145 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS F 144 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL F 319 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY F 146 " --> pdb=" O VAL F 319 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 134 through 136 removed outlier: 4.218A pdb=" N ALA G 134 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE G 175 " --> pdb=" O SER G 179 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER G 179 " --> pdb=" O ILE G 175 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 206 through 207 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 206 through 207 current: chain 'H' and resid 14 through 20 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 14 through 20 current: chain 'H' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 32 through 34 current: chain 'H' and resid 61 through 70 removed outlier: 6.943A pdb=" N ILE H 62 " --> pdb=" O ARG H 85 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ARG H 85 " --> pdb=" O ILE H 62 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU H 64 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA H 83 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY H 66 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 27 through 29 removed outlier: 3.566A pdb=" N SER a 27 " --> pdb=" O ASP a 22 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLN a 20 " --> pdb=" O VAL a 29 " (cutoff:3.500A) 2249 hydrogen bonds defined for protein. 6582 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.79 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6327 1.31 - 1.44: 8796 1.44 - 1.57: 21964 1.57 - 1.69: 27 1.69 - 1.82: 358 Bond restraints: 37472 Sorted by residual: bond pdb=" C PRO F 23 " pdb=" O PRO F 23 " ideal model delta sigma weight residual 1.234 1.187 0.046 1.14e-02 7.69e+03 1.63e+01 bond pdb=" CA SER B 375 " pdb=" CB SER B 375 " ideal model delta sigma weight residual 1.532 1.474 0.058 1.58e-02 4.01e+03 1.34e+01 bond pdb=" CA SER B 373 " pdb=" CB SER B 373 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.48e-02 4.57e+03 1.29e+01 bond pdb=" C ILE Q 63 " pdb=" N PRO Q 64 " ideal model delta sigma weight residual 1.335 1.372 -0.037 1.19e-02 7.06e+03 9.88e+00 bond pdb=" N LEU O 45 " pdb=" CA LEU O 45 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.32e-02 5.74e+03 8.88e+00 ... (remaining 37467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 49415 2.26 - 4.52: 1138 4.52 - 6.78: 140 6.78 - 9.04: 21 9.04 - 11.30: 7 Bond angle restraints: 50721 Sorted by residual: angle pdb=" N THR A 148 " pdb=" CA THR A 148 " pdb=" C THR A 148 " ideal model delta sigma weight residual 109.96 101.16 8.80 1.68e+00 3.54e-01 2.75e+01 angle pdb=" N VAL E 198 " pdb=" CA VAL E 198 " pdb=" C VAL E 198 " ideal model delta sigma weight residual 113.20 108.20 5.00 9.60e-01 1.09e+00 2.71e+01 angle pdb=" C HIS A 479 " pdb=" N ALA A 480 " pdb=" CA ALA A 480 " ideal model delta sigma weight residual 120.58 126.21 -5.63 1.32e+00 5.74e-01 1.82e+01 angle pdb=" C VAL A 146 " pdb=" N GLN A 147 " pdb=" CA GLN A 147 " ideal model delta sigma weight residual 122.84 117.31 5.53 1.30e+00 5.92e-01 1.81e+01 angle pdb=" N ILE O 46 " pdb=" CA ILE O 46 " pdb=" CB ILE O 46 " ideal model delta sigma weight residual 110.50 112.94 -2.44 6.30e-01 2.52e+00 1.50e+01 ... (remaining 50716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 22316 35.49 - 70.98: 409 70.98 - 106.47: 54 106.47 - 141.96: 3 141.96 - 177.45: 2 Dihedral angle restraints: 22784 sinusoidal: 9019 harmonic: 13765 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 300.00 122.55 177.45 1 2.00e+01 2.50e-03 4.80e+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 300.00 125.32 174.69 1 2.00e+01 2.50e-03 4.79e+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 300.00 179.58 120.43 1 2.00e+01 2.50e-03 3.62e+01 ... (remaining 22781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 5503 0.099 - 0.197: 399 0.197 - 0.296: 7 0.296 - 0.394: 3 0.394 - 0.493: 2 Chirality restraints: 5914 Sorted by residual: chirality pdb=" CB ILE Q 63 " pdb=" CA ILE Q 63 " pdb=" CG1 ILE Q 63 " pdb=" CG2 ILE Q 63 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.07e+00 chirality pdb=" CA THR A 148 " pdb=" N THR A 148 " pdb=" C THR A 148 " pdb=" CB THR A 148 " both_signs ideal model delta sigma weight residual False 2.53 2.96 -0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA TYR F 26 " pdb=" N TYR F 26 " pdb=" C TYR F 26 " pdb=" CB TYR F 26 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 5911 not shown) Planarity restraints: 6540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG W 169 " -0.241 9.50e-02 1.11e+02 1.09e-01 9.44e+00 pdb=" NE ARG W 169 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG W 169 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG W 169 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG W 169 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 59 " 0.214 9.50e-02 1.11e+02 9.72e-02 8.76e+00 pdb=" NE ARG A 59 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 59 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG A 59 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 59 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 296 " 0.015 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C ARG A 296 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG A 296 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU A 297 " 0.017 2.00e-02 2.50e+03 ... (remaining 6537 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 63 2.50 - 3.10: 27767 3.10 - 3.70: 55379 3.70 - 4.30: 83326 4.30 - 4.90: 136635 Nonbonded interactions: 303170 Sorted by model distance: nonbonded pdb="MG MG D 501 " pdb=" O1G ATP D 502 " model vdw 1.900 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.006 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 2.062 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 2.101 2.170 nonbonded pdb=" OG1 THR D 156 " pdb="MG MG D 501 " model vdw 2.115 2.170 ... (remaining 303165 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' selection = (chain 'B' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) selection = (chain 'C' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 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' selection = (chain 'Y' and (resid 1 through 47 or resid 50 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 33.400 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 0.072 37472 Z= 0.230 Angle : 0.833 11.300 50721 Z= 0.461 Chirality : 0.052 0.493 5914 Planarity : 0.009 0.109 6540 Dihedral : 14.469 177.445 13978 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.58 % Favored : 98.40 % Rotamer: Outliers : 0.76 % Allowed : 4.88 % Favored : 94.36 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.11), residues: 4799 helix: 0.28 (0.09), residues: 2614 sheet: 0.25 (0.21), residues: 528 loop : -0.42 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.004 ARG A 59 TYR 0.035 0.006 TYR G 205 PHE 0.042 0.003 PHE O 54 TRP 0.033 0.005 TRP G 203 HIS 0.009 0.002 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00428 (37472) covalent geometry : angle 0.83345 (50721) hydrogen bonds : bond 0.12999 ( 2249) hydrogen bonds : angle 6.26370 ( 6582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 517 time to evaluate : 1.476 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: symmetry clash REVERT: C 386 MET cc_start: 0.8727 (mmm) cc_final: 0.8355 (mmt) REVERT: D 445 MET cc_start: 0.8889 (mmt) cc_final: 0.8677 (mmm) REVERT: E 56 MET cc_start: 0.9133 (mmm) cc_final: 0.8868 (mmp) REVERT: E 242 ASP cc_start: 0.7159 (t70) cc_final: 0.6163 (t70) REVERT: E 397 GLN cc_start: 0.8584 (tt0) cc_final: 0.8069 (tm-30) REVERT: F 136 MET cc_start: 0.8363 (mmm) cc_final: 0.8030 (mmm) REVERT: G 48 MET cc_start: 0.8608 (mmt) cc_final: 0.8213 (mmm) REVERT: H 53 VAL cc_start: 0.8848 (p) cc_final: 0.8578 (p) REVERT: H 63 TYR cc_start: 0.6661 (t80) cc_final: 0.6289 (t80) REVERT: H 127 GLN cc_start: 0.8194 (mt0) cc_final: 0.7871 (tt0) REVERT: J 11 MET cc_start: 0.5319 (tpp) cc_final: 0.5093 (tmm) REVERT: J 65 MET cc_start: 0.3343 (OUTLIER) cc_final: 0.3131 (mmp) REVERT: L 6 MET cc_start: 0.6287 (ttp) cc_final: 0.5968 (mtm) REVERT: L 17 MET cc_start: 0.7017 (mtm) cc_final: 0.6698 (tpp) REVERT: L 57 MET cc_start: 0.0866 (tmm) cc_final: 0.0394 (tpp) REVERT: M 17 MET cc_start: 0.6233 (mtm) cc_final: 0.3680 (tpt) REVERT: M 44 ASP cc_start: 0.6857 (m-30) cc_final: 0.5948 (t70) REVERT: M 75 MET cc_start: 0.3690 (ttp) cc_final: 0.3057 (tmm) REVERT: N 65 MET cc_start: 0.0914 (mtt) cc_final: 0.0644 (mtm) REVERT: O 37 GLU cc_start: 0.6882 (tt0) cc_final: 0.6577 (tp30) REVERT: O 65 MET cc_start: 0.4916 (mmt) cc_final: 0.4432 (mmm) REVERT: P 6 MET cc_start: 0.4010 (mmt) cc_final: 0.3586 (ptp) REVERT: P 11 MET cc_start: 0.5183 (tpp) cc_final: 0.4658 (mpp) REVERT: P 47 PRO cc_start: 0.5615 (Cg_endo) cc_final: 0.5050 (Cg_exo) REVERT: Q 11 MET cc_start: 0.7515 (tpt) cc_final: 0.6697 (mmp) REVERT: Q 17 MET cc_start: 0.7185 (mtm) cc_final: 0.6320 (tpt) REVERT: S 4 LEU cc_start: 0.3890 (tp) cc_final: 0.3626 (pt) REVERT: S 31 LEU cc_start: 0.6715 (tp) cc_final: 0.6093 (pp) REVERT: X 74 VAL cc_start: 0.8539 (m) cc_final: 0.8312 (m) REVERT: X 136 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6651 (mm) REVERT: X 150 ASP cc_start: 0.8174 (t0) cc_final: 0.7763 (m-30) REVERT: Y 24 TYR cc_start: 0.2664 (m-80) cc_final: 0.1869 (t80) REVERT: Y 26 TRP cc_start: 0.4381 (t60) cc_final: 0.3085 (m100) REVERT: Y 37 GLN cc_start: 0.5105 (mt0) cc_final: 0.4798 (tp40) REVERT: Y 73 GLN cc_start: 0.7455 (tp40) cc_final: 0.6664 (pt0) REVERT: Y 113 ARG cc_start: 0.7593 (ttt180) cc_final: 0.7317 (ttt180) REVERT: Y 115 ARG cc_start: 0.8810 (ttp80) cc_final: 0.8590 (tpt90) REVERT: a 65 LYS cc_start: 0.2966 (tttt) cc_final: 0.2478 (pttt) REVERT: a 168 MET cc_start: 0.6152 (mmt) cc_final: 0.5500 (tpp) outliers start: 29 outliers final: 5 residues processed: 535 average time/residue: 0.2666 time to fit residues: 221.8721 Evaluate side-chains 314 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 307 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain J residue 65 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 106 GLN Chi-restraints excluded: chain X residue 136 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.0000 chunk 470 optimal weight: 4.9990 overall best weight: 3.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN C 220 ASN C 358 ASN C 479 HIS E 365 GLN G 57 HIS ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN O 42 GLN P 3 ASN R 52 GLN S 52 GLN Y 73 GLN Y 123 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.083382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052973 restraints weight = 150977.071| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.20 r_work: 0.2853 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37472 Z= 0.198 Angle : 0.651 8.147 50721 Z= 0.343 Chirality : 0.045 0.308 5914 Planarity : 0.005 0.083 6540 Dihedral : 8.339 165.961 5373 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.46 % Favored : 98.52 % Rotamer: Outliers : 1.20 % Allowed : 8.72 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.12), residues: 4799 helix: 0.85 (0.10), residues: 2697 sheet: 0.48 (0.21), residues: 548 loop : -0.22 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 85 TYR 0.018 0.002 TYR P 10 PHE 0.020 0.002 PHE G 125 TRP 0.038 0.003 TRP G 203 HIS 0.006 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00439 (37472) covalent geometry : angle 0.65060 (50721) hydrogen bonds : bond 0.06182 ( 2249) hydrogen bonds : angle 5.05091 ( 6582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 324 time to evaluate : 1.404 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 456 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8105 (mm) REVERT: B 1 MET cc_start: 0.4130 (ttm) cc_final: 0.3471 (mmm) REVERT: B 10 GLU cc_start: 0.9333 (tm-30) cc_final: 0.8982 (mp0) REVERT: C 180 ILE cc_start: 0.9375 (pt) cc_final: 0.9139 (mm) REVERT: C 181 ASP cc_start: 0.8814 (m-30) cc_final: 0.8612 (m-30) REVERT: E 56 MET cc_start: 0.9484 (mmm) cc_final: 0.9092 (mmp) REVERT: E 397 GLN cc_start: 0.8997 (tt0) cc_final: 0.8308 (tm-30) REVERT: E 445 MET cc_start: 0.8964 (mmt) cc_final: 0.8447 (mmm) REVERT: F 0 MET cc_start: 0.7930 (pmm) cc_final: 0.7589 (pmm) REVERT: F 384 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8400 (tm-30) REVERT: G 63 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6880 (tmtt) REVERT: H 49 MET cc_start: 0.6243 (ppp) cc_final: 0.5929 (ppp) REVERT: H 98 LYS cc_start: 0.6182 (tppt) cc_final: 0.5870 (mmmt) REVERT: L 6 MET cc_start: 0.6522 (ttp) cc_final: 0.6256 (mtm) REVERT: L 65 MET cc_start: 0.0866 (mmm) cc_final: -0.0325 (ptm) REVERT: M 16 MET cc_start: 0.6824 (mtp) cc_final: 0.6427 (mmm) REVERT: M 17 MET cc_start: 0.5596 (mtm) cc_final: 0.3374 (tpt) REVERT: N 3 ASN cc_start: 0.7507 (t0) cc_final: 0.6077 (m-40) REVERT: N 11 MET cc_start: 0.4975 (tpt) cc_final: 0.4493 (ttp) REVERT: N 16 MET cc_start: 0.5571 (mmm) cc_final: 0.4375 (tpp) REVERT: P 6 MET cc_start: 0.3774 (mmt) cc_final: 0.3250 (ptp) REVERT: P 11 MET cc_start: 0.5186 (tpp) cc_final: 0.4684 (mpp) REVERT: Q 11 MET cc_start: 0.7188 (tpt) cc_final: 0.6730 (mmm) REVERT: Q 17 MET cc_start: 0.7297 (mtm) cc_final: 0.6273 (tpt) REVERT: Q 37 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8292 (tm-30) REVERT: Y 24 TYR cc_start: 0.2539 (m-80) cc_final: 0.2112 (t80) REVERT: Y 26 TRP cc_start: 0.3672 (t60) cc_final: 0.2783 (m100) REVERT: Y 73 GLN cc_start: 0.7143 (tp-100) cc_final: 0.6535 (pt0) REVERT: Y 89 GLU cc_start: 0.8669 (tp30) cc_final: 0.8409 (tm-30) REVERT: Y 115 ARG cc_start: 0.8868 (ttp80) cc_final: 0.8648 (tpt90) REVERT: a 65 LYS cc_start: 0.2395 (tttt) cc_final: 0.2100 (pttt) REVERT: a 168 MET cc_start: 0.6108 (mmt) cc_final: 0.5532 (tpp) outliers start: 46 outliers final: 21 residues processed: 357 average time/residue: 0.2419 time to fit residues: 140.1842 Evaluate side-chains 298 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 275 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 30 ILE Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain a residue 121 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 403 optimal weight: 5.9990 chunk 378 optimal weight: 6.9990 chunk 440 optimal weight: 8.9990 chunk 333 optimal weight: 30.0000 chunk 116 optimal weight: 3.9990 chunk 460 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 366 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 433 optimal weight: 20.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 243 ASN F 368 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 104 GLN X 106 GLN Y 64 GLN a 15 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.081615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.051648 restraints weight = 151404.199| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.14 r_work: 0.2807 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 37472 Z= 0.254 Angle : 0.656 10.304 50721 Z= 0.341 Chirality : 0.045 0.344 5914 Planarity : 0.005 0.081 6540 Dihedral : 7.867 149.117 5365 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.06 % Allowed : 9.27 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.12), residues: 4799 helix: 1.17 (0.10), residues: 2679 sheet: 0.41 (0.21), residues: 566 loop : -0.24 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 50 TYR 0.018 0.002 TYR E 247 PHE 0.017 0.002 PHE M 35 TRP 0.031 0.002 TRP G 203 HIS 0.008 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00576 (37472) covalent geometry : angle 0.65585 (50721) hydrogen bonds : bond 0.05786 ( 2249) hydrogen bonds : angle 4.87914 ( 6582) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 290 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.7287 (t80) REVERT: B 10 GLU cc_start: 0.9302 (tm-30) cc_final: 0.8973 (mp0) REVERT: C 181 ASP cc_start: 0.8893 (m-30) cc_final: 0.8647 (m-30) REVERT: C 187 ARG cc_start: 0.9431 (OUTLIER) cc_final: 0.9195 (ptp-170) REVERT: D 379 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7923 (mpp) REVERT: E 46 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8980 (pp) REVERT: E 397 GLN cc_start: 0.9048 (tt0) cc_final: 0.8379 (tm-30) REVERT: F 243 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.8090 (m-40) REVERT: G 48 MET cc_start: 0.8603 (tpt) cc_final: 0.8324 (mmm) REVERT: G 116 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8449 (mmp) REVERT: I 17 MET cc_start: 0.4140 (ppp) cc_final: 0.3917 (ppp) REVERT: L 6 MET cc_start: 0.6502 (ttp) cc_final: 0.6189 (mtm) REVERT: L 65 MET cc_start: 0.0994 (mmm) cc_final: 0.0503 (ptt) REVERT: L 75 MET cc_start: 0.3873 (tmm) cc_final: 0.3644 (tmm) REVERT: M 11 MET cc_start: 0.4041 (tpt) cc_final: 0.3756 (tpt) REVERT: N 3 ASN cc_start: 0.7500 (t0) cc_final: 0.5959 (m110) REVERT: O 75 MET cc_start: 0.3026 (tmm) cc_final: 0.2797 (tmm) REVERT: P 6 MET cc_start: 0.3801 (mmt) cc_final: 0.3557 (ptp) REVERT: P 11 MET cc_start: 0.4818 (tpp) cc_final: 0.4204 (mpp) REVERT: Q 17 MET cc_start: 0.7417 (mtm) cc_final: 0.6311 (tpt) REVERT: R 75 MET cc_start: 0.2728 (ptm) cc_final: 0.2432 (ptm) REVERT: S 17 MET cc_start: 0.0821 (mtp) cc_final: 0.0544 (mtp) REVERT: X 104 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8224 (pt0) REVERT: X 147 ASP cc_start: 0.7382 (m-30) cc_final: 0.6927 (t70) REVERT: Y 24 TYR cc_start: 0.2835 (m-80) cc_final: 0.2609 (t80) REVERT: Y 26 TRP cc_start: 0.3764 (t60) cc_final: 0.2789 (m100) REVERT: Y 73 GLN cc_start: 0.7013 (tp-100) cc_final: 0.6384 (pt0) REVERT: Y 82 ARG cc_start: 0.7158 (mmm160) cc_final: 0.6649 (mmm160) REVERT: Y 115 ARG cc_start: 0.8928 (ttp80) cc_final: 0.8657 (tpt90) REVERT: a 65 LYS cc_start: 0.2288 (tttt) cc_final: 0.2018 (pttt) REVERT: a 168 MET cc_start: 0.6492 (mmt) cc_final: 0.5542 (tpp) outliers start: 79 outliers final: 41 residues processed: 346 average time/residue: 0.2322 time to fit residues: 132.7260 Evaluate side-chains 314 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 266 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain F residue 243 ASN Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain Q residue 30 ILE Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 104 GLN Chi-restraints excluded: chain X residue 106 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 228 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 5 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 326 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 167 optimal weight: 0.8980 chunk 371 optimal weight: 9.9990 chunk 352 optimal weight: 30.0000 chunk 110 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 253 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 GLN A 488 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 GLN X 106 GLN Y 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.082295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.051531 restraints weight = 151007.353| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.98 r_work: 0.2849 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 37472 Z= 0.171 Angle : 0.589 11.567 50721 Z= 0.304 Chirality : 0.042 0.248 5914 Planarity : 0.004 0.059 6540 Dihedral : 7.458 145.903 5365 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.46 % Allowed : 10.91 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.12 (0.12), residues: 4799 helix: 1.42 (0.10), residues: 2677 sheet: 0.44 (0.21), residues: 570 loop : -0.22 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 129 TYR 0.015 0.001 TYR E 247 PHE 0.030 0.001 PHE F 189 TRP 0.014 0.001 TRP G 203 HIS 0.005 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00379 (37472) covalent geometry : angle 0.58942 (50721) hydrogen bonds : bond 0.05213 ( 2249) hydrogen bonds : angle 4.64911 ( 6582) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 280 time to evaluate : 1.482 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: B 1 MET cc_start: 0.4530 (mmt) cc_final: 0.4311 (mmt) REVERT: B 10 GLU cc_start: 0.9298 (tm-30) cc_final: 0.9005 (mp0) REVERT: C 187 ARG cc_start: 0.9375 (OUTLIER) cc_final: 0.9124 (ptp-170) REVERT: D 379 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7896 (mpp) REVERT: E 46 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8927 (pp) REVERT: E 397 GLN cc_start: 0.9043 (tt0) cc_final: 0.8407 (tm-30) REVERT: E 445 MET cc_start: 0.8916 (mmt) cc_final: 0.8481 (mmm) REVERT: G 48 MET cc_start: 0.8637 (tpt) cc_final: 0.8385 (mmm) REVERT: I 11 MET cc_start: -0.0458 (ttt) cc_final: -0.0847 (ttt) REVERT: L 6 MET cc_start: 0.6504 (ttp) cc_final: 0.6251 (mtm) REVERT: L 17 MET cc_start: 0.6386 (OUTLIER) cc_final: 0.5998 (tpp) REVERT: L 65 MET cc_start: 0.2007 (mmm) cc_final: 0.1577 (ptm) REVERT: N 3 ASN cc_start: 0.7537 (t0) cc_final: 0.6020 (m110) REVERT: N 16 MET cc_start: 0.4823 (mmm) cc_final: 0.4208 (tpp) REVERT: P 6 MET cc_start: 0.3943 (mmt) cc_final: 0.3692 (ptp) REVERT: P 11 MET cc_start: 0.4616 (tpp) cc_final: 0.4044 (mpp) REVERT: Q 17 MET cc_start: 0.7238 (mtm) cc_final: 0.6111 (tpt) REVERT: X 115 ARG cc_start: 0.8602 (ptp-110) cc_final: 0.8354 (ptt-90) REVERT: X 147 ASP cc_start: 0.7494 (m-30) cc_final: 0.7043 (t70) REVERT: Y 24 TYR cc_start: 0.2905 (m-80) cc_final: 0.2668 (t80) REVERT: Y 26 TRP cc_start: 0.3858 (t60) cc_final: 0.2839 (m100) REVERT: Y 73 GLN cc_start: 0.6993 (tp-100) cc_final: 0.6325 (pt0) REVERT: Y 115 ARG cc_start: 0.8947 (ttp80) cc_final: 0.8653 (tpt90) REVERT: a 65 LYS cc_start: 0.2442 (tttt) cc_final: 0.2154 (pttt) REVERT: a 168 MET cc_start: 0.6507 (mmt) cc_final: 0.5478 (tpp) outliers start: 56 outliers final: 34 residues processed: 319 average time/residue: 0.2286 time to fit residues: 122.0767 Evaluate side-chains 301 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 263 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain Y residue 83 ARG Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 228 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 321 optimal weight: 30.0000 chunk 65 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 395 optimal weight: 30.0000 chunk 210 optimal weight: 0.9980 chunk 351 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 298 optimal weight: 0.9980 chunk 374 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 479 HIS ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Y 96 GLN a 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.082679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.053085 restraints weight = 149779.632| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.16 r_work: 0.2845 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 37472 Z= 0.143 Angle : 0.563 8.122 50721 Z= 0.290 Chirality : 0.041 0.247 5914 Planarity : 0.004 0.050 6540 Dihedral : 7.089 142.189 5365 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.70 % Allowed : 11.30 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.34 (0.12), residues: 4799 helix: 1.62 (0.10), residues: 2670 sheet: 0.50 (0.21), residues: 568 loop : -0.14 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 121 TYR 0.013 0.001 TYR A 270 PHE 0.022 0.001 PHE F 189 TRP 0.013 0.001 TRP a 235 HIS 0.004 0.001 HIS H 104 Details of bonding type rmsd covalent geometry : bond 0.00312 (37472) covalent geometry : angle 0.56274 (50721) hydrogen bonds : bond 0.04818 ( 2249) hydrogen bonds : angle 4.48325 ( 6582) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 278 time to evaluate : 1.280 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: B 10 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8999 (mp0) REVERT: B 236 TYR cc_start: 0.9471 (OUTLIER) cc_final: 0.8551 (t80) REVERT: B 504 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8996 (mm) REVERT: C 187 ARG cc_start: 0.9368 (OUTLIER) cc_final: 0.9108 (ptp-170) REVERT: D 379 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8064 (mpp) REVERT: E 46 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8960 (pp) REVERT: E 397 GLN cc_start: 0.9058 (tt0) cc_final: 0.8382 (tm-30) REVERT: E 445 MET cc_start: 0.8942 (mmt) cc_final: 0.8494 (mmm) REVERT: F 445 MET cc_start: 0.8844 (mmm) cc_final: 0.8528 (mmm) REVERT: G 48 MET cc_start: 0.8706 (tpt) cc_final: 0.8453 (mmm) REVERT: I 11 MET cc_start: -0.0866 (ttt) cc_final: -0.1256 (ttt) REVERT: L 6 MET cc_start: 0.6280 (ttp) cc_final: 0.5898 (mtm) REVERT: L 17 MET cc_start: 0.6412 (OUTLIER) cc_final: 0.6011 (tpp) REVERT: L 65 MET cc_start: 0.2061 (mmm) cc_final: 0.1812 (ptm) REVERT: N 16 MET cc_start: 0.5260 (mmm) cc_final: 0.4165 (tpp) REVERT: P 6 MET cc_start: 0.3821 (mmt) cc_final: 0.3597 (ptp) REVERT: P 11 MET cc_start: 0.4594 (tpp) cc_final: 0.3975 (mpp) REVERT: Q 17 MET cc_start: 0.7153 (mtm) cc_final: 0.6025 (tpt) REVERT: X 115 ARG cc_start: 0.8582 (ptp-110) cc_final: 0.8360 (ptt-90) REVERT: X 147 ASP cc_start: 0.7384 (m-30) cc_final: 0.6924 (t70) REVERT: Y 26 TRP cc_start: 0.3706 (t60) cc_final: 0.2794 (m100) REVERT: Y 73 GLN cc_start: 0.7079 (tp-100) cc_final: 0.6526 (pt0) REVERT: Y 82 ARG cc_start: 0.6826 (mmm160) cc_final: 0.5856 (mmp-170) REVERT: Y 115 ARG cc_start: 0.8932 (ttp80) cc_final: 0.8638 (tpt90) REVERT: a 65 LYS cc_start: 0.2452 (tttt) cc_final: 0.2155 (pttt) REVERT: a 168 MET cc_start: 0.6487 (mmt) cc_final: 0.5414 (tpp) REVERT: a 215 MET cc_start: 0.3429 (mmp) cc_final: 0.2637 (mmp) REVERT: a 252 GLN cc_start: 0.7579 (mt0) cc_final: 0.7372 (mt0) outliers start: 65 outliers final: 37 residues processed: 325 average time/residue: 0.2288 time to fit residues: 123.1734 Evaluate side-chains 302 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 259 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 83 ARG Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 228 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 449 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 412 optimal weight: 5.9990 chunk 306 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 GLN a 15 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.081524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.050691 restraints weight = 153536.047| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.93 r_work: 0.2844 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 37472 Z= 0.218 Angle : 0.618 12.924 50721 Z= 0.316 Chirality : 0.043 0.268 5914 Planarity : 0.004 0.049 6540 Dihedral : 7.104 141.898 5365 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.14 % Allowed : 12.11 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.28 (0.12), residues: 4799 helix: 1.62 (0.10), residues: 2667 sheet: 0.38 (0.21), residues: 563 loop : -0.21 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 129 TYR 0.016 0.001 TYR E 247 PHE 0.014 0.001 PHE L 76 TRP 0.013 0.001 TRP a 235 HIS 0.006 0.001 HIS H 104 Details of bonding type rmsd covalent geometry : bond 0.00498 (37472) covalent geometry : angle 0.61833 (50721) hydrogen bonds : bond 0.05038 ( 2249) hydrogen bonds : angle 4.54669 ( 6582) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 272 time to evaluate : 1.477 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: B 504 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8954 (mm) REVERT: C 187 ARG cc_start: 0.9383 (OUTLIER) cc_final: 0.9100 (ptp-170) REVERT: D 379 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8057 (mpp) REVERT: D 445 MET cc_start: 0.9058 (mmm) cc_final: 0.8294 (mpp) REVERT: E 46 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8888 (pp) REVERT: E 397 GLN cc_start: 0.8975 (tt0) cc_final: 0.8308 (tm-30) REVERT: E 408 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7926 (tp30) REVERT: E 434 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: E 445 MET cc_start: 0.8941 (mmt) cc_final: 0.8501 (mmm) REVERT: G 48 MET cc_start: 0.8651 (tpt) cc_final: 0.8370 (mmm) REVERT: H 95 MET cc_start: 0.7100 (mmm) cc_final: 0.6807 (mmm) REVERT: I 11 MET cc_start: -0.0588 (ttt) cc_final: -0.0947 (ttt) REVERT: L 6 MET cc_start: 0.6300 (ttp) cc_final: 0.5929 (mtm) REVERT: L 17 MET cc_start: 0.6491 (ttt) cc_final: 0.6099 (tpp) REVERT: L 65 MET cc_start: 0.2329 (mmm) cc_final: 0.1822 (ptm) REVERT: N 16 MET cc_start: 0.5228 (mmm) cc_final: 0.4168 (tpp) REVERT: P 6 MET cc_start: 0.3947 (mmt) cc_final: 0.3416 (ptp) REVERT: P 11 MET cc_start: 0.4483 (tpp) cc_final: 0.3692 (mpp) REVERT: Q 17 MET cc_start: 0.7292 (mtm) cc_final: 0.6058 (tpt) REVERT: Q 34 LYS cc_start: 0.8341 (mmmm) cc_final: 0.8104 (mppt) REVERT: Q 54 PHE cc_start: 0.5985 (m-80) cc_final: 0.5700 (m-80) REVERT: Q 65 MET cc_start: 0.5684 (tpt) cc_final: 0.5426 (tpt) REVERT: Q 72 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5683 (mm) REVERT: S 31 LEU cc_start: 0.6593 (tp) cc_final: 0.5968 (mt) REVERT: W 109 ASP cc_start: 0.7948 (t0) cc_final: 0.7564 (t0) REVERT: W 123 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8398 (tptp) REVERT: X 106 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8662 (mp10) REVERT: X 115 ARG cc_start: 0.8558 (ptp-110) cc_final: 0.8290 (ptt-90) REVERT: X 147 ASP cc_start: 0.7280 (m-30) cc_final: 0.6827 (t70) REVERT: Y 26 TRP cc_start: 0.3774 (t60) cc_final: 0.2766 (m100) REVERT: Y 73 GLN cc_start: 0.7109 (tp-100) cc_final: 0.6495 (pt0) REVERT: Y 115 ARG cc_start: 0.8923 (ttp80) cc_final: 0.8629 (tpt90) REVERT: Y 121 ARG cc_start: 0.8993 (tmm-80) cc_final: 0.8640 (tmm160) REVERT: a 65 LYS cc_start: 0.2361 (tttt) cc_final: 0.2071 (pttt) REVERT: a 168 MET cc_start: 0.6528 (mmt) cc_final: 0.5493 (tpp) REVERT: a 215 MET cc_start: 0.3539 (mmp) cc_final: 0.2718 (mmp) outliers start: 82 outliers final: 61 residues processed: 336 average time/residue: 0.2221 time to fit residues: 124.5966 Evaluate side-chains 325 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 257 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 83 ARG Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 228 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 150 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 163 optimal weight: 0.3980 chunk 171 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 386 optimal weight: 5.9990 chunk 344 optimal weight: 20.0000 chunk 210 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 288 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.082048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.052535 restraints weight = 154388.798| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.14 r_work: 0.2851 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 37472 Z= 0.173 Angle : 0.587 13.845 50721 Z= 0.299 Chirality : 0.042 0.271 5914 Planarity : 0.004 0.049 6540 Dihedral : 6.931 140.755 5365 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.14 % Allowed : 12.84 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.38 (0.12), residues: 4799 helix: 1.72 (0.10), residues: 2671 sheet: 0.43 (0.22), residues: 562 loop : -0.22 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 51 TYR 0.015 0.001 TYR E 247 PHE 0.016 0.001 PHE L 76 TRP 0.013 0.001 TRP a 235 HIS 0.005 0.001 HIS H 104 Details of bonding type rmsd covalent geometry : bond 0.00391 (37472) covalent geometry : angle 0.58667 (50721) hydrogen bonds : bond 0.04740 ( 2249) hydrogen bonds : angle 4.44974 ( 6582) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 265 time to evaluate : 1.505 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: B 504 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8947 (mm) REVERT: C 187 ARG cc_start: 0.9338 (OUTLIER) cc_final: 0.9052 (ptp-170) REVERT: D 379 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8100 (mpp) REVERT: E 46 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8859 (pp) REVERT: E 397 GLN cc_start: 0.9012 (tt0) cc_final: 0.8310 (tm-30) REVERT: E 408 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8000 (tp30) REVERT: E 434 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: E 445 MET cc_start: 0.8906 (mmt) cc_final: 0.8490 (mmm) REVERT: F 379 MET cc_start: 0.8226 (tpp) cc_final: 0.8008 (tpt) REVERT: G 48 MET cc_start: 0.8711 (tpt) cc_final: 0.8457 (mmm) REVERT: H 95 MET cc_start: 0.7256 (mmm) cc_final: 0.6978 (mmm) REVERT: H 98 LYS cc_start: 0.6123 (tppt) cc_final: 0.5911 (tppt) REVERT: I 11 MET cc_start: -0.0515 (ttt) cc_final: -0.0801 (ttt) REVERT: L 17 MET cc_start: 0.6455 (ttt) cc_final: 0.6053 (tpp) REVERT: L 37 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7101 (mm-30) REVERT: L 65 MET cc_start: 0.2245 (mmm) cc_final: 0.1877 (ptm) REVERT: N 16 MET cc_start: 0.5273 (mmm) cc_final: 0.4303 (tpp) REVERT: N 75 MET cc_start: -0.0657 (OUTLIER) cc_final: -0.0963 (ttt) REVERT: P 6 MET cc_start: 0.4031 (mmt) cc_final: 0.3524 (ptp) REVERT: P 11 MET cc_start: 0.4603 (tpp) cc_final: 0.3897 (mpp) REVERT: Q 11 MET cc_start: 0.6811 (tpt) cc_final: 0.6459 (mmm) REVERT: Q 17 MET cc_start: 0.7191 (mtm) cc_final: 0.5861 (tpp) REVERT: Q 34 LYS cc_start: 0.8361 (mmmm) cc_final: 0.8133 (mptt) REVERT: Q 54 PHE cc_start: 0.5881 (m-80) cc_final: 0.5649 (m-80) REVERT: Q 65 MET cc_start: 0.5728 (tpt) cc_final: 0.5448 (tpt) REVERT: Q 72 LEU cc_start: 0.5962 (OUTLIER) cc_final: 0.5415 (mm) REVERT: S 31 LEU cc_start: 0.6566 (tp) cc_final: 0.5916 (mt) REVERT: X 104 GLN cc_start: 0.8569 (pp30) cc_final: 0.8317 (pt0) REVERT: X 106 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8612 (mp10) REVERT: X 115 ARG cc_start: 0.8532 (ptp-110) cc_final: 0.8278 (ptt-90) REVERT: X 147 ASP cc_start: 0.7304 (m-30) cc_final: 0.6884 (t70) REVERT: Y 26 TRP cc_start: 0.3842 (t60) cc_final: 0.2794 (m100) REVERT: Y 73 GLN cc_start: 0.7070 (tp-100) cc_final: 0.6493 (pt0) REVERT: Y 82 ARG cc_start: 0.7194 (mmm160) cc_final: 0.6275 (mmp-170) REVERT: Y 115 ARG cc_start: 0.8984 (ttp80) cc_final: 0.8669 (tpt90) REVERT: Y 121 ARG cc_start: 0.8977 (tmm-80) cc_final: 0.8597 (tmm160) REVERT: a 168 MET cc_start: 0.6537 (mmt) cc_final: 0.5464 (tpp) outliers start: 82 outliers final: 59 residues processed: 326 average time/residue: 0.2282 time to fit residues: 124.5598 Evaluate side-chains 327 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 260 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 83 ARG Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 228 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 244 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 445 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 286 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 377 optimal weight: 8.9990 chunk 153 optimal weight: 0.0050 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 96 GLN a 15 HIS ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.082795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.053374 restraints weight = 153389.237| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.15 r_work: 0.2877 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37472 Z= 0.125 Angle : 0.579 15.145 50721 Z= 0.291 Chirality : 0.041 0.253 5914 Planarity : 0.004 0.048 6540 Dihedral : 6.693 138.833 5365 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.62 % Allowed : 13.60 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.51 (0.12), residues: 4799 helix: 1.81 (0.10), residues: 2675 sheet: 0.52 (0.22), residues: 560 loop : -0.14 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 210 TYR 0.012 0.001 TYR E 247 PHE 0.014 0.001 PHE R 35 TRP 0.013 0.001 TRP a 235 HIS 0.005 0.001 HIS H 104 Details of bonding type rmsd covalent geometry : bond 0.00268 (37472) covalent geometry : angle 0.57856 (50721) hydrogen bonds : bond 0.04459 ( 2249) hydrogen bonds : angle 4.35542 ( 6582) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 272 time to evaluate : 1.492 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: B 504 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8978 (mm) REVERT: C 187 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.9052 (ptp-170) REVERT: E 46 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8829 (pp) REVERT: E 397 GLN cc_start: 0.8948 (tt0) cc_final: 0.8273 (tm-30) REVERT: E 408 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8011 (tp30) REVERT: E 445 MET cc_start: 0.8913 (mmt) cc_final: 0.8526 (mmm) REVERT: F 379 MET cc_start: 0.8195 (tpp) cc_final: 0.7988 (tpt) REVERT: F 386 ASP cc_start: 0.8493 (m-30) cc_final: 0.8181 (m-30) REVERT: G 48 MET cc_start: 0.8702 (tpt) cc_final: 0.8467 (mmm) REVERT: H 95 MET cc_start: 0.7255 (mmm) cc_final: 0.6991 (mmm) REVERT: H 98 LYS cc_start: 0.6040 (tppt) cc_final: 0.5815 (tppt) REVERT: I 11 MET cc_start: -0.0288 (ttt) cc_final: -0.0632 (ttt) REVERT: L 17 MET cc_start: 0.6390 (OUTLIER) cc_final: 0.6037 (tpp) REVERT: L 65 MET cc_start: 0.1984 (mmm) cc_final: 0.1500 (ptm) REVERT: N 16 MET cc_start: 0.5230 (mmm) cc_final: 0.4251 (tpp) REVERT: P 6 MET cc_start: 0.4068 (mmt) cc_final: 0.3575 (ptp) REVERT: P 11 MET cc_start: 0.4529 (tpp) cc_final: 0.3916 (mpp) REVERT: Q 17 MET cc_start: 0.7095 (mtm) cc_final: 0.5891 (tpt) REVERT: Q 34 LYS cc_start: 0.8363 (mmmm) cc_final: 0.8158 (mppt) REVERT: Q 65 MET cc_start: 0.5628 (tpt) cc_final: 0.5346 (tpt) REVERT: R 17 MET cc_start: 0.2790 (ttt) cc_final: 0.2318 (tmm) REVERT: S 31 LEU cc_start: 0.6543 (tp) cc_final: 0.5945 (mt) REVERT: S 41 ARG cc_start: 0.1949 (OUTLIER) cc_final: 0.1576 (ttp-110) REVERT: X 104 GLN cc_start: 0.8579 (pp30) cc_final: 0.8278 (pt0) REVERT: X 106 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8646 (mp10) REVERT: X 115 ARG cc_start: 0.8520 (ptp-110) cc_final: 0.8257 (ptt-90) REVERT: X 150 ASP cc_start: 0.7965 (t0) cc_final: 0.7384 (m-30) REVERT: Y 26 TRP cc_start: 0.3807 (t60) cc_final: 0.2706 (m100) REVERT: Y 73 GLN cc_start: 0.7070 (tp-100) cc_final: 0.6513 (pt0) REVERT: Y 82 ARG cc_start: 0.7078 (mmm160) cc_final: 0.6244 (mmp-170) REVERT: Y 115 ARG cc_start: 0.8996 (ttp80) cc_final: 0.8695 (tpt90) REVERT: Y 121 ARG cc_start: 0.9027 (tmm-80) cc_final: 0.8615 (tmm160) REVERT: a 168 MET cc_start: 0.6515 (mmt) cc_final: 0.5441 (tpp) outliers start: 62 outliers final: 47 residues processed: 315 average time/residue: 0.2269 time to fit residues: 119.2882 Evaluate side-chains 312 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain S residue 41 ARG Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 83 ARG Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 228 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 270 optimal weight: 5.9990 chunk 428 optimal weight: 20.0000 chunk 401 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 202 optimal weight: 0.0010 chunk 203 optimal weight: 3.9990 chunk 301 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 429 optimal weight: 9.9990 chunk 351 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.082346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.052990 restraints weight = 154770.310| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.19 r_work: 0.2867 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 37472 Z= 0.154 Angle : 0.597 13.610 50721 Z= 0.300 Chirality : 0.042 0.326 5914 Planarity : 0.004 0.050 6540 Dihedral : 6.626 139.879 5365 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.98 % Favored : 98.00 % Rotamer: Outliers : 1.91 % Allowed : 13.55 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.51 (0.12), residues: 4799 helix: 1.79 (0.10), residues: 2693 sheet: 0.50 (0.22), residues: 560 loop : -0.12 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 210 TYR 0.013 0.001 TYR E 247 PHE 0.039 0.001 PHE a 254 TRP 0.017 0.001 TRP a 111 HIS 0.005 0.001 HIS H 104 Details of bonding type rmsd covalent geometry : bond 0.00344 (37472) covalent geometry : angle 0.59694 (50721) hydrogen bonds : bond 0.04518 ( 2249) hydrogen bonds : angle 4.37948 ( 6582) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 262 time to evaluate : 1.432 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: B 504 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8997 (mm) REVERT: C 187 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.9056 (ptp-170) REVERT: E 46 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8842 (pp) REVERT: E 397 GLN cc_start: 0.8986 (tt0) cc_final: 0.8297 (tm-30) REVERT: E 408 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8045 (tp30) REVERT: E 434 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: E 445 MET cc_start: 0.8945 (mmt) cc_final: 0.8551 (mmm) REVERT: F 379 MET cc_start: 0.8130 (tpp) cc_final: 0.7915 (tpt) REVERT: G 48 MET cc_start: 0.8700 (tpt) cc_final: 0.8461 (mmm) REVERT: H 54 LYS cc_start: 0.8229 (mtmm) cc_final: 0.8006 (mptt) REVERT: H 95 MET cc_start: 0.7266 (mmm) cc_final: 0.7008 (mmm) REVERT: H 98 LYS cc_start: 0.6217 (tppt) cc_final: 0.5984 (tppt) REVERT: I 11 MET cc_start: -0.0480 (ttt) cc_final: -0.0837 (ttt) REVERT: L 17 MET cc_start: 0.6401 (OUTLIER) cc_final: 0.6137 (tpp) REVERT: L 65 MET cc_start: 0.2027 (mmm) cc_final: 0.1627 (ptm) REVERT: N 16 MET cc_start: 0.5203 (mmm) cc_final: 0.4358 (tpp) REVERT: P 6 MET cc_start: 0.4082 (mmt) cc_final: 0.3559 (ptp) REVERT: P 11 MET cc_start: 0.4518 (tpp) cc_final: 0.3890 (mpp) REVERT: Q 17 MET cc_start: 0.7152 (mtm) cc_final: 0.6056 (tpp) REVERT: Q 34 LYS cc_start: 0.8389 (mmmm) cc_final: 0.7835 (mptt) REVERT: Q 65 MET cc_start: 0.5893 (tpt) cc_final: 0.5575 (tpt) REVERT: R 17 MET cc_start: 0.2971 (ttt) cc_final: 0.2513 (tmm) REVERT: S 31 LEU cc_start: 0.6530 (tp) cc_final: 0.5936 (mt) REVERT: S 41 ARG cc_start: 0.1969 (OUTLIER) cc_final: 0.1585 (ttp-110) REVERT: X 104 GLN cc_start: 0.8655 (pp30) cc_final: 0.8329 (pt0) REVERT: X 106 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8632 (mp10) REVERT: Y 26 TRP cc_start: 0.3836 (t60) cc_final: 0.2912 (m100) REVERT: Y 73 GLN cc_start: 0.6952 (tp-100) cc_final: 0.6351 (pt0) REVERT: Y 82 ARG cc_start: 0.7084 (mmm160) cc_final: 0.6282 (mmp-170) REVERT: Y 115 ARG cc_start: 0.8972 (ttp80) cc_final: 0.8656 (tpt90) REVERT: Y 121 ARG cc_start: 0.9010 (tmm-80) cc_final: 0.8638 (tmm160) REVERT: a 168 MET cc_start: 0.6540 (mmt) cc_final: 0.5425 (tpp) outliers start: 73 outliers final: 56 residues processed: 316 average time/residue: 0.2268 time to fit residues: 120.6128 Evaluate side-chains 322 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 259 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 53 PHE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain S residue 41 ARG Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 83 ARG Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 228 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 229 optimal weight: 7.9990 chunk 366 optimal weight: 10.0000 chunk 443 optimal weight: 9.9990 chunk 462 optimal weight: 9.9990 chunk 421 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 chunk 399 optimal weight: 30.0000 chunk 370 optimal weight: 7.9990 chunk 258 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN F 210 ASN F 361 GLN G 59 ASN ** O 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 GLN a 15 HIS ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.080714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.051110 restraints weight = 155306.271| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.09 r_work: 0.2812 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 37472 Z= 0.289 Angle : 0.715 15.592 50721 Z= 0.360 Chirality : 0.045 0.280 5914 Planarity : 0.005 0.057 6540 Dihedral : 7.003 143.499 5365 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.73 % Favored : 97.25 % Rotamer: Outliers : 1.80 % Allowed : 13.83 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.15 (0.12), residues: 4799 helix: 1.53 (0.10), residues: 2687 sheet: 0.27 (0.22), residues: 554 loop : -0.31 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG X 115 TYR 0.017 0.002 TYR E 247 PHE 0.041 0.002 PHE a 254 TRP 0.014 0.002 TRP a 235 HIS 0.011 0.001 HIS H 104 Details of bonding type rmsd covalent geometry : bond 0.00662 (37472) covalent geometry : angle 0.71540 (50721) hydrogen bonds : bond 0.05247 ( 2249) hydrogen bonds : angle 4.68556 ( 6582) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 268 time to evaluate : 1.506 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: B 504 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9000 (mm) REVERT: C 187 ARG cc_start: 0.9364 (OUTLIER) cc_final: 0.9108 (ptp-170) REVERT: E 46 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8895 (pp) REVERT: E 397 GLN cc_start: 0.9024 (tt0) cc_final: 0.8356 (tm-30) REVERT: E 434 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: E 445 MET cc_start: 0.8906 (mmt) cc_final: 0.8466 (mmm) REVERT: F 379 MET cc_start: 0.8284 (tpp) cc_final: 0.7987 (tpt) REVERT: G 31 MET cc_start: 0.8878 (ttp) cc_final: 0.8564 (ttp) REVERT: G 48 MET cc_start: 0.8575 (tpt) cc_final: 0.8374 (mmm) REVERT: G 155 MET cc_start: 0.7808 (tpt) cc_final: 0.7330 (tpp) REVERT: H 95 MET cc_start: 0.7082 (mmm) cc_final: 0.6770 (mmm) REVERT: H 98 LYS cc_start: 0.5851 (tppt) cc_final: 0.5624 (tppt) REVERT: I 11 MET cc_start: -0.0030 (ttt) cc_final: -0.0276 (ttt) REVERT: I 17 MET cc_start: 0.4768 (ppp) cc_final: 0.4511 (ppp) REVERT: L 17 MET cc_start: 0.6228 (OUTLIER) cc_final: 0.5906 (tpp) REVERT: L 65 MET cc_start: 0.2098 (mmm) cc_final: 0.1664 (ptm) REVERT: N 16 MET cc_start: 0.4871 (mmm) cc_final: 0.4052 (tpp) REVERT: P 6 MET cc_start: 0.4240 (mmt) cc_final: 0.3509 (ptp) REVERT: P 11 MET cc_start: 0.4751 (tpp) cc_final: 0.4093 (mpp) REVERT: Q 11 MET cc_start: 0.7143 (tpt) cc_final: 0.6430 (mmp) REVERT: Q 17 MET cc_start: 0.7168 (mtm) cc_final: 0.5882 (tpp) REVERT: Q 65 MET cc_start: 0.5920 (tpt) cc_final: 0.5642 (tpt) REVERT: R 17 MET cc_start: 0.3333 (ttt) cc_final: 0.2921 (tmm) REVERT: S 31 LEU cc_start: 0.6664 (tp) cc_final: 0.6031 (mt) REVERT: S 41 ARG cc_start: 0.2047 (OUTLIER) cc_final: 0.1649 (ttp-110) REVERT: X 104 GLN cc_start: 0.8660 (pp30) cc_final: 0.8284 (pt0) REVERT: X 106 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8651 (mp10) REVERT: Y 26 TRP cc_start: 0.3835 (t60) cc_final: 0.2757 (m100) REVERT: Y 73 GLN cc_start: 0.7028 (tp-100) cc_final: 0.6406 (pt0) REVERT: Y 115 ARG cc_start: 0.9040 (ttp80) cc_final: 0.8692 (tpt90) REVERT: Y 121 ARG cc_start: 0.9089 (tmm-80) cc_final: 0.8667 (tmm160) REVERT: a 168 MET cc_start: 0.6555 (mmt) cc_final: 0.5455 (tpp) outliers start: 69 outliers final: 56 residues processed: 318 average time/residue: 0.2258 time to fit residues: 119.5803 Evaluate side-chains 321 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 259 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 53 PHE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain S residue 41 ARG Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 83 ARG Chi-restraints excluded: chain Y residue 96 GLN Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 344 optimal weight: 0.9980 chunk 435 optimal weight: 8.9990 chunk 357 optimal weight: 0.0770 chunk 324 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 379 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 GLN M 52 GLN ** O 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 GLN ** a 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS ** a 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** 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 = 0.3828 r_free = 0.3828 target = 0.082471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.052975 restraints weight = 153898.731| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.07 r_work: 0.2871 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 37472 Z= 0.135 Angle : 0.625 14.591 50721 Z= 0.313 Chirality : 0.042 0.295 5914 Planarity : 0.004 0.049 6540 Dihedral : 6.651 137.026 5365 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.85 % Favored : 98.12 % Rotamer: Outliers : 1.62 % Allowed : 13.99 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.37 (0.12), residues: 4799 helix: 1.70 (0.10), residues: 2692 sheet: 0.41 (0.22), residues: 547 loop : -0.21 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 51 TYR 0.015 0.001 TYR a 94 PHE 0.046 0.001 PHE a 254 TRP 0.014 0.001 TRP a 235 HIS 0.005 0.001 HIS H 104 Details of bonding type rmsd covalent geometry : bond 0.00292 (37472) covalent geometry : angle 0.62505 (50721) hydrogen bonds : bond 0.04569 ( 2249) hydrogen bonds : angle 4.45740 ( 6582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11335.09 seconds wall clock time: 193 minutes 56.62 seconds (11636.62 seconds total)