Starting phenix.real_space_refine on Tue Sep 15 02:25:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6n2y_9333/09_2026/6n2y_9333.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n2y_9333/09_2026/6n2y_9333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6n2y_9333/09_2026/6n2y_9333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n2y_9333/09_2026/6n2y_9333.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6n2y_9333/09_2026/6n2y_9333.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6n2y_9333/09_2026/6n2y_9333.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n2y_9333/09_2026/6n2y_9333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n2y_9333/09_2026/6n2y_9333.map" } resolution = 3.0 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= 0.009 sd= 0.229 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 12 5.49 5 Mg 4 5.21 5 S 98 5.16 5 C 22291 2.51 5 N 6106 2.21 5 O 6532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35043 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3827 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 476} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3787 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 476} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3766 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 470} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3622 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3593 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 3621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3621 Classifications: {'peptide': 471} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2187 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 928 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 122} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "I" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1284 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 78 Chain: "b2" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 770 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 1, 'TRANS': 132} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU:plan': 22, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 186 Chain: "b2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 84 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 18 Chain: "b1" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 889 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 1, 'TRANS': 155} Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ARG:plan': 11, 'GLN:plan1': 14, 'GLU:plan': 27, 'ASN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 238 Chain: "a" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1486 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 5, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 62 Chain: "c0" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c1" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c2" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c3" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c4" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c5" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c6" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c7" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c8" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c9" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} 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: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.11, per 1000 atoms: 0.23 Number of scatterers: 35043 At special positions: 0 Unit cell: (128.26, 137.8, 227.9, 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 98 16.00 P 12 15.00 Mg 4 11.99 O 6532 8.00 N 6106 7.00 C 22291 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.47 Conformation dependent library (CDL) restraints added in 1.6 seconds 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8582 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 25 sheets defined 58.9% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 removed outlier: 3.551A pdb=" N GLN A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.655A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.727A pdb=" N HIS A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 219 removed outlier: 3.638A pdb=" N ASP A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 231 through 252 Proline residue: A 239 - end of helix removed outlier: 4.192A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.715A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.778A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 420 removed outlier: 3.630A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 467 removed outlier: 3.777A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 removed outlier: 3.632A pdb=" N LEU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.838A pdb=" N LEU A 487 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 20 removed outlier: 3.617A pdb=" N TYR B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.802A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.591A pdb=" N ASN B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.669A pdb=" N HIS B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 219 removed outlier: 3.813A pdb=" N ASP B 219 " --> pdb=" O GLY B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 237 through 252 removed outlier: 4.151A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.829A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.539A pdb=" N ALA B 285 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.827A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 removed outlier: 3.731A pdb=" N GLY B 309 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 374 through 393 removed outlier: 4.651A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 402 through 408 removed outlier: 4.346A pdb=" N GLN B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 420 removed outlier: 4.310A pdb=" N ARG B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 467 removed outlier: 4.019A pdb=" N GLN B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 removed outlier: 3.585A pdb=" N LEU B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.910A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 18 Processing helix chain 'C' and resid 78 through 82 removed outlier: 4.363A pdb=" N GLY C 81 " --> pdb=" O PRO C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.830A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 156 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.561A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 219 removed outlier: 4.058A pdb=" N ASP C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 231 through 237 Processing helix chain 'C' and resid 237 through 251 removed outlier: 3.996A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.744A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) 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: 3.872A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 336 removed outlier: 3.553A pdb=" N SER C 336 " --> pdb=" O THR C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 372 through 393 removed outlier: 3.568A pdb=" N LYS C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 396 No H-bonds generated for 'chain 'C' and resid 394 through 396' Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 429 through 442 removed outlier: 3.765A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 467 removed outlier: 3.602A pdb=" N LEU C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 479 Processing helix chain 'C' and resid 485 through 498 removed outlier: 3.610A pdb=" N THR C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.523A pdb=" N LEU D 92 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 163 through 179 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 242 removed outlier: 5.098A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.622A pdb=" N GLY D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 277 removed outlier: 3.562A pdb=" N TYR D 277 " --> pdb=" O ALA D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 removed outlier: 3.703A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 315 through 323 Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 360 through 378 Processing helix chain 'D' and resid 380 through 388 Processing helix chain 'D' and resid 395 through 410 removed outlier: 3.564A pdb=" N VAL D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'E' and resid 139 through 145 Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 191 through 205 Processing helix chain 'E' and resid 206 through 209 removed outlier: 3.897A pdb=" N SER E 209 " --> pdb=" O GLY E 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 206 through 209' Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 227 through 242 removed outlier: 3.907A pdb=" N MET E 235 " --> pdb=" O THR E 231 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'E' and resid 273 through 277 removed outlier: 3.659A pdb=" N TYR E 277 " --> pdb=" O ALA E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 322 Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 360 through 387 removed outlier: 4.571A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 410 removed outlier: 4.169A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 460 through 470 Processing helix chain 'F' and resid 124 through 128 Processing helix chain 'F' and resid 139 through 145 Processing helix chain 'F' and resid 163 through 176 Processing helix chain 'F' and resid 191 through 206 WARNING: missing atoms! Processing helix chain 'F' and resid 221 through 243 removed outlier: 3.880A pdb=" N ARG F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.960A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL F 264 " --> pdb=" O ALA F 260 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 277 Processing helix chain 'F' and resid 282 through 290 removed outlier: 3.554A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 320 Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 360 through 379 Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 395 through 410 removed outlier: 3.754A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.502A pdb=" N GLU F 418 " --> pdb=" O HIS F 415 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 442 Processing helix chain 'F' and resid 449 through 453 Processing helix chain 'F' and resid 458 through 470 Processing helix chain 'G' and resid 3 through 58 Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.559A pdb=" N ASN G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG G 106 " --> pdb=" O THR G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 146 through 162 removed outlier: 4.222A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 283 removed outlier: 3.767A pdb=" N ILE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Proline residue: G 218 - end of helix Processing helix chain 'H' and resid 88 through 131 removed outlier: 3.541A pdb=" N ARG H 92 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP H 110 " --> pdb=" O SER H 106 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE H 113 " --> pdb=" O ASP H 109 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA H 116 " --> pdb=" O ASP H 112 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 22 Processing helix chain 'I' and resid 23 through 41 Processing helix chain 'I' and resid 42 through 49 removed outlier: 4.253A pdb=" N SER I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 66 Processing helix chain 'I' and resid 70 through 83 Processing helix chain 'I' and resid 85 through 87 No H-bonds generated for 'chain 'I' and resid 85 through 87' Processing helix chain 'I' and resid 88 through 105 removed outlier: 3.654A pdb=" N ASP I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 134 removed outlier: 3.586A pdb=" N ARG I 123 " --> pdb=" O ASP I 119 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN I 131 " --> pdb=" O ASP I 127 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS I 132 " --> pdb=" O VAL I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 176 removed outlier: 3.767A pdb=" N LEU I 176 " --> pdb=" O ILE I 172 " (cutoff:3.500A) Processing helix chain 'b2' and resid 10 through 29 Processing helix chain 'b2' and resid 29 through 123 removed outlier: 3.518A pdb=" N ILEb2 44 " --> pdb=" O ARGb2 40 " (cutoff:3.500A) Processing helix chain 'b2' and resid 124 through 140 removed outlier: 3.534A pdb=" N ALAb2 129 " --> pdb=" O ARGb2 125 " (cutoff:3.500A) Processing helix chain 'b2' and resid 601 through 616 Processing helix chain 'b1' and resid 9 through 143 removed outlier: 3.610A pdb=" N TYRb1 13 " --> pdb=" O GLYb1 9 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRPb1 30 " --> pdb=" O ARGb1 26 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLNb1 31 " --> pdb=" O LYSb1 27 " (cutoff:3.500A) Proline residue: b1 32 - end of helix removed outlier: 3.958A pdb=" N ALAb1 51 " --> pdb=" O GLUb1 47 " (cutoff:3.500A) Processing helix chain 'b1' and resid 145 through 163 Processing helix chain 'a' and resid 16 through 38 removed outlier: 3.582A pdb=" N MET a 20 " --> pdb=" O ASN a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 67 Processing helix chain 'a' and resid 68 through 73 Processing helix chain 'a' and resid 75 through 92 removed outlier: 3.745A pdb=" N THR a 81 " --> pdb=" O THR a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 112 through 130 Processing helix chain 'a' and resid 153 through 191 removed outlier: 4.630A pdb=" N GLY a 177 " --> pdb=" O ASN a 173 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR a 191 " --> pdb=" O LEU a 187 " (cutoff:3.500A) Processing helix chain 'a' and resid 199 through 234 removed outlier: 4.263A pdb=" N MET a 203 " --> pdb=" O ALA a 199 " (cutoff:3.500A) Processing helix chain 'c0' and resid 3 through 37 Processing helix chain 'c0' and resid 40 through 72 removed outlier: 4.001A pdb=" N THRc0 47 " --> pdb=" O VALc0 43 " (cutoff:3.500A) Proline residue: c0 59 - end of helix removed outlier: 3.923A pdb=" N PHEc0 67 " --> pdb=" O VALc0 63 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILEc0 68 " --> pdb=" O VALc0 64 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARGc0 72 " --> pdb=" O ILEc0 68 " (cutoff:3.500A) Processing helix chain 'c1' and resid 3 through 37 Processing helix chain 'c1' and resid 40 through 72 removed outlier: 4.525A pdb=" N LEUc1 58 " --> pdb=" O LEUc1 54 " (cutoff:3.500A) Proline residue: c1 59 - end of helix Processing helix chain 'c2' and resid 3 through 37 Processing helix chain 'c2' and resid 40 through 56 Processing helix chain 'c2' and resid 56 through 72 Processing helix chain 'c3' and resid 3 through 37 Processing helix chain 'c3' and resid 40 through 71 Proline residue: c3 59 - end of helix Processing helix chain 'c4' and resid 3 through 37 Processing helix chain 'c4' and resid 40 through 56 Processing helix chain 'c4' and resid 56 through 72 removed outlier: 4.032A pdb=" N ILEc4 68 " --> pdb=" O VALc4 64 " (cutoff:3.500A) Processing helix chain 'c5' and resid 3 through 37 Processing helix chain 'c5' and resid 40 through 72 removed outlier: 4.290A pdb=" N LEUc5 58 " --> pdb=" O LEUc5 54 " (cutoff:3.500A) Proline residue: c5 59 - end of helix Processing helix chain 'c6' and resid 3 through 37 Processing helix chain 'c6' and resid 40 through 72 removed outlier: 4.372A pdb=" N LEUc6 58 " --> pdb=" O LEUc6 54 " (cutoff:3.500A) Proline residue: c6 59 - end of helix removed outlier: 3.635A pdb=" N GLYc6 71 " --> pdb=" O PHEc6 67 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARGc6 72 " --> pdb=" O ILEc6 68 " (cutoff:3.500A) Processing helix chain 'c7' and resid 3 through 37 Processing helix chain 'c7' and resid 40 through 56 removed outlier: 3.664A pdb=" N LEUc7 44 " --> pdb=" O LEUc7 40 " (cutoff:3.500A) Processing helix chain 'c7' and resid 56 through 72 removed outlier: 3.504A pdb=" N ILEc7 60 " --> pdb=" O GLUc7 56 " (cutoff:3.500A) Processing helix chain 'c8' and resid 3 through 37 Processing helix chain 'c8' and resid 40 through 71 removed outlier: 4.938A pdb=" N LEUc8 58 " --> pdb=" O LEUc8 54 " (cutoff:3.500A) Proline residue: c8 59 - end of helix Processing helix chain 'c9' and resid 3 through 37 removed outlier: 3.525A pdb=" N GLNc9 37 " --> pdb=" O GLYc9 33 " (cutoff:3.500A) Processing helix chain 'c9' and resid 40 through 71 removed outlier: 3.827A pdb=" N THRc9 47 " --> pdb=" O VALc9 43 " (cutoff:3.500A) Proline residue: c9 59 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.696A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.682A pdb=" N ARG A 127 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.381A pdb=" N VAL A 256 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU A 316 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 258 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N PHE A 318 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR A 260 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLU A 320 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 169 " --> pdb=" O VAL A 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.436A pdb=" N ILE A 159 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 76 through 78 removed outlier: 6.880A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET B 60 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.000A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.292A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP B 261 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL B 196 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL B 256 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU B 316 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 258 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N PHE B 318 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR B 260 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N GLU B 320 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 319 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.395A pdb=" N ILE B 159 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 24 through 27 removed outlier: 3.999A pdb=" N SER I 113 " --> pdb=" O ILE I 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 31 through 35 removed outlier: 6.399A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C 91 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.409A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.200A pdb=" N ILE C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL C 259 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE C 194 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP C 261 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 196 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL C 256 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU C 316 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL C 258 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE C 318 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TYR C 260 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLU C 320 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 319 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 10 removed outlier: 5.699A pdb=" N VAL D 6 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS D 17 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASN D 28 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA D 29 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR D 79 " --> pdb=" O ALA D 29 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB6, first strand: chain 'D' and resid 95 through 96 removed outlier: 3.628A pdb=" N ILE D 303 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 251 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS D 153 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR D 329 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY D 155 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.383A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 10 removed outlier: 5.575A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AC1, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.004A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 188 " --> pdb=" O ASP E 252 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS E 153 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N THR E 329 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLY E 155 " --> pdb=" O THR E 329 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC3, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.653A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.092A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 113 through 118 removed outlier: 6.362A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR G 172 " --> pdb=" O THR G 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 204 through 205 removed outlier: 6.477A pdb=" N GLU G 204 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N HIS H 5 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE H 77 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER H 7 " --> pdb=" O ILE H 77 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR H 16 " --> pdb=" O VAL H 8 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 48 through 52 removed outlier: 3.629A pdb=" N SER H 48 " --> pdb=" O VAL H 63 " (cutoff:3.500A) 2207 hydrogen bonds defined for protein. 6477 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: 6.70 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5932 1.30 - 1.43: 8273 1.43 - 1.56: 21039 1.56 - 1.68: 139 1.68 - 1.81: 195 Bond restraints: 35578 Sorted by residual: bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.75e+01 bond pdb=" CA GLUb1 75 " pdb=" CB GLUb1 75 " ideal model delta sigma weight residual 1.528 1.655 -0.127 1.56e-02 4.11e+03 6.60e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.47e+01 bond pdb=" CA LEUb2 131 " pdb=" CB LEUb2 131 " ideal model delta sigma weight residual 1.528 1.656 -0.127 1.59e-02 3.96e+03 6.40e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.34e+01 ... (remaining 35573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 47254 3.57 - 7.14: 910 7.14 - 10.71: 156 10.71 - 14.28: 10 14.28 - 17.85: 3 Bond angle restraints: 48333 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 122.02 17.85 1.00e+00 1.00e+00 3.19e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 122.36 17.51 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 121.10 15.73 1.00e+00 1.00e+00 2.47e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 125.97 13.90 1.00e+00 1.00e+00 1.93e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 123.73 13.10 1.00e+00 1.00e+00 1.72e+02 ... (remaining 48328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.32: 20830 23.32 - 46.65: 531 46.65 - 69.97: 18 69.97 - 93.30: 27 93.30 - 116.62: 1 Dihedral angle restraints: 21407 sinusoidal: 8021 harmonic: 13386 Sorted by residual: dihedral pdb=" C ARGb1 99 " pdb=" N ARGb1 99 " pdb=" CA ARGb1 99 " pdb=" CB ARGb1 99 " ideal model delta harmonic sigma weight residual -122.60 -138.06 15.46 0 2.50e+00 1.60e-01 3.83e+01 dihedral pdb=" N ARGb1 99 " pdb=" C ARGb1 99 " pdb=" CA ARGb1 99 " pdb=" CB ARGb1 99 " ideal model delta harmonic sigma weight residual 122.80 138.26 -15.46 0 2.50e+00 1.60e-01 3.82e+01 dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 -176.62 116.62 1 2.00e+01 2.50e-03 3.48e+01 ... (remaining 21404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 5534 0.141 - 0.283: 215 0.283 - 0.424: 31 0.424 - 0.565: 6 0.565 - 0.707: 2 Chirality restraints: 5788 Sorted by residual: chirality pdb=" CA ARGb1 99 " pdb=" N ARGb1 99 " pdb=" C ARGb1 99 " pdb=" CB ARGb1 99 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" CA GLNb2 90 " pdb=" N GLNb2 90 " pdb=" C GLNb2 90 " pdb=" CB GLNb2 90 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA ILEb1 157 " pdb=" N ILEb1 157 " pdb=" C ILEb1 157 " pdb=" CB ILEb1 157 " both_signs ideal model delta sigma weight residual False 2.43 1.88 0.55 2.00e-01 2.50e+01 7.52e+00 ... (remaining 5785 not shown) Planarity restraints: 6254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEUb1 144 " -0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C LEUb1 144 " 0.079 2.00e-02 2.50e+03 pdb=" O LEUb1 144 " -0.032 2.00e-02 2.50e+03 pdb=" N THRb1 145 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLNb1 127 " 0.019 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C GLNb1 127 " -0.069 2.00e-02 2.50e+03 pdb=" O GLNb1 127 " 0.025 2.00e-02 2.50e+03 pdb=" N VALb1 128 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLUb1 64 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C GLUb1 64 " 0.065 2.00e-02 2.50e+03 pdb=" O GLUb1 64 " -0.025 2.00e-02 2.50e+03 pdb=" N GLNb1 65 " -0.022 2.00e-02 2.50e+03 ... (remaining 6251 not shown) Histogram of nonbonded interaction distances: 0.76 - 1.59: 5 1.59 - 2.42: 91 2.42 - 3.25: 34055 3.25 - 4.07: 91322 4.07 - 4.90: 167437 Warning: very small nonbonded interaction distances. Nonbonded interactions: 292910 Sorted by model distance: nonbonded pdb=" O PRO H 36 " pdb=" OE2 GLUc5 39 " model vdw 0.765 3.040 nonbonded pdb=" N LEU H 32 " pdb=" NE2 GLNc4 37 " model vdw 1.152 3.200 nonbonded pdb=" O PRO H 36 " pdb=" CD GLUc5 39 " model vdw 1.382 3.270 nonbonded pdb=" CA LEU H 32 " pdb=" NE2 GLNc4 37 " model vdw 1.441 3.550 nonbonded pdb=" O ASNb1 46 " pdb=" OD1 ASPb1 49 " model vdw 1.500 3.040 ... (remaining 292905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 12 or (resid 13 through 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 16 or (resid 17 and (nam \ e N or name CA or name C or name O or name CB )) or resid 18 or (resid 19 and (n \ ame N or name CA or name C or name O or name CB )) or resid 20 through 187 or (r \ esid 188 and (name N or name CA or name C or name O or name CB )) or resid 189 t \ hrough 352 or (resid 353 and (name N or name CA or name C or name CB or name CG1 \ or name CG2)) or resid 354 through 394 or (resid 395 through 398 and (name N or \ name CA or name C or name O or name CB )) or resid 399 through 405 or (resid 40 \ 6 through 408 and (name N or name CA or name C or name O or name CB )) or resid \ 409 through 483 or (resid 484 through 485 and (name N or name CA or name C or na \ me O or name CB )) or resid 486 through 495 or (resid 496 and (name N or name CA \ or name C or name O or name CB )) or resid 497 through 601)) selection = (chain 'B' and (resid 8 through 12 or (resid 13 through 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 16 or (resid 17 and (nam \ e N or name CA or name C or name O or name CB )) or resid 18 or (resid 19 and (n \ ame N or name CA or name C or name O or name CB )) or resid 20 through 38 or (re \ sid 39 and (name N or name CA or name C or name CB )) or resid 40 through 187 or \ (resid 188 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 9 through 393 or (resid 394 and (name N or name CA or name C or name CB )) or re \ sid 395 through 601)) selection = (chain 'C' and (resid 8 through 38 or (resid 39 and (name N or name CA or name C \ or name CB )) or resid 40 through 352 or (resid 353 and (name N or name CA or n \ ame C or name CB or name CG1 or name CG2)) or resid 354 through 393 or (resid 39 \ 4 and (name N or name CA or name C or name CB )) or (resid 395 through 398 and ( \ name N or name CA or name C or name O or name CB )) or resid 399 through 402 or \ (resid 403 through 408 and (name N or name CA or name C or name O or name CB )) \ or resid 409 through 450 or (resid 451 and (name N or name CA or name C or name \ O or name CB )) or resid 452 through 483 or (resid 484 through 485 and (name N o \ r name CA or name C or name O or name CB )) or resid 486 through 495 or (resid 4 \ 96 and (name N or name CA or name C or name O or name CB )) or resid 497 through \ 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name CB or name CG or name OD1 or name ND2)) or resid 197 through 208 or ( \ resid 209 and (name N or name CA or name C or name CB or name OG )) or resid 210 \ through 296 or (resid 297 and (name N or name CA or name C or name CB or name C \ G or name CD or name CE or name NZ )) or resid 298 through 385 or (resid 386 and \ (name N or name CA or name C or name O or name CB )) or resid 387 through 388 o \ r (resid 389 through 392 and (name N or name CA or name C or name O or name CB ) \ ) or resid 393 or (resid 394 through 395 and (name N or name CA or name C or nam \ e O or name CB )) or resid 396 or (resid 397 and (name N or name CA or name C or \ name O or name CB )) or resid 398 through 420 or (resid 421 and (name N or name \ CA or name C or name CB or name OG1 or name CG2)) or (resid 422 and (name N or \ name CA or name C )) or resid 423 through 430 or (resid 431 and (name N or name \ CA or name C or name O or name CB )) or resid 432 through 468 or (resid 469 and \ (name N or name CA or name C or name O or name CB )) or resid 470)) selection = (chain 'E' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name CB or name CG or name OD1 or name ND2)) or resid 197 through 208 or ( \ resid 209 and (name N or name CA or name C or name CB or name OG )) or resid 210 \ through 296 or (resid 297 and (name N or name CA or name C or name CB or name C \ G or name CD or name CE or name NZ )) or resid 298 through 420 or (resid 421 and \ (name N or name CA or name C or name CB or name OG1 or name CG2)) or (resid 422 \ and (name N or name CA or name C )) or resid 423 through 430 or (resid 431 and \ (name N or name CA or name C or name O or name CB )) or resid 432 through 470)) selection = (chain 'F' and (resid 2 through 385 or (resid 386 and (name N or name CA or name \ C or name O or name CB )) or resid 387 through 388 or (resid 389 through 392 an \ d (name N or name CA or name C or name O or name CB )) or resid 393 or (resid 39 \ 4 through 395 and (name N or name CA or name C or name O or name CB )) or resid \ 396 or (resid 397 and (name N or name CA or name C or name O or name CB )) or re \ sid 398 through 468 or (resid 469 and (name N or name CA or name C or name O or \ name CB )) or resid 470)) } ncs_group { reference = (chain 'b1' and ((resid 7 and (name N or name CA or name C or name O or name CB \ )) or resid 8 through 19 or (resid 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 38 or (resid 39 and (name N or name CA or nam \ e C or name O or name CB )) or resid 40 through 43 or (resid 44 through 139 and \ (name N or name CA or name C or name O or name CB )) or (resid 140 and (name N o \ r name CA or name C or name CB )))) selection = (chain 'b2' and (resid 7 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 30 or (resid 31 and (name N or nam \ e CA or name C or name O or name CB )) or resid 32 through 33 or (resid 34 and ( \ name N or name CA or name C or name O or name CB )) or resid 35 through 140)) } ncs_group { reference = chain 'c0' selection = chain 'c1' selection = chain 'c2' selection = chain 'c3' selection = chain 'c4' selection = chain 'c5' selection = chain 'c6' selection = chain 'c7' selection = chain 'c8' selection = chain 'c9' } 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.910 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 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 : 0.009 0.127 35580 Z= 0.543 Angle : 1.188 17.851 48333 Z= 0.733 Chirality : 0.072 0.707 5788 Planarity : 0.008 0.077 6254 Dihedral : 10.480 116.619 12825 Min Nonbonded Distance : 0.765 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.38 % Favored : 96.49 % Rotamer: Outliers : 0.40 % Allowed : 5.43 % Favored : 94.17 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.11), residues: 4648 helix: -1.55 (0.09), residues: 2510 sheet: -1.02 (0.22), residues: 508 loop : -1.74 (0.14), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 283 TYR 0.045 0.003 TYR C 329 PHE 0.043 0.003 PHEc6 65 TRP 0.023 0.002 TRP a 206 HIS 0.027 0.002 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00887 / 0.54 (35578) covalent geometry : angle 1.18763 / 0.73 (48333) hydrogen bonds : bond 0.15754 / 10.51 ( 2207) hydrogen bonds : angle 6.83519 / 4.76 ( 6477) Misc. bond : bond 0.00088 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 780 time to evaluate : 1.360 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR F 421 " (corrupted residue). Skipping it. 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 11 LEU cc_start: 0.8169 (mt) cc_final: 0.7969 (mp) REVERT: A 214 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8142 (tttp) REVERT: A 250 MET cc_start: 0.8756 (ttp) cc_final: 0.8314 (ttp) REVERT: A 252 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8427 (mtpp) REVERT: A 262 ASP cc_start: 0.7469 (m-30) cc_final: 0.7121 (m-30) REVERT: A 347 ASP cc_start: 0.7443 (m-30) cc_final: 0.7179 (m-30) REVERT: A 373 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7973 (ttpp) REVERT: A 385 ASP cc_start: 0.7847 (m-30) cc_final: 0.7533 (m-30) REVERT: A 458 LYS cc_start: 0.8239 (ttpp) cc_final: 0.7804 (tttp) REVERT: A 489 LYS cc_start: 0.8337 (mtmt) cc_final: 0.8096 (mtmt) REVERT: B 28 VAL cc_start: 0.8942 (t) cc_final: 0.8624 (p) REVERT: B 214 LYS cc_start: 0.8519 (mtmt) cc_final: 0.8285 (mtmm) REVERT: C 95 MET cc_start: 0.8381 (tpt) cc_final: 0.7896 (tpt) REVERT: C 250 MET cc_start: 0.9070 (ttp) cc_final: 0.8732 (ttm) REVERT: C 262 ASP cc_start: 0.7546 (m-30) cc_final: 0.7248 (m-30) REVERT: C 465 ASP cc_start: 0.7514 (m-30) cc_final: 0.7300 (m-30) REVERT: C 467 ASN cc_start: 0.7244 (m-40) cc_final: 0.6881 (m110) REVERT: D 75 GLU cc_start: 0.7717 (tt0) cc_final: 0.7237 (tm-30) REVERT: D 98 VAL cc_start: 0.8807 (t) cc_final: 0.8592 (p) REVERT: D 332 GLU cc_start: 0.7506 (tp30) cc_final: 0.7265 (tp30) REVERT: D 381 GLN cc_start: 0.7929 (tt0) cc_final: 0.6929 (tp40) REVERT: D 431 LYS cc_start: 0.7624 (mtpm) cc_final: 0.7370 (mtpp) REVERT: D 467 LYS cc_start: 0.7622 (mtmt) cc_final: 0.6881 (mptt) REVERT: E 39 GLU cc_start: 0.7959 (pm20) cc_final: 0.7746 (pm20) REVERT: E 90 VAL cc_start: 0.8593 (m) cc_final: 0.8342 (p) REVERT: E 375 GLN cc_start: 0.8002 (tp-100) cc_final: 0.7506 (tp40) REVERT: E 427 TYR cc_start: 0.8740 (t80) cc_final: 0.8473 (t80) REVERT: F 30 LEU cc_start: 0.8791 (mt) cc_final: 0.8556 (mp) REVERT: F 281 LEU cc_start: 0.8806 (tm) cc_final: 0.8590 (tp) REVERT: F 337 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8190 (mt-10) REVERT: F 438 LYS cc_start: 0.7967 (tttt) cc_final: 0.7654 (ttpp) REVERT: F 469 MET cc_start: 0.8003 (mtp) cc_final: 0.7548 (mtm) REVERT: G 8 LYS cc_start: 0.8216 (tptt) cc_final: 0.7962 (tptt) REVERT: G 15 LYS cc_start: 0.8234 (mttt) cc_final: 0.7920 (mttm) REVERT: G 40 LYS cc_start: 0.7982 (mtpm) cc_final: 0.7559 (ttpp) REVERT: I 32 ARG cc_start: 0.8110 (mtt-85) cc_final: 0.7846 (mtt-85) REVERT: b2 33 LEU cc_start: 0.8225 (tm) cc_final: 0.7916 (tm) REVERT: b1 40 ARG cc_start: 0.5785 (ttt90) cc_final: 0.5365 (ptp-170) REVERT: c9 58 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6417 (mm) outliers start: 14 outliers final: 4 residues processed: 793 average time/residue: 0.7524 time to fit residues: 708.3774 Evaluate side-chains 511 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 506 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain c9 residue 58 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0070 chunk 401 optimal weight: 2.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 GLN A 147 GLN A 186 GLN A 215 HIS A 358 ASN A 422 GLN A 425 HIS B 46 ASN B 57 ASN B 147 GLN B 186 GLN B 215 HIS ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 HIS C 18 ASN C 186 GLN C 333 ASN C 397 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 HIS D 28 ASN D 34 HIS D 179 HIS D 217 GLN D 289 GLN D 304 GLN D 324 HIS ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS E 196 ASN E 381 GLN E 415 HIS F 28 ASN F 177 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 GLN G 33 ASN G 94 ASN G 107 HIS G 130 ASN G 282 ASN H 125 ASN a 16 ASN a 49 GLN a 128 HIS a 173 ASN a 217 GLN a 231 HIS c4 37 GLN c5 23 ASN c7 23 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.191561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137204 restraints weight = 37128.972| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.15 r_work: 0.3126 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35580 Z= 0.176 Angle : 0.669 12.131 48333 Z= 0.341 Chirality : 0.046 0.213 5788 Planarity : 0.006 0.060 6254 Dihedral : 5.749 78.911 5085 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 3.69 % Allowed : 11.86 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.68 (0.12), residues: 4648 helix: 0.20 (0.10), residues: 2516 sheet: -0.75 (0.21), residues: 547 loop : -1.23 (0.14), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 104 TYR 0.044 0.002 TYRc6 69 PHE 0.019 0.002 PHE a 87 TRP 0.020 0.002 TRP a 206 HIS 0.010 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (35578) covalent geometry : angle 0.66899 / 0.34 (48333) hydrogen bonds : bond 0.05029 / 3.36 ( 2207) hydrogen bonds : angle 4.88508 / 3.45 ( 6477) Misc. bond : bond 0.00050 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 544 time to evaluate : 1.355 Fit side-chains TARDY: cannot create tardy model for: "THR F 421 " (corrupted residue). Skipping it. 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 11 LEU cc_start: 0.8465 (mt) cc_final: 0.8259 (mp) REVERT: A 101 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: A 214 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8530 (tttm) REVERT: A 250 MET cc_start: 0.9103 (ttp) cc_final: 0.8868 (ttp) REVERT: A 385 ASP cc_start: 0.8149 (m-30) cc_final: 0.7911 (m-30) REVERT: A 446 ASP cc_start: 0.7967 (m-30) cc_final: 0.7743 (m-30) REVERT: A 458 LYS cc_start: 0.8601 (ttpp) cc_final: 0.8247 (tttp) REVERT: B 40 ARG cc_start: 0.9052 (ttm170) cc_final: 0.8845 (ttm170) REVERT: B 161 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8804 (mtt90) REVERT: B 214 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8498 (mtmt) REVERT: B 306 ASP cc_start: 0.8722 (m-30) cc_final: 0.8442 (m-30) REVERT: B 452 ASP cc_start: 0.8386 (m-30) cc_final: 0.8084 (m-30) REVERT: B 473 GLU cc_start: 0.7907 (tp30) cc_final: 0.7637 (mm-30) REVERT: C 54 GLU cc_start: 0.8577 (pt0) cc_final: 0.8367 (pt0) REVERT: C 62 MET cc_start: 0.8833 (ttt) cc_final: 0.8573 (ttm) REVERT: C 250 MET cc_start: 0.9147 (ttp) cc_final: 0.8853 (ttm) REVERT: C 262 ASP cc_start: 0.8182 (m-30) cc_final: 0.7907 (m-30) REVERT: C 467 ASN cc_start: 0.7537 (m-40) cc_final: 0.7170 (m110) REVERT: C 469 GLN cc_start: 0.6968 (tm-30) cc_final: 0.6661 (tm-30) REVERT: C 484 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7688 (mt-10) REVERT: D 75 GLU cc_start: 0.8672 (tt0) cc_final: 0.8318 (tm-30) REVERT: D 332 GLU cc_start: 0.8384 (tp30) cc_final: 0.8035 (mm-30) REVERT: D 381 GLN cc_start: 0.8554 (tt0) cc_final: 0.7435 (tp40) REVERT: D 431 LYS cc_start: 0.8262 (mtpm) cc_final: 0.8046 (mtpt) REVERT: D 467 LYS cc_start: 0.7751 (mtmt) cc_final: 0.6893 (mptt) REVERT: E 77 ILE cc_start: 0.9152 (pt) cc_final: 0.8783 (mp) REVERT: E 90 VAL cc_start: 0.8991 (m) cc_final: 0.8665 (p) REVERT: E 135 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8541 (tp) REVERT: E 167 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8611 (tp) REVERT: E 243 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.7827 (mp10) REVERT: E 249 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8741 (tp) REVERT: E 368 ARG cc_start: 0.8702 (mtp85) cc_final: 0.8310 (mmt-90) REVERT: E 375 GLN cc_start: 0.8583 (tp-100) cc_final: 0.8336 (mm-40) REVERT: E 379 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8131 (mt-10) REVERT: F 89 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: F 201 GLU cc_start: 0.7737 (tp30) cc_final: 0.7471 (tp30) REVERT: F 438 LYS cc_start: 0.8548 (tttt) cc_final: 0.8201 (ttpp) REVERT: F 469 MET cc_start: 0.7876 (mtp) cc_final: 0.7649 (mtm) REVERT: G 6 ASP cc_start: 0.8392 (m-30) cc_final: 0.8092 (m-30) REVERT: G 40 LYS cc_start: 0.8246 (mtpm) cc_final: 0.7871 (ttpp) REVERT: b2 14 GLN cc_start: 0.5362 (mm-40) cc_final: 0.5054 (mm-40) REVERT: b2 26 ARG cc_start: 0.7437 (ttp-110) cc_final: 0.7221 (ptm160) REVERT: b2 33 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8167 (tm) REVERT: b1 40 ARG cc_start: 0.5656 (ttt90) cc_final: 0.5271 (ptt180) REVERT: a 157 ILE cc_start: 0.9246 (pp) cc_final: 0.8964 (pp) REVERT: a 160 PHE cc_start: 0.8462 (m-80) cc_final: 0.8028 (m-80) REVERT: a 171 PHE cc_start: 0.7218 (t80) cc_final: 0.6742 (t80) REVERT: c1 58 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6609 (tt) REVERT: c6 48 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6260 (ttt) REVERT: c9 40 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8093 (pp) REVERT: c9 58 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5884 (mm) outliers start: 129 outliers final: 41 residues processed: 635 average time/residue: 0.6559 time to fit residues: 503.7310 Evaluate side-chains 519 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 466 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain b2 residue 12 ILE Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b2 residue 40 ARG Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain c1 residue 58 LEU Chi-restraints excluded: chain c6 residue 48 MET Chi-restraints excluded: chain c7 residue 10 ILE Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 58 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 299 optimal weight: 0.5980 chunk 437 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 313 optimal weight: 4.9990 chunk 385 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 253 optimal weight: 0.0970 chunk 164 optimal weight: 3.9990 chunk 462 optimal weight: 4.9990 chunk 68 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 172 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 HIS C 345 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 HIS E 217 GLN E 381 GLN F 28 ASN F 169 GLN F 177 GLN F 217 GLN G 130 ASN a 49 GLN a 90 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.192646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138100 restraints weight = 37107.829| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.02 r_work: 0.3180 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35580 Z= 0.134 Angle : 0.617 18.339 48333 Z= 0.309 Chirality : 0.045 0.279 5788 Planarity : 0.005 0.058 6254 Dihedral : 5.297 64.699 5084 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 3.54 % Allowed : 13.83 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.18 (0.12), residues: 4648 helix: 0.98 (0.10), residues: 2525 sheet: -0.60 (0.21), residues: 563 loop : -0.93 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGb2 26 TYR 0.029 0.001 TYRc6 69 PHE 0.032 0.001 PHE a 209 TRP 0.020 0.002 TRP a 105 HIS 0.007 0.001 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (35578) covalent geometry : angle 0.61688 / 0.31 (48333) hydrogen bonds : bond 0.04454 / 2.97 ( 2207) hydrogen bonds : angle 4.58734 / 3.25 ( 6477) Misc. bond : bond 0.00050 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 524 time to evaluate : 1.349 Fit side-chains TARDY: cannot create tardy model for: "THR F 421 " (corrupted residue). Skipping it. 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 67 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: A 214 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8522 (tttp) REVERT: A 250 MET cc_start: 0.9067 (ttp) cc_final: 0.8844 (ttp) REVERT: A 351 SER cc_start: 0.8743 (OUTLIER) cc_final: 0.8523 (m) REVERT: A 385 ASP cc_start: 0.8045 (m-30) cc_final: 0.7525 (m-30) REVERT: A 422 GLN cc_start: 0.8836 (mt0) cc_final: 0.8630 (mt0) REVERT: A 446 ASP cc_start: 0.7874 (m-30) cc_final: 0.7629 (m-30) REVERT: A 458 LYS cc_start: 0.8513 (ttpp) cc_final: 0.8148 (tttp) REVERT: B 161 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8779 (mtt90) REVERT: B 214 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8485 (mtmm) REVERT: B 219 ASP cc_start: 0.8736 (m-30) cc_final: 0.8453 (m-30) REVERT: B 306 ASP cc_start: 0.8717 (m-30) cc_final: 0.8497 (m-30) REVERT: B 452 ASP cc_start: 0.8337 (m-30) cc_final: 0.8025 (m-30) REVERT: B 473 GLU cc_start: 0.7794 (tp30) cc_final: 0.7560 (mm-30) REVERT: C 62 MET cc_start: 0.8790 (ttt) cc_final: 0.8561 (ttm) REVERT: C 89 ARG cc_start: 0.8305 (ttp-110) cc_final: 0.7409 (ttp80) REVERT: C 190 ASN cc_start: 0.7422 (m-40) cc_final: 0.7192 (m-40) REVERT: C 250 MET cc_start: 0.9146 (ttp) cc_final: 0.8877 (ttm) REVERT: C 383 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7666 (ttp-110) REVERT: C 467 ASN cc_start: 0.7392 (m-40) cc_final: 0.6984 (m110) REVERT: C 469 GLN cc_start: 0.6710 (tm-30) cc_final: 0.6443 (tm-30) REVERT: D 75 GLU cc_start: 0.8624 (tt0) cc_final: 0.8074 (tm-30) REVERT: D 332 GLU cc_start: 0.8391 (tp30) cc_final: 0.8033 (mm-30) REVERT: D 381 GLN cc_start: 0.8547 (tt0) cc_final: 0.7387 (tp40) REVERT: D 420 PHE cc_start: 0.8617 (m-10) cc_final: 0.8415 (m-10) REVERT: D 432 GLU cc_start: 0.8054 (mp0) cc_final: 0.7542 (mt-10) REVERT: E 39 GLU cc_start: 0.8226 (pm20) cc_final: 0.8004 (pm20) REVERT: E 52 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8998 (mt) REVERT: E 77 ILE cc_start: 0.9225 (pt) cc_final: 0.8914 (mp) REVERT: E 90 VAL cc_start: 0.9019 (m) cc_final: 0.8692 (p) REVERT: E 167 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8629 (tp) REVERT: E 375 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8322 (mm-40) REVERT: E 407 GLN cc_start: 0.8466 (tt0) cc_final: 0.8232 (tt0) REVERT: F 10 MET cc_start: 0.8298 (mtm) cc_final: 0.8065 (mtm) REVERT: F 89 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: F 201 GLU cc_start: 0.7663 (tp30) cc_final: 0.7342 (tp30) REVERT: F 226 MET cc_start: 0.8909 (mtp) cc_final: 0.8638 (mtp) REVERT: F 365 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7833 (mp10) REVERT: F 438 LYS cc_start: 0.8555 (tttt) cc_final: 0.8199 (ttpp) REVERT: G 8 LYS cc_start: 0.8816 (tptt) cc_final: 0.8566 (tptt) REVERT: G 40 LYS cc_start: 0.8242 (mtpm) cc_final: 0.7852 (ttpp) REVERT: I 9 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7650 (mtp180) REVERT: b1 40 ARG cc_start: 0.5371 (ttt90) cc_final: 0.5018 (ptt180) REVERT: a 84 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7887 (mmm) REVERT: a 157 ILE cc_start: 0.9248 (pp) cc_final: 0.8958 (pp) REVERT: a 160 PHE cc_start: 0.8507 (m-80) cc_final: 0.8065 (m-80) REVERT: a 171 PHE cc_start: 0.7359 (t80) cc_final: 0.6991 (t80) REVERT: c1 58 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6527 (tt) REVERT: c6 6 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7442 (mt) REVERT: c6 48 MET cc_start: 0.6566 (ttm) cc_final: 0.6358 (ttt) REVERT: c9 40 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8023 (pp) REVERT: c9 67 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8428 (m-10) outliers start: 124 outliers final: 41 residues processed: 611 average time/residue: 0.6678 time to fit residues: 496.9838 Evaluate side-chains 532 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 478 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain b2 residue 12 ILE Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 84 MET Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c1 residue 58 LEU Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c5 residue 58 LEU Chi-restraints excluded: chain c6 residue 6 LEU Chi-restraints excluded: chain c7 residue 10 ILE Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 67 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 249 optimal weight: 0.2980 chunk 271 optimal weight: 0.5980 chunk 366 optimal weight: 40.0000 chunk 313 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 379 optimal weight: 20.0000 chunk 248 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 488 ASN B 46 ASN B 172 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN B 470 HIS ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 GLN E 401 HIS F 28 ASN F 169 GLN F 177 GLN F 324 HIS G 38 ASN I 41 ASN a 207 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.192592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.138806 restraints weight = 37140.034| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.14 r_work: 0.3161 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 35580 Z= 0.140 Angle : 0.607 15.701 48333 Z= 0.303 Chirality : 0.045 0.335 5788 Planarity : 0.004 0.055 6254 Dihedral : 5.041 58.962 5081 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 3.40 % Allowed : 15.14 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.56 (0.12), residues: 4648 helix: 1.32 (0.10), residues: 2523 sheet: -0.60 (0.21), residues: 576 loop : -0.73 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 90 TYR 0.024 0.001 TYR B 438 PHE 0.015 0.001 PHE C 494 TRP 0.008 0.001 TRP a 206 HIS 0.007 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (35578) covalent geometry : angle 0.60650 / 0.30 (48333) hydrogen bonds : bond 0.04247 / 2.83 ( 2207) hydrogen bonds : angle 4.44010 / 3.15 ( 6477) Misc. bond : bond 0.00053 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 501 time to evaluate : 1.222 Fit side-chains TARDY: cannot create tardy model for: "THR F 421 " (corrupted residue). Skipping it. 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 67 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: A 250 MET cc_start: 0.9052 (ttp) cc_final: 0.8773 (ttp) REVERT: A 385 ASP cc_start: 0.8063 (m-30) cc_final: 0.7817 (m-30) REVERT: A 422 GLN cc_start: 0.8908 (mt0) cc_final: 0.8698 (mt0) REVERT: A 430 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7767 (p) REVERT: A 458 LYS cc_start: 0.8494 (ttpp) cc_final: 0.8126 (tttp) REVERT: B 17 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: B 161 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8824 (mtt90) REVERT: B 214 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8488 (mtmm) REVERT: B 306 ASP cc_start: 0.8672 (m-30) cc_final: 0.8446 (m-30) REVERT: B 473 GLU cc_start: 0.7880 (tp30) cc_final: 0.7656 (mm-30) REVERT: C 62 MET cc_start: 0.8803 (ttt) cc_final: 0.8583 (ttm) REVERT: C 250 MET cc_start: 0.9212 (ttp) cc_final: 0.8916 (ttm) REVERT: C 383 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8027 (ttp-110) REVERT: C 467 ASN cc_start: 0.7370 (m-40) cc_final: 0.6955 (m110) REVERT: C 469 GLN cc_start: 0.6733 (tm-30) cc_final: 0.6454 (tm-30) REVERT: D 85 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8638 (p) REVERT: D 332 GLU cc_start: 0.8509 (tp30) cc_final: 0.8144 (mm-30) REVERT: D 381 GLN cc_start: 0.8597 (tt0) cc_final: 0.7431 (tp40) REVERT: D 431 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8050 (ttpp) REVERT: E 39 GLU cc_start: 0.8216 (pm20) cc_final: 0.8004 (pm20) REVERT: E 52 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9041 (mt) REVERT: E 77 ILE cc_start: 0.9257 (pt) cc_final: 0.8912 (mp) REVERT: E 90 VAL cc_start: 0.9050 (m) cc_final: 0.8730 (p) REVERT: E 167 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8663 (tp) REVERT: E 332 GLU cc_start: 0.7827 (tp30) cc_final: 0.7611 (tp30) REVERT: E 407 GLN cc_start: 0.8488 (tt0) cc_final: 0.8217 (tt0) REVERT: F 10 MET cc_start: 0.8447 (mtm) cc_final: 0.8233 (mtm) REVERT: F 35 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7705 (mmmm) REVERT: F 89 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: F 201 GLU cc_start: 0.7730 (tp30) cc_final: 0.7447 (tp30) REVERT: F 326 ASP cc_start: 0.8876 (m-30) cc_final: 0.8601 (m-30) REVERT: F 365 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7871 (mp10) REVERT: F 381 GLN cc_start: 0.8527 (tp40) cc_final: 0.8233 (mm-40) REVERT: F 438 LYS cc_start: 0.8637 (tttt) cc_final: 0.8273 (ttpp) REVERT: G 40 LYS cc_start: 0.8297 (mtpm) cc_final: 0.7863 (ttpp) REVERT: I 9 ARG cc_start: 0.8037 (mtt180) cc_final: 0.7714 (mtp180) REVERT: I 61 LEU cc_start: 0.8076 (tp) cc_final: 0.7844 (tt) REVERT: I 64 GLU cc_start: 0.8260 (tt0) cc_final: 0.7431 (mp0) REVERT: I 131 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8381 (pm20) REVERT: I 143 ILE cc_start: 0.7238 (pt) cc_final: 0.7038 (pp) REVERT: I 155 ARG cc_start: 0.7816 (ttt90) cc_final: 0.7298 (tpt-90) REVERT: I 169 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7392 (mm) REVERT: b2 21 LEU cc_start: 0.4204 (OUTLIER) cc_final: 0.3913 (mm) REVERT: b2 26 ARG cc_start: 0.7621 (ttp80) cc_final: 0.7382 (ttp-110) REVERT: b2 31 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7869 (mm110) REVERT: b1 27 LYS cc_start: 0.8715 (tptt) cc_final: 0.8509 (tptp) REVERT: b1 40 ARG cc_start: 0.5185 (ttt90) cc_final: 0.4859 (ptt180) REVERT: a 160 PHE cc_start: 0.8568 (m-80) cc_final: 0.8102 (m-80) REVERT: c1 58 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6657 (tt) REVERT: c2 48 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7515 (tpt) REVERT: c6 6 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7398 (mt) REVERT: c6 48 MET cc_start: 0.6699 (ttm) cc_final: 0.6394 (ttt) REVERT: c9 40 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7947 (pp) REVERT: c9 67 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8464 (m-10) outliers start: 119 outliers final: 54 residues processed: 581 average time/residue: 0.6756 time to fit residues: 475.6331 Evaluate side-chains 540 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 467 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain b2 residue 21 LEU Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 39 GLN Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 23 ILE Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c1 residue 58 LEU Chi-restraints excluded: chain c2 residue 48 MET Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c6 residue 6 LEU Chi-restraints excluded: chain c7 residue 10 ILE Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 67 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 28 optimal weight: 0.5980 chunk 349 optimal weight: 50.0000 chunk 45 optimal weight: 4.9990 chunk 364 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 414 optimal weight: 7.9990 chunk 296 optimal weight: 0.8980 chunk 360 optimal weight: 50.0000 chunk 375 optimal weight: 8.9990 chunk 269 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 GLN B 172 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN F 28 ASN F 177 GLN F 330 ASN G 38 ASN I 95 GLN c3 23 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.189818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134965 restraints weight = 37022.314| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.33 r_work: 0.3109 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35580 Z= 0.180 Angle : 0.632 9.854 48333 Z= 0.316 Chirality : 0.046 0.234 5788 Planarity : 0.005 0.057 6254 Dihedral : 5.046 60.523 5081 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 4.20 % Allowed : 15.57 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.70 (0.12), residues: 4648 helix: 1.42 (0.10), residues: 2533 sheet: -0.56 (0.21), residues: 563 loop : -0.64 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 89 TYR 0.021 0.001 TYR B 438 PHE 0.016 0.002 PHE C 494 TRP 0.007 0.001 TRPb2 30 HIS 0.010 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (35578) covalent geometry : angle 0.63206 / 0.32 (48333) hydrogen bonds : bond 0.04364 / 2.91 ( 2207) hydrogen bonds : angle 4.44447 / 3.15 ( 6477) Misc. bond : bond 0.00102 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 477 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR F 421 " (corrupted residue). Skipping it. 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 250 MET cc_start: 0.9105 (ttp) cc_final: 0.8855 (ttp) REVERT: A 385 ASP cc_start: 0.8101 (m-30) cc_final: 0.7816 (m-30) REVERT: A 430 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7788 (p) REVERT: A 458 LYS cc_start: 0.8482 (ttpp) cc_final: 0.8105 (tttp) REVERT: B 122 GLU cc_start: 0.7277 (pm20) cc_final: 0.6894 (mp0) REVERT: B 161 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8873 (mtt90) REVERT: B 214 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8536 (mtmm) REVERT: B 306 ASP cc_start: 0.8669 (m-30) cc_final: 0.8436 (m-30) REVERT: B 473 GLU cc_start: 0.7844 (tp30) cc_final: 0.7613 (mm-30) REVERT: C 62 MET cc_start: 0.8901 (ttt) cc_final: 0.8675 (ttm) REVERT: C 262 ASP cc_start: 0.8334 (m-30) cc_final: 0.8056 (m-30) REVERT: C 383 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8089 (ttp-110) REVERT: C 467 ASN cc_start: 0.7330 (m-40) cc_final: 0.6904 (m110) REVERT: C 469 GLN cc_start: 0.6824 (tm-30) cc_final: 0.6557 (tm-30) REVERT: D 85 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8640 (p) REVERT: D 131 GLU cc_start: 0.8529 (pt0) cc_final: 0.8251 (pm20) REVERT: D 254 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7942 (pp) REVERT: D 332 GLU cc_start: 0.8486 (tp30) cc_final: 0.8127 (mm-30) REVERT: D 381 GLN cc_start: 0.8670 (tt0) cc_final: 0.7502 (tp40) REVERT: E 39 GLU cc_start: 0.8230 (pm20) cc_final: 0.7950 (pm20) REVERT: E 52 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9050 (mt) REVERT: E 77 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8842 (mp) REVERT: E 90 VAL cc_start: 0.9121 (m) cc_final: 0.8834 (p) REVERT: E 256 ARG cc_start: 0.8531 (mmt90) cc_final: 0.7964 (mmp80) REVERT: E 332 GLU cc_start: 0.7853 (tp30) cc_final: 0.7564 (tp30) REVERT: E 407 GLN cc_start: 0.8512 (tt0) cc_final: 0.8263 (tt0) REVERT: F 35 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7090 (ttmt) REVERT: F 89 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: F 201 GLU cc_start: 0.7799 (tp30) cc_final: 0.7469 (tp30) REVERT: F 226 MET cc_start: 0.8935 (mtp) cc_final: 0.8655 (mtp) REVERT: F 365 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7854 (mp10) REVERT: F 381 GLN cc_start: 0.8614 (tp40) cc_final: 0.8349 (mm-40) REVERT: F 438 LYS cc_start: 0.8650 (tttt) cc_final: 0.8281 (ttpp) REVERT: F 460 GLU cc_start: 0.8481 (mp0) cc_final: 0.8203 (mp0) REVERT: G 40 LYS cc_start: 0.8366 (mtpm) cc_final: 0.7865 (ttpp) REVERT: G 98 LEU cc_start: 0.8283 (tp) cc_final: 0.8029 (tp) REVERT: I 9 ARG cc_start: 0.8119 (mtt180) cc_final: 0.7799 (mtp180) REVERT: I 83 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7875 (mtt180) REVERT: I 131 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8197 (pm20) REVERT: I 155 ARG cc_start: 0.7819 (ttt90) cc_final: 0.7300 (tpt-90) REVERT: b1 24 LEU cc_start: 0.9229 (mm) cc_final: 0.9019 (mm) REVERT: b1 40 ARG cc_start: 0.5154 (ttt90) cc_final: 0.4868 (ptt180) REVERT: a 157 ILE cc_start: 0.9176 (pp) cc_final: 0.8879 (pp) REVERT: a 160 PHE cc_start: 0.8584 (m-80) cc_final: 0.8117 (m-80) REVERT: c1 58 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6613 (tt) REVERT: c1 61 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7192 (pp) REVERT: c2 34 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7128 (mp) REVERT: c2 48 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7499 (tpt) REVERT: c6 6 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7276 (mt) REVERT: c6 48 MET cc_start: 0.6668 (ttm) cc_final: 0.6367 (ttt) REVERT: c9 67 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8571 (m-10) outliers start: 147 outliers final: 70 residues processed: 586 average time/residue: 0.6875 time to fit residues: 487.6852 Evaluate side-chains 548 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 461 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain I residue 83 ARG Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 25 LEU Chi-restraints excluded: chain b1 residue 39 GLN Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c1 residue 58 LEU Chi-restraints excluded: chain c1 residue 61 ILE Chi-restraints excluded: chain c2 residue 34 ILE Chi-restraints excluded: chain c2 residue 48 MET Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c6 residue 6 LEU Chi-restraints excluded: chain c7 residue 10 ILE Chi-restraints excluded: chain c9 residue 6 LEU Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 67 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 232 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 376 optimal weight: 40.0000 chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 303 optimal weight: 20.0000 chunk 366 optimal weight: 20.0000 chunk 429 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 141 optimal weight: 0.0270 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN F 28 ASN F 177 GLN F 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.187575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.128967 restraints weight = 37045.217| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.67 r_work: 0.3119 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 35580 Z= 0.219 Angle : 0.662 11.558 48333 Z= 0.332 Chirality : 0.047 0.243 5788 Planarity : 0.005 0.060 6254 Dihedral : 5.140 60.597 5081 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.67 % Rotamer: Outliers : 3.77 % Allowed : 16.31 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.66 (0.12), residues: 4648 helix: 1.39 (0.10), residues: 2530 sheet: -0.65 (0.22), residues: 538 loop : -0.63 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 104 TYR 0.021 0.002 TYR B 438 PHE 0.023 0.002 PHE a 31 TRP 0.015 0.001 TRP a 206 HIS 0.010 0.002 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 (35578) covalent geometry : angle 0.66151 / 0.33 (48333) hydrogen bonds : bond 0.04487 / 2.99 ( 2207) hydrogen bonds : angle 4.48776 / 3.18 ( 6477) Misc. bond : bond 0.00119 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 464 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR F 421 " (corrupted residue). Skipping it. 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 250 MET cc_start: 0.9115 (ttp) cc_final: 0.8907 (ttp) REVERT: A 385 ASP cc_start: 0.8085 (m-30) cc_final: 0.7787 (m-30) REVERT: A 392 LEU cc_start: 0.7987 (mt) cc_final: 0.7748 (mt) REVERT: A 430 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7775 (p) REVERT: A 458 LYS cc_start: 0.8506 (ttpp) cc_final: 0.8122 (tttp) REVERT: B 122 GLU cc_start: 0.7162 (pm20) cc_final: 0.6836 (mp0) REVERT: B 161 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8847 (mtt90) REVERT: B 214 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8438 (mtmm) REVERT: B 306 ASP cc_start: 0.8571 (m-30) cc_final: 0.8347 (m-30) REVERT: B 473 GLU cc_start: 0.7752 (tp30) cc_final: 0.7497 (mm-30) REVERT: C 62 MET cc_start: 0.8882 (ttt) cc_final: 0.8661 (ttm) REVERT: C 262 ASP cc_start: 0.8309 (m-30) cc_final: 0.8015 (m-30) REVERT: C 383 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8129 (ttp-110) REVERT: C 467 ASN cc_start: 0.7402 (m-40) cc_final: 0.6970 (m110) REVERT: C 469 GLN cc_start: 0.6843 (tm-30) cc_final: 0.6570 (tm-30) REVERT: D 85 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8593 (p) REVERT: D 131 GLU cc_start: 0.8494 (pt0) cc_final: 0.8237 (pm20) REVERT: D 254 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8116 (pp) REVERT: D 381 GLN cc_start: 0.8638 (tt0) cc_final: 0.7494 (tp40) REVERT: D 391 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7784 (mt-10) REVERT: D 420 PHE cc_start: 0.8701 (m-10) cc_final: 0.8437 (m-10) REVERT: D 432 GLU cc_start: 0.8400 (mp0) cc_final: 0.7998 (mp0) REVERT: E 39 GLU cc_start: 0.8161 (pm20) cc_final: 0.7879 (pm20) REVERT: E 52 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8980 (mt) REVERT: E 64 MET cc_start: 0.9327 (mmt) cc_final: 0.9002 (mmm) REVERT: E 77 ILE cc_start: 0.9117 (pt) cc_final: 0.8857 (mp) REVERT: E 90 VAL cc_start: 0.9115 (m) cc_final: 0.8862 (p) REVERT: E 332 GLU cc_start: 0.7801 (tp30) cc_final: 0.7518 (tp30) REVERT: F 35 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7052 (ttmt) REVERT: F 89 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: F 108 ASP cc_start: 0.8170 (t0) cc_final: 0.7876 (m-30) REVERT: F 201 GLU cc_start: 0.7796 (tp30) cc_final: 0.7452 (tp30) REVERT: F 365 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7770 (mp10) REVERT: F 381 GLN cc_start: 0.8496 (tp40) cc_final: 0.8229 (mm-40) REVERT: F 438 LYS cc_start: 0.8662 (tttt) cc_final: 0.8269 (ttpp) REVERT: G 40 LYS cc_start: 0.8355 (mtpm) cc_final: 0.7868 (ttpp) REVERT: G 98 LEU cc_start: 0.8354 (tp) cc_final: 0.8072 (tp) REVERT: G 100 TYR cc_start: 0.8328 (t80) cc_final: 0.8054 (t80) REVERT: G 137 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7246 (tt) REVERT: G 189 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8177 (pp) REVERT: I 9 ARG cc_start: 0.8153 (mtt180) cc_final: 0.7827 (mtp180) REVERT: I 64 GLU cc_start: 0.8201 (tt0) cc_final: 0.7468 (mp0) REVERT: I 131 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8194 (mp10) REVERT: I 155 ARG cc_start: 0.7831 (ttt90) cc_final: 0.7290 (tpt-90) REVERT: b2 21 LEU cc_start: 0.4087 (OUTLIER) cc_final: 0.3617 (mm) REVERT: b2 26 ARG cc_start: 0.7619 (ptm160) cc_final: 0.7418 (ttp-110) REVERT: b1 24 LEU cc_start: 0.9274 (mm) cc_final: 0.9068 (mm) REVERT: b1 40 ARG cc_start: 0.5126 (ttt90) cc_final: 0.4897 (ptt180) REVERT: a 84 MET cc_start: 0.7931 (mmm) cc_final: 0.7635 (mmm) REVERT: a 157 ILE cc_start: 0.9225 (pp) cc_final: 0.9021 (pp) REVERT: a 160 PHE cc_start: 0.8662 (m-80) cc_final: 0.8201 (m-80) REVERT: c1 58 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6650 (tt) REVERT: c2 34 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7195 (mp) REVERT: c2 48 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7720 (tpt) REVERT: c6 6 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7286 (tp) REVERT: c9 67 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8625 (m-10) outliers start: 132 outliers final: 74 residues processed: 562 average time/residue: 0.6785 time to fit residues: 458.2701 Evaluate side-chains 534 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 443 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain b2 residue 21 LEU Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 25 LEU Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 225 THR Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c1 residue 58 LEU Chi-restraints excluded: chain c2 residue 34 ILE Chi-restraints excluded: chain c2 residue 48 MET Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c6 residue 6 LEU Chi-restraints excluded: chain c7 residue 10 ILE Chi-restraints excluded: chain c9 residue 6 LEU Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 67 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 198 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 252 optimal weight: 0.5980 chunk 433 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 390 optimal weight: 40.0000 chunk 449 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 412 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 GLN B 172 GLN E 259 GLN F 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.181735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.121531 restraints weight = 36912.837| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.62 r_work: 0.2858 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35580 Z= 0.179 Angle : 0.632 12.099 48333 Z= 0.315 Chirality : 0.046 0.207 5788 Planarity : 0.005 0.056 6254 Dihedral : 5.033 59.989 5081 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.21 % Favored : 96.75 % Rotamer: Outliers : 3.66 % Allowed : 16.71 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.78 (0.12), residues: 4648 helix: 1.49 (0.10), residues: 2530 sheet: -0.58 (0.21), residues: 556 loop : -0.59 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 104 TYR 0.021 0.001 TYR B 438 PHE 0.025 0.001 PHE a 31 TRP 0.009 0.001 TRP a 206 HIS 0.008 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (35578) covalent geometry : angle 0.63179 / 0.32 (48333) hydrogen bonds : bond 0.04253 / 2.83 ( 2207) hydrogen bonds : angle 4.43818 / 3.14 ( 6477) Misc. bond : bond 0.00101 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 457 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR F 421 " (corrupted residue). Skipping it. 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 4 ARG cc_start: 0.8088 (mtt90) cc_final: 0.7869 (mtt90) REVERT: A 250 MET cc_start: 0.9148 (ttp) cc_final: 0.8916 (ttp) REVERT: A 385 ASP cc_start: 0.8037 (m-30) cc_final: 0.7704 (m-30) REVERT: A 430 VAL cc_start: 0.7894 (OUTLIER) cc_final: 0.7692 (p) REVERT: A 458 LYS cc_start: 0.8311 (ttpp) cc_final: 0.7930 (tttp) REVERT: B 28 VAL cc_start: 0.8786 (t) cc_final: 0.8485 (p) REVERT: B 122 GLU cc_start: 0.7056 (pm20) cc_final: 0.6738 (mp0) REVERT: B 161 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8903 (mtt90) REVERT: B 214 LYS cc_start: 0.8697 (mtmt) cc_final: 0.8397 (mtmm) REVERT: B 306 ASP cc_start: 0.8601 (m-30) cc_final: 0.8350 (m-30) REVERT: B 446 ASP cc_start: 0.7720 (m-30) cc_final: 0.7495 (m-30) REVERT: B 473 GLU cc_start: 0.7756 (tp30) cc_final: 0.7443 (mm-30) REVERT: C 62 MET cc_start: 0.8818 (ttt) cc_final: 0.8581 (ttm) REVERT: C 262 ASP cc_start: 0.8225 (m-30) cc_final: 0.7909 (m-30) REVERT: C 383 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.8021 (ttp-110) REVERT: C 469 GLN cc_start: 0.6729 (tm-30) cc_final: 0.6417 (tm-30) REVERT: C 484 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7584 (mt-10) REVERT: D 3 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7583 (ttm170) REVERT: D 85 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8488 (p) REVERT: D 131 GLU cc_start: 0.8576 (pt0) cc_final: 0.8165 (pm20) REVERT: D 254 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7956 (pp) REVERT: D 381 GLN cc_start: 0.8432 (tt0) cc_final: 0.7214 (tp40) REVERT: D 391 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7729 (mt-10) REVERT: E 5 ARG cc_start: 0.8367 (ppt170) cc_final: 0.8104 (ppt170) REVERT: E 39 GLU cc_start: 0.8043 (pm20) cc_final: 0.7734 (pm20) REVERT: E 52 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8984 (mt) REVERT: E 64 MET cc_start: 0.9343 (mmt) cc_final: 0.9056 (mmm) REVERT: E 77 ILE cc_start: 0.9126 (pt) cc_final: 0.8722 (mp) REVERT: E 90 VAL cc_start: 0.9057 (m) cc_final: 0.8808 (p) REVERT: E 167 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8544 (tp) REVERT: F 35 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.6897 (ttmt) REVERT: F 201 GLU cc_start: 0.7610 (tp30) cc_final: 0.7206 (tp30) REVERT: F 365 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7598 (mp10) REVERT: F 381 GLN cc_start: 0.8320 (tp40) cc_final: 0.8045 (mm-40) REVERT: F 438 LYS cc_start: 0.8445 (tttt) cc_final: 0.7959 (ttpp) REVERT: F 460 GLU cc_start: 0.8535 (mp0) cc_final: 0.8260 (mp0) REVERT: G 40 LYS cc_start: 0.8310 (mtpm) cc_final: 0.7703 (ttpp) REVERT: G 98 LEU cc_start: 0.8100 (tp) cc_final: 0.7805 (tp) REVERT: G 189 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7879 (pp) REVERT: I 131 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8057 (pm20) REVERT: I 155 ARG cc_start: 0.7653 (ttt90) cc_final: 0.7106 (tpt-90) REVERT: b2 17 MET cc_start: 0.4124 (pp-130) cc_final: 0.3799 (ppp) REVERT: b1 24 LEU cc_start: 0.9231 (mm) cc_final: 0.9026 (mm) REVERT: a 84 MET cc_start: 0.8022 (mmm) cc_final: 0.7757 (mmm) REVERT: a 119 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7799 (mp) REVERT: a 157 ILE cc_start: 0.9209 (pp) cc_final: 0.9002 (pp) REVERT: a 160 PHE cc_start: 0.8638 (m-80) cc_final: 0.8179 (m-80) REVERT: c1 58 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6711 (tt) REVERT: c2 30 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7927 (t) REVERT: c2 34 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7022 (mp) REVERT: c2 48 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7578 (tpt) REVERT: c7 10 ILE cc_start: 0.4110 (OUTLIER) cc_final: 0.3874 (tt) REVERT: c9 67 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8576 (m-10) outliers start: 128 outliers final: 69 residues processed: 557 average time/residue: 0.6891 time to fit residues: 464.2647 Evaluate side-chains 530 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 444 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain b2 residue 31 GLN Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 25 LEU Chi-restraints excluded: chain b1 residue 39 GLN Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 119 LEU Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c1 residue 58 LEU Chi-restraints excluded: chain c2 residue 30 THR Chi-restraints excluded: chain c2 residue 34 ILE Chi-restraints excluded: chain c2 residue 48 MET Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c7 residue 10 ILE Chi-restraints excluded: chain c7 residue 43 VAL Chi-restraints excluded: chain c9 residue 6 LEU Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 67 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 165 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 414 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 416 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 417 optimal weight: 30.0000 chunk 393 optimal weight: 8.9990 chunk 362 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS B 172 GLN E 259 GLN E 289 GLN F 177 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.183148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.123362 restraints weight = 36901.609| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.61 r_work: 0.2895 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35580 Z= 0.143 Angle : 0.616 10.341 48333 Z= 0.307 Chirality : 0.045 0.226 5788 Planarity : 0.005 0.087 6254 Dihedral : 4.906 59.284 5081 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 2.91 % Allowed : 18.00 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.93 (0.12), residues: 4648 helix: 1.61 (0.10), residues: 2538 sheet: -0.54 (0.21), residues: 557 loop : -0.51 (0.16), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGb2 26 TYR 0.019 0.001 TYR B 438 PHE 0.027 0.001 PHE a 31 TRP 0.010 0.001 TRPb2 30 HIS 0.006 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (35578) covalent geometry : angle 0.61626 / 0.31 (48333) hydrogen bonds : bond 0.04046 / 2.69 ( 2207) hydrogen bonds : angle 4.36150 / 3.09 ( 6477) Misc. bond : bond 0.00070 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 466 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR F 421 " (corrupted residue). Skipping it. 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 4 ARG cc_start: 0.8069 (mtt90) cc_final: 0.7807 (mtt90) REVERT: A 250 MET cc_start: 0.9120 (ttp) cc_final: 0.8842 (ttp) REVERT: A 385 ASP cc_start: 0.8017 (m-30) cc_final: 0.7725 (m-30) REVERT: A 430 VAL cc_start: 0.7928 (OUTLIER) cc_final: 0.7715 (p) REVERT: A 458 LYS cc_start: 0.8309 (ttpp) cc_final: 0.7921 (tttp) REVERT: B 28 VAL cc_start: 0.8767 (t) cc_final: 0.8464 (p) REVERT: B 122 GLU cc_start: 0.7090 (pm20) cc_final: 0.6816 (mp0) REVERT: B 161 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8855 (mtt90) REVERT: B 214 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8382 (mtmm) REVERT: B 289 ASP cc_start: 0.7848 (t70) cc_final: 0.7542 (t0) REVERT: B 306 ASP cc_start: 0.8631 (m-30) cc_final: 0.8400 (m-30) REVERT: B 473 GLU cc_start: 0.7627 (tp30) cc_final: 0.7344 (mm-30) REVERT: B 483 ASN cc_start: 0.7896 (m110) cc_final: 0.7344 (t0) REVERT: C 62 MET cc_start: 0.8780 (ttt) cc_final: 0.8553 (ttm) REVERT: C 262 ASP cc_start: 0.8127 (m-30) cc_final: 0.7804 (m-30) REVERT: C 383 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7986 (ttp-110) REVERT: C 469 GLN cc_start: 0.6652 (tm-30) cc_final: 0.6354 (tm-30) REVERT: C 484 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7594 (mt-10) REVERT: D 85 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8477 (p) REVERT: D 131 GLU cc_start: 0.8579 (pt0) cc_final: 0.8181 (pm20) REVERT: D 254 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7827 (pp) REVERT: D 381 GLN cc_start: 0.8427 (tt0) cc_final: 0.7205 (tp40) REVERT: D 391 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7707 (mt-10) REVERT: D 420 PHE cc_start: 0.8641 (m-10) cc_final: 0.8433 (m-10) REVERT: E 39 GLU cc_start: 0.8078 (pm20) cc_final: 0.7770 (pm20) REVERT: E 64 MET cc_start: 0.9320 (mmt) cc_final: 0.9062 (mmm) REVERT: E 77 ILE cc_start: 0.9123 (pt) cc_final: 0.8719 (mp) REVERT: E 90 VAL cc_start: 0.9074 (m) cc_final: 0.8825 (p) REVERT: E 167 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8547 (tp) REVERT: F 35 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.6887 (ttmt) REVERT: F 201 GLU cc_start: 0.7559 (tp30) cc_final: 0.7199 (tp30) REVERT: F 381 GLN cc_start: 0.8291 (tp40) cc_final: 0.8018 (mm-40) REVERT: F 438 LYS cc_start: 0.8441 (tttt) cc_final: 0.7952 (ttpp) REVERT: F 460 GLU cc_start: 0.8435 (mp0) cc_final: 0.8063 (mp0) REVERT: G 40 LYS cc_start: 0.8297 (mtpm) cc_final: 0.7685 (ttpp) REVERT: G 49 ILE cc_start: 0.7423 (tp) cc_final: 0.7162 (tt) REVERT: G 98 LEU cc_start: 0.8063 (tp) cc_final: 0.7763 (tp) REVERT: I 64 GLU cc_start: 0.8155 (tt0) cc_final: 0.7394 (mp0) REVERT: I 131 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8096 (pm20) REVERT: I 155 ARG cc_start: 0.7587 (ttt90) cc_final: 0.7111 (tpt-90) REVERT: b2 31 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8021 (mm-40) REVERT: a 91 MET cc_start: 0.6516 (mtm) cc_final: 0.6281 (pmm) REVERT: a 119 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7566 (mp) REVERT: a 157 ILE cc_start: 0.9216 (pp) cc_final: 0.8869 (pp) REVERT: a 160 PHE cc_start: 0.8653 (m-80) cc_final: 0.8219 (m-80) REVERT: c1 58 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6716 (tt) REVERT: c2 34 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7031 (mp) REVERT: c8 50 ILE cc_start: 0.5945 (OUTLIER) cc_final: 0.5580 (tp) REVERT: c9 67 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8569 (m-10) outliers start: 102 outliers final: 63 residues processed: 540 average time/residue: 0.6945 time to fit residues: 450.5737 Evaluate side-chains 526 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 451 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain b2 residue 19 ILE Chi-restraints excluded: chain b2 residue 36 ILE Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 25 LEU Chi-restraints excluded: chain b1 residue 39 GLN Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 119 LEU Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c1 residue 58 LEU Chi-restraints excluded: chain c2 residue 34 ILE Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c7 residue 43 VAL Chi-restraints excluded: chain c8 residue 50 ILE Chi-restraints excluded: chain c9 residue 6 LEU Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 67 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 362 optimal weight: 30.0000 chunk 159 optimal weight: 0.9980 chunk 147 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 379 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 407 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN A 422 GLN A 426 GLN B 172 GLN F 34 HIS F 177 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.183636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124017 restraints weight = 36767.845| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.61 r_work: 0.2918 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35580 Z= 0.141 Angle : 0.622 15.845 48333 Z= 0.308 Chirality : 0.045 0.224 5788 Planarity : 0.004 0.085 6254 Dihedral : 4.853 59.046 5081 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.90 % Rotamer: Outliers : 2.60 % Allowed : 18.69 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.04 (0.12), residues: 4648 helix: 1.68 (0.10), residues: 2545 sheet: -0.47 (0.21), residues: 546 loop : -0.46 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 104 TYR 0.020 0.001 TYR C 438 PHE 0.022 0.001 PHE a 31 TRP 0.011 0.001 TRPb2 30 HIS 0.006 0.001 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (35578) covalent geometry : angle 0.62165 / 0.31 (48333) hydrogen bonds : bond 0.03991 / 2.66 ( 2207) hydrogen bonds : angle 4.32768 / 3.06 ( 6477) Misc. bond : bond 0.00065 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 458 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR F 421 " (corrupted residue). Skipping it. 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 250 MET cc_start: 0.9094 (ttp) cc_final: 0.8831 (ttp) REVERT: A 339 ASP cc_start: 0.8485 (m-30) cc_final: 0.8262 (m-30) REVERT: A 385 ASP cc_start: 0.8014 (m-30) cc_final: 0.7722 (m-30) REVERT: A 458 LYS cc_start: 0.8307 (ttpp) cc_final: 0.7927 (tttp) REVERT: B 28 VAL cc_start: 0.8723 (t) cc_final: 0.8392 (p) REVERT: B 122 GLU cc_start: 0.7173 (pm20) cc_final: 0.6928 (mp0) REVERT: B 161 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8851 (mtt90) REVERT: B 289 ASP cc_start: 0.7839 (t70) cc_final: 0.7533 (t0) REVERT: B 306 ASP cc_start: 0.8623 (m-30) cc_final: 0.8387 (m-30) REVERT: B 473 GLU cc_start: 0.7712 (tp30) cc_final: 0.7428 (mm-30) REVERT: B 483 ASN cc_start: 0.7843 (m110) cc_final: 0.7290 (t0) REVERT: C 62 MET cc_start: 0.8816 (ttt) cc_final: 0.8559 (ttm) REVERT: C 383 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7984 (ttp-110) REVERT: C 469 GLN cc_start: 0.6603 (tm-30) cc_final: 0.6299 (tm-30) REVERT: C 484 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7571 (mt-10) REVERT: D 85 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8493 (p) REVERT: D 131 GLU cc_start: 0.8566 (pt0) cc_final: 0.8136 (pm20) REVERT: D 254 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7814 (pp) REVERT: D 332 GLU cc_start: 0.8317 (tp30) cc_final: 0.7914 (mm-30) REVERT: D 381 GLN cc_start: 0.8402 (tt0) cc_final: 0.7195 (tp40) REVERT: D 391 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7699 (mt-10) REVERT: D 420 PHE cc_start: 0.8688 (m-10) cc_final: 0.8470 (m-10) REVERT: E 39 GLU cc_start: 0.8068 (pm20) cc_final: 0.7721 (pm20) REVERT: E 64 MET cc_start: 0.9307 (mmt) cc_final: 0.9058 (mmm) REVERT: E 77 ILE cc_start: 0.9121 (pt) cc_final: 0.8698 (mp) REVERT: E 90 VAL cc_start: 0.9071 (m) cc_final: 0.8827 (p) REVERT: E 167 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8564 (tp) REVERT: F 201 GLU cc_start: 0.7561 (tp30) cc_final: 0.7204 (tp30) REVERT: F 381 GLN cc_start: 0.8303 (tp40) cc_final: 0.8033 (mm-40) REVERT: F 438 LYS cc_start: 0.8434 (tttt) cc_final: 0.7939 (ttpp) REVERT: G 40 LYS cc_start: 0.8299 (mtpm) cc_final: 0.7699 (ttpp) REVERT: G 49 ILE cc_start: 0.7488 (tp) cc_final: 0.7218 (tt) REVERT: G 98 LEU cc_start: 0.8043 (tp) cc_final: 0.7763 (tp) REVERT: I 64 GLU cc_start: 0.8166 (tt0) cc_final: 0.7429 (mp0) REVERT: I 131 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8097 (pm20) REVERT: I 155 ARG cc_start: 0.7624 (ttt90) cc_final: 0.7211 (tpt-90) REVERT: b2 26 ARG cc_start: 0.7765 (ptm-80) cc_final: 0.7215 (ttp-110) REVERT: b2 27 LYS cc_start: 0.8624 (tptm) cc_final: 0.8163 (mmpt) REVERT: b2 31 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7902 (mm110) REVERT: a 91 MET cc_start: 0.6444 (mtm) cc_final: 0.6163 (pmm) REVERT: a 119 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7433 (mp) REVERT: a 157 ILE cc_start: 0.9225 (pp) cc_final: 0.8882 (pp) REVERT: a 160 PHE cc_start: 0.8607 (m-80) cc_final: 0.8161 (m-80) REVERT: c1 58 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6702 (tt) REVERT: c2 34 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7046 (mp) REVERT: c9 67 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8530 (m-10) outliers start: 91 outliers final: 64 residues processed: 527 average time/residue: 0.7045 time to fit residues: 448.1600 Evaluate side-chains 511 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 438 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 39 GLN Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 119 LEU Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c1 residue 58 LEU Chi-restraints excluded: chain c2 residue 34 ILE Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c7 residue 43 VAL Chi-restraints excluded: chain c9 residue 6 LEU Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 67 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 333 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 220 optimal weight: 4.9990 chunk 389 optimal weight: 8.9990 chunk 237 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 254 optimal weight: 0.0170 chunk 146 optimal weight: 0.9980 chunk 448 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 GLN B 172 GLN F 177 GLN a 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.183642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.123974 restraints weight = 36699.587| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.59 r_work: 0.3037 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35580 Z= 0.143 Angle : 0.629 16.337 48333 Z= 0.311 Chirality : 0.045 0.254 5788 Planarity : 0.004 0.074 6254 Dihedral : 4.845 59.898 5081 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 2.37 % Allowed : 19.14 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.10 (0.12), residues: 4648 helix: 1.73 (0.10), residues: 2545 sheet: -0.46 (0.21), residues: 547 loop : -0.42 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 186 TYR 0.019 0.001 TYR E 427 PHE 0.022 0.001 PHE a 31 TRP 0.019 0.001 TRP a 206 HIS 0.006 0.001 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (35578) covalent geometry : angle 0.62875 / 0.31 (48333) hydrogen bonds : bond 0.03984 / 2.66 ( 2207) hydrogen bonds : angle 4.30866 / 3.05 ( 6477) Misc. bond : bond 0.00066 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 451 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR F 421 " (corrupted residue). Skipping it. 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 250 MET cc_start: 0.9078 (ttp) cc_final: 0.8793 (ttp) REVERT: A 278 ARG cc_start: 0.8538 (mtp85) cc_final: 0.8307 (mtp85) REVERT: A 339 ASP cc_start: 0.8444 (m-30) cc_final: 0.8239 (m-30) REVERT: A 385 ASP cc_start: 0.7913 (m-30) cc_final: 0.7648 (m-30) REVERT: A 402 LEU cc_start: 0.7072 (mp) cc_final: 0.6700 (tt) REVERT: A 458 LYS cc_start: 0.8326 (ttpp) cc_final: 0.7941 (tttp) REVERT: B 28 VAL cc_start: 0.8760 (t) cc_final: 0.8445 (p) REVERT: B 122 GLU cc_start: 0.7216 (pm20) cc_final: 0.6883 (mp0) REVERT: B 161 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8840 (mtt90) REVERT: B 289 ASP cc_start: 0.7889 (t70) cc_final: 0.7585 (t0) REVERT: B 306 ASP cc_start: 0.8579 (m-30) cc_final: 0.8340 (m-30) REVERT: B 350 PHE cc_start: 0.7657 (m-10) cc_final: 0.7128 (t80) REVERT: B 473 GLU cc_start: 0.7743 (tp30) cc_final: 0.7464 (mm-30) REVERT: B 483 ASN cc_start: 0.7845 (m110) cc_final: 0.7325 (t0) REVERT: C 62 MET cc_start: 0.8842 (ttt) cc_final: 0.8603 (ttm) REVERT: C 113 GLN cc_start: 0.8485 (mp10) cc_final: 0.8026 (mt0) REVERT: C 383 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7991 (ttp-110) REVERT: C 469 GLN cc_start: 0.6623 (tm-30) cc_final: 0.6335 (tm-30) REVERT: C 484 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7567 (mt-10) REVERT: D 85 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8501 (p) REVERT: D 131 GLU cc_start: 0.8479 (pt0) cc_final: 0.8077 (pm20) REVERT: D 254 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7795 (pp) REVERT: D 332 GLU cc_start: 0.8334 (tp30) cc_final: 0.7928 (mm-30) REVERT: D 381 GLN cc_start: 0.8459 (tt0) cc_final: 0.7245 (tp40) REVERT: D 391 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7739 (mt-10) REVERT: D 420 PHE cc_start: 0.8730 (m-10) cc_final: 0.8459 (m-10) REVERT: E 39 GLU cc_start: 0.8091 (pm20) cc_final: 0.7810 (pm20) REVERT: E 64 MET cc_start: 0.9296 (mmt) cc_final: 0.9044 (mmm) REVERT: E 77 ILE cc_start: 0.9138 (pt) cc_final: 0.8726 (mp) REVERT: E 90 VAL cc_start: 0.9084 (m) cc_final: 0.8855 (p) REVERT: E 167 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8563 (tp) REVERT: F 381 GLN cc_start: 0.8250 (tp40) cc_final: 0.7965 (mm-40) REVERT: F 438 LYS cc_start: 0.8457 (tttt) cc_final: 0.7962 (ttpp) REVERT: G 40 LYS cc_start: 0.8248 (mtpm) cc_final: 0.7682 (ttpp) REVERT: G 49 ILE cc_start: 0.7550 (tp) cc_final: 0.7280 (tt) REVERT: G 127 ARG cc_start: 0.8085 (mpt-90) cc_final: 0.7832 (mpt-90) REVERT: I 64 GLU cc_start: 0.8214 (tt0) cc_final: 0.7479 (mp0) REVERT: I 131 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8083 (pm20) REVERT: I 155 ARG cc_start: 0.7650 (ttt90) cc_final: 0.7265 (tpt-90) REVERT: I 169 LEU cc_start: 0.7138 (mm) cc_final: 0.6937 (mm) REVERT: b2 26 ARG cc_start: 0.7774 (ptm-80) cc_final: 0.7157 (ttp-110) REVERT: b2 27 LYS cc_start: 0.8638 (tptm) cc_final: 0.8166 (mmpt) REVERT: b2 31 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7952 (mm110) REVERT: a 91 MET cc_start: 0.6492 (mtm) cc_final: 0.6246 (pmm) REVERT: a 119 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7458 (mp) REVERT: a 157 ILE cc_start: 0.9210 (pp) cc_final: 0.8869 (pp) REVERT: a 160 PHE cc_start: 0.8598 (m-80) cc_final: 0.8139 (m-80) REVERT: c1 58 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6743 (tt) REVERT: c2 34 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7082 (mp) REVERT: c9 67 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8508 (m-10) outliers start: 83 outliers final: 65 residues processed: 515 average time/residue: 0.6894 time to fit residues: 427.4158 Evaluate side-chains 514 residues out of total 3799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 440 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 39 GLN Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 119 LEU Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c1 residue 58 LEU Chi-restraints excluded: chain c2 residue 34 ILE Chi-restraints excluded: chain c4 residue 67 PHE Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c7 residue 43 VAL Chi-restraints excluded: chain c9 residue 6 LEU Chi-restraints excluded: chain c9 residue 40 LEU Chi-restraints excluded: chain c9 residue 67 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 260 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 163 optimal weight: 0.0870 chunk 456 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 85 optimal weight: 0.0370 chunk 162 optimal weight: 0.9990 chunk 406 optimal weight: 6.9990 chunk 422 optimal weight: 6.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 172 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.184865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.125536 restraints weight = 36685.235| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.57 r_work: 0.3060 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35580 Z= 0.128 Angle : 0.616 14.717 48333 Z= 0.304 Chirality : 0.044 0.204 5788 Planarity : 0.004 0.065 6254 Dihedral : 4.762 58.941 5081 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.12 % Favored : 96.86 % Rotamer: Outliers : 2.26 % Allowed : 19.51 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.21 (0.13), residues: 4648 helix: 1.84 (0.10), residues: 2528 sheet: -0.42 (0.22), residues: 548 loop : -0.40 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 186 TYR 0.023 0.001 TYR C 438 PHE 0.021 0.001 PHE a 31 TRP 0.011 0.001 TRP a 206 HIS 0.006 0.001 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (35578) covalent geometry : angle 0.61624 / 0.30 (48333) hydrogen bonds : bond 0.03861 / 2.57 ( 2207) hydrogen bonds : angle 4.25668 / 3.01 ( 6477) Misc. bond : bond 0.00054 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13688.72 seconds wall clock time: 233 minutes 24.03 seconds (14004.03 seconds total)