Starting phenix.real_space_refine on Sat Aug 8 22:51:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q3k_72200/08_2026/9q3k_72200.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q3k_72200/08_2026/9q3k_72200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q3k_72200/08_2026/9q3k_72200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q3k_72200/08_2026/9q3k_72200.map" model { file = "/net/cci-nas-00/data/ceres_data/9q3k_72200/08_2026/9q3k_72200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q3k_72200/08_2026/9q3k_72200.cif" } resolution = 2.2 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= 0.001 sd= 0.033 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 Ni 8 6.56 5 P 8 5.49 5 S 229 5.16 5 C 19331 2.51 5 N 5099 2.21 5 O 5657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30332 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3753 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 453} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ASP:plan': 1, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 3762 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 480, 3759 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 453} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 480, 3759 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 453} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3851 Chain: "A" Number of atoms: 3764 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 480, 3761 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 453} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 480, 3761 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 453} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 3854 Chain: "H" Number of atoms: 3772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3772 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 453} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "E" Number of atoms: 3772 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 480, 3769 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 453} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 480, 3769 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 453} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3862 Chain: "F" Number of atoms: 3772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3772 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 453} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "C" Number of atoms: 3764 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 480, 3761 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 453} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 480, 3761 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 453} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 3854 Chain: "G" Number of atoms: 3773 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 480, 3770 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 453} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Conformer: "B" Number of residues, atoms: 480, 3770 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 453} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 bond proxies already assigned to first conformer: 3863 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {' NI': 1, '4EY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {' NI': 1, '4EY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {' NI': 1, '4EY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {' NI': 1, '4EY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {' NI': 1, '4EY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {' NI': 1, '4EY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {' NI': 1, '4EY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {' NI': 1, '4EY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.98, per 1000 atoms: 0.36 Number of scatterers: 30332 At special positions: 0 Unit cell: (130.242, 130.242, 119.61, 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) Ni 8 28.00 S 229 16.00 P 8 15.00 O 5657 8.00 N 5099 7.00 C 19331 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 2.1 seconds 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7082 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 49 sheets defined 45.9% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'B' and resid 36 through 50 removed outlier: 4.536A pdb=" N GLU B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ALA B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 83 through 99 Processing helix chain 'B' and resid 119 through 136 Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.666A pdb=" N CYS B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE B 201 " --> pdb=" O CYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 209 removed outlier: 3.508A pdb=" N SER B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 228 through 246 Processing helix chain 'B' and resid 269 through 285 removed outlier: 4.655A pdb=" N LYS B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 329 Processing helix chain 'B' and resid 355 through 368 removed outlier: 4.619A pdb=" N GLU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 376 removed outlier: 4.287A pdb=" N GLN B 376 " --> pdb=" O ASP B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 383 Processing helix chain 'B' and resid 384 through 393 Processing helix chain 'B' and resid 398 through 416 removed outlier: 3.937A pdb=" N GLY B 402 " --> pdb=" O HIS B 398 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE B 403 " --> pdb=" O PRO B 399 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA B 412 " --> pdb=" O CYS B 408 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 433 removed outlier: 4.137A pdb=" N ALA B 430 " --> pdb=" O LYS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 452 Processing helix chain 'D' and resid 36 through 50 removed outlier: 4.197A pdb=" N GLU D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 83 through 99 Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 119 through 136 Proline residue: D 129 - end of helix Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.901A pdb=" N CYS D 197 " --> pdb=" O GLY D 193 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE D 201 " --> pdb=" O CYS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 211 removed outlier: 3.610A pdb=" N SER D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N HIS D 210 " --> pdb=" O SER D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 218 through 222 Processing helix chain 'D' and resid 228 through 246 Processing helix chain 'D' and resid 269 through 285 removed outlier: 4.389A pdb=" N LYS D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU D 280 " --> pdb=" O LYS D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 330 Processing helix chain 'D' and resid 355 through 367 removed outlier: 4.672A pdb=" N GLU D 359 " --> pdb=" O PRO D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 376 removed outlier: 4.271A pdb=" N GLN D 376 " --> pdb=" O ASP D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 383 Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 398 through 416 removed outlier: 3.930A pdb=" N GLY D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE D 403 " --> pdb=" O PRO D 399 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU D 411 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA D 412 " --> pdb=" O CYS D 408 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU D 413 " --> pdb=" O ALA D 409 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 433 removed outlier: 4.142A pdb=" N ALA D 430 " --> pdb=" O LYS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 452 Processing helix chain 'A' and resid 36 through 50 removed outlier: 4.226A pdb=" N GLU A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 119 through 136 Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.854A pdb=" N CYS A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 201 " --> pdb=" O CYS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 211 removed outlier: 4.137A pdb=" N HIS A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 228 through 246 Processing helix chain 'A' and resid 269 through 285 removed outlier: 4.553A pdb=" N LYS A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 330 Processing helix chain 'A' and resid 355 through 367 removed outlier: 4.629A pdb=" N GLU A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 4.277A pdb=" N GLN A 376 " --> pdb=" O ASP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 Processing helix chain 'A' and resid 384 through 393 Processing helix chain 'A' and resid 398 through 416 removed outlier: 3.932A pdb=" N GLY A 402 " --> pdb=" O HIS A 398 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A 403 " --> pdb=" O PRO A 399 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 412 " --> pdb=" O CYS A 408 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 433 removed outlier: 4.092A pdb=" N ALA A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'H' and resid 36 through 50 removed outlier: 4.334A pdb=" N GLU H 41 " --> pdb=" O GLU H 37 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ALA H 42 " --> pdb=" O ASP H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 61 Processing helix chain 'H' and resid 83 through 99 Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 119 through 136 Proline residue: H 129 - end of helix Processing helix chain 'H' and resid 148 through 150 No H-bonds generated for 'chain 'H' and resid 148 through 150' Processing helix chain 'H' and resid 168 through 173 Processing helix chain 'H' and resid 193 through 201 removed outlier: 3.770A pdb=" N CYS H 197 " --> pdb=" O GLY H 193 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE H 201 " --> pdb=" O CYS H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 208 Processing helix chain 'H' and resid 212 through 217 Processing helix chain 'H' and resid 228 through 246 Processing helix chain 'H' and resid 269 through 285 removed outlier: 4.283A pdb=" N LYS H 279 " --> pdb=" O LYS H 275 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU H 280 " --> pdb=" O LYS H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 330 Processing helix chain 'H' and resid 356 through 367 Processing helix chain 'H' and resid 370 through 376 removed outlier: 4.309A pdb=" N GLN H 376 " --> pdb=" O ASP H 373 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 383 Processing helix chain 'H' and resid 384 through 393 Processing helix chain 'H' and resid 398 through 415 removed outlier: 3.977A pdb=" N GLY H 402 " --> pdb=" O HIS H 398 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE H 403 " --> pdb=" O PRO H 399 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU H 411 " --> pdb=" O SER H 407 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA H 412 " --> pdb=" O CYS H 408 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU H 413 " --> pdb=" O ALA H 409 " (cutoff:3.500A) Processing helix chain 'H' and resid 426 through 433 removed outlier: 4.150A pdb=" N ALA H 430 " --> pdb=" O LYS H 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 452 Processing helix chain 'E' and resid 36 through 50 removed outlier: 4.349A pdb=" N GLU E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ALA E 42 " --> pdb=" O ASP E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 83 through 100 Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 119 through 128 Processing helix chain 'E' and resid 128 through 136 Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 168 through 173 Processing helix chain 'E' and resid 193 through 201 removed outlier: 3.845A pdb=" N CYS E 197 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE E 201 " --> pdb=" O CYS E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 208 Processing helix chain 'E' and resid 212 through 217 Processing helix chain 'E' and resid 228 through 246 Processing helix chain 'E' and resid 269 through 285 removed outlier: 4.426A pdb=" N LYS E 279 " --> pdb=" O LYS E 275 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU E 280 " --> pdb=" O LYS E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 330 Processing helix chain 'E' and resid 355 through 367 removed outlier: 4.696A pdb=" N GLU E 359 " --> pdb=" O PRO E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 376 removed outlier: 4.327A pdb=" N GLN E 376 " --> pdb=" O ASP E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 383 Processing helix chain 'E' and resid 384 through 393 Processing helix chain 'E' and resid 398 through 415 removed outlier: 3.999A pdb=" N GLY E 402 " --> pdb=" O HIS E 398 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE E 403 " --> pdb=" O PRO E 399 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU E 411 " --> pdb=" O SER E 407 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA E 412 " --> pdb=" O CYS E 408 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU E 413 " --> pdb=" O ALA E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 433 removed outlier: 4.141A pdb=" N ALA E 430 " --> pdb=" O LYS E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 452 Processing helix chain 'F' and resid 36 through 50 removed outlier: 4.332A pdb=" N GLU F 41 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA F 42 " --> pdb=" O ASP F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 83 through 100 Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 119 through 128 Processing helix chain 'F' and resid 128 through 136 Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 193 through 201 removed outlier: 3.715A pdb=" N CYS F 197 " --> pdb=" O GLY F 193 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE F 201 " --> pdb=" O CYS F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 208 Processing helix chain 'F' and resid 212 through 217 Processing helix chain 'F' and resid 228 through 246 Processing helix chain 'F' and resid 269 through 285 removed outlier: 4.083A pdb=" N LYS F 279 " --> pdb=" O LYS F 275 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA F 283 " --> pdb=" O LYS F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 330 Processing helix chain 'F' and resid 356 through 367 Processing helix chain 'F' and resid 370 through 376 removed outlier: 4.324A pdb=" N GLN F 376 " --> pdb=" O ASP F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 383 Processing helix chain 'F' and resid 384 through 394 Processing helix chain 'F' and resid 398 through 415 removed outlier: 3.994A pdb=" N GLY F 402 " --> pdb=" O HIS F 398 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE F 403 " --> pdb=" O PRO F 399 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU F 411 " --> pdb=" O SER F 407 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA F 412 " --> pdb=" O CYS F 408 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 433 removed outlier: 4.169A pdb=" N ALA F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 452 Processing helix chain 'C' and resid 36 through 50 removed outlier: 4.152A pdb=" N GLU C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA C 42 " --> pdb=" O ASP C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 83 through 99 Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 119 through 136 Proline residue: C 129 - end of helix Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.958A pdb=" N CYS C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE C 201 " --> pdb=" O CYS C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 212 through 217 Processing helix chain 'C' and resid 228 through 246 Processing helix chain 'C' and resid 269 through 285 removed outlier: 4.618A pdb=" N LYS C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU C 280 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 330 Processing helix chain 'C' and resid 355 through 368 removed outlier: 4.686A pdb=" N GLU C 359 " --> pdb=" O PRO C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 376 removed outlier: 4.246A pdb=" N GLN C 376 " --> pdb=" O ASP C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 383 Processing helix chain 'C' and resid 384 through 393 Processing helix chain 'C' and resid 398 through 416 removed outlier: 3.934A pdb=" N GLY C 402 " --> pdb=" O HIS C 398 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE C 403 " --> pdb=" O PRO C 399 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA C 412 " --> pdb=" O CYS C 408 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU C 413 " --> pdb=" O ALA C 409 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 433 removed outlier: 4.174A pdb=" N ALA C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 452 Processing helix chain 'G' and resid 36 through 50 removed outlier: 4.337A pdb=" N GLU G 41 " --> pdb=" O GLU G 37 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA G 42 " --> pdb=" O ASP G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 83 through 99 removed outlier: 3.518A pdb=" N VAL G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'G' and resid 119 through 136 Proline residue: G 129 - end of helix Processing helix chain 'G' and resid 148 through 150 No H-bonds generated for 'chain 'G' and resid 148 through 150' Processing helix chain 'G' and resid 168 through 173 Processing helix chain 'G' and resid 193 through 201 removed outlier: 3.914A pdb=" N CYS G 197 " --> pdb=" O GLY G 193 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE G 201 " --> pdb=" O CYS G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 208 Processing helix chain 'G' and resid 212 through 217 Processing helix chain 'G' and resid 228 through 246 Processing helix chain 'G' and resid 269 through 285 removed outlier: 4.081A pdb=" N LYS G 279 " --> pdb=" O LYS G 275 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU G 280 " --> pdb=" O LYS G 276 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA G 283 " --> pdb=" O LYS G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 330 Processing helix chain 'G' and resid 355 through 368 removed outlier: 4.714A pdb=" N GLU G 359 " --> pdb=" O PRO G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 376 removed outlier: 4.319A pdb=" N GLN G 376 " --> pdb=" O ASP G 373 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 383 Processing helix chain 'G' and resid 384 through 394 Processing helix chain 'G' and resid 398 through 415 removed outlier: 4.081A pdb=" N GLY G 402 " --> pdb=" O HIS G 398 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE G 403 " --> pdb=" O PRO G 399 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU G 411 " --> pdb=" O SER G 407 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA G 412 " --> pdb=" O CYS G 408 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU G 413 " --> pdb=" O ALA G 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 433 removed outlier: 4.151A pdb=" N ALA G 430 " --> pdb=" O LYS G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 452 Processing sheet with id=AA1, first strand: chain 'B' and resid 10 through 14 removed outlier: 12.901A pdb=" N ASP B 4 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE B 299 " --> pdb=" O ASP B 4 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLU B 6 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY B 300 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASP B 21 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 14 removed outlier: 12.901A pdb=" N ASP B 4 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE B 299 " --> pdb=" O ASP B 4 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLU B 6 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP B 295 " --> pdb=" O ASN B 336 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ALA B 418 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS B 337 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N TYR B 420 " --> pdb=" O CYS B 337 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE B 339 " --> pdb=" O TYR B 420 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL B 422 " --> pdb=" O PHE B 339 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N CYS B 341 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 141 through 143 removed outlier: 6.718A pdb=" N VAL B 67 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE B 109 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE B 69 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER B 111 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N PHE B 71 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR B 68 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 179 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL B 70 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N HIS B 181 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA B 176 " --> pdb=" O PHE B 250 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N CYS B 252 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU B 178 " --> pdb=" O CYS B 252 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ALA B 254 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY B 180 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU B 256 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR B 182 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU B 264 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 152 through 157 removed outlier: 6.084A pdb=" N VAL B 164 " --> pdb=" O LEU B 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 184 through 185 Processing sheet with id=AA6, first strand: chain 'B' and resid 286 through 290 removed outlier: 6.108A pdb=" N VAL B 287 " --> pdb=" O MET B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 14 removed outlier: 12.866A pdb=" N ASP D 4 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N PHE D 299 " --> pdb=" O ASP D 4 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLU D 6 " --> pdb=" O PHE D 299 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY D 300 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASP D 21 " --> pdb=" O ALA D 461 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 14 removed outlier: 12.866A pdb=" N ASP D 4 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N PHE D 299 " --> pdb=" O ASP D 4 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLU D 6 " --> pdb=" O PHE D 299 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP D 295 " --> pdb=" O ASN D 336 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ALA D 418 " --> pdb=" O ASP D 335 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N CYS D 337 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TYR D 420 " --> pdb=" O CYS D 337 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE D 339 " --> pdb=" O TYR D 420 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL D 422 " --> pdb=" O PHE D 339 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS D 341 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 141 through 143 removed outlier: 6.700A pdb=" N VAL D 67 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE D 109 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE D 69 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER D 111 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N PHE D 71 " --> pdb=" O SER D 111 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR D 68 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE D 179 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL D 70 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N HIS D 181 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ALA D 176 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N CYS D 252 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU D 178 " --> pdb=" O CYS D 252 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ALA D 254 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY D 180 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU D 256 " --> pdb=" O GLY D 180 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR D 182 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU D 264 " --> pdb=" O VAL D 255 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 157 removed outlier: 6.096A pdb=" N VAL D 164 " --> pdb=" O LEU D 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 184 through 185 Processing sheet with id=AB3, first strand: chain 'D' and resid 286 through 290 removed outlier: 6.122A pdb=" N VAL D 287 " --> pdb=" O MET D 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 10 through 14 removed outlier: 12.966A pdb=" N ASP A 4 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE A 299 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLU A 6 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY A 300 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP A 21 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 10 through 14 removed outlier: 12.966A pdb=" N ASP A 4 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE A 299 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLU A 6 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP A 295 " --> pdb=" O ASN A 336 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA A 418 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N CYS A 337 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N TYR A 420 " --> pdb=" O CYS A 337 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE A 339 " --> pdb=" O TYR A 420 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL A 422 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N CYS A 341 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 141 through 143 removed outlier: 6.735A pdb=" N VAL A 67 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE A 109 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE A 69 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER A 111 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N PHE A 71 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR A 68 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 179 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 70 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N HIS A 181 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA A 176 " --> pdb=" O PHE A 250 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N CYS A 252 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 178 " --> pdb=" O CYS A 252 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ALA A 254 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY A 180 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU A 256 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR A 182 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU A 264 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 152 through 157 removed outlier: 6.100A pdb=" N VAL A 164 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AB9, first strand: chain 'A' and resid 286 through 290 removed outlier: 6.161A pdb=" N VAL A 287 " --> pdb=" O MET A 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 14 removed outlier: 12.811A pdb=" N ASP H 4 " --> pdb=" O ILE H 297 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE H 299 " --> pdb=" O ASP H 4 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLU H 6 " --> pdb=" O PHE H 299 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY H 300 " --> pdb=" O LEU H 462 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP H 21 " --> pdb=" O ALA H 461 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 14 removed outlier: 12.811A pdb=" N ASP H 4 " --> pdb=" O ILE H 297 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE H 299 " --> pdb=" O ASP H 4 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLU H 6 " --> pdb=" O PHE H 299 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP H 295 " --> pdb=" O ASN H 336 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ALA H 418 " --> pdb=" O ASP H 335 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS H 337 " --> pdb=" O ALA H 418 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR H 420 " --> pdb=" O CYS H 337 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE H 339 " --> pdb=" O TYR H 420 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL H 422 " --> pdb=" O PHE H 339 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N CYS H 341 " --> pdb=" O VAL H 422 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 141 through 143 removed outlier: 6.747A pdb=" N VAL H 67 " --> pdb=" O LEU H 107 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE H 109 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE H 69 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA H 176 " --> pdb=" O PHE H 250 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N CYS H 252 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU H 178 " --> pdb=" O CYS H 252 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ALA H 254 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY H 180 " --> pdb=" O ALA H 254 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU H 256 " --> pdb=" O GLY H 180 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU H 264 " --> pdb=" O VAL H 255 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 152 through 157 removed outlier: 5.646A pdb=" N VAL H 164 " --> pdb=" O LEU H 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 184 through 185 Processing sheet with id=AC6, first strand: chain 'H' and resid 286 through 290 removed outlier: 6.273A pdb=" N VAL H 287 " --> pdb=" O MET H 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'E' and resid 21 through 22 removed outlier: 6.429A pdb=" N ASP E 21 " --> pdb=" O ALA E 461 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY E 300 " --> pdb=" O LEU E 462 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP E 295 " --> pdb=" O ASN E 336 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA E 418 " --> pdb=" O ASP E 335 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N CYS E 337 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N TYR E 420 " --> pdb=" O CYS E 337 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE E 339 " --> pdb=" O TYR E 420 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL E 422 " --> pdb=" O PHE E 339 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS E 341 " --> pdb=" O VAL E 422 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 25 through 26 removed outlier: 3.551A pdb=" N GLY E 26 " --> pdb=" O VAL E 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 141 through 143 removed outlier: 6.779A pdb=" N VAL E 67 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE E 109 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE E 69 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR E 68 " --> pdb=" O ILE E 177 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE E 179 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL E 70 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N HIS E 181 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA E 176 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N CYS E 252 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU E 178 " --> pdb=" O CYS E 252 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA E 254 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY E 180 " --> pdb=" O ALA E 254 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU E 256 " --> pdb=" O GLY E 180 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU E 264 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 152 through 157 removed outlier: 5.565A pdb=" N VAL E 164 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 184 through 185 Processing sheet with id=AD4, first strand: chain 'E' and resid 286 through 290 removed outlier: 6.237A pdb=" N VAL E 287 " --> pdb=" O MET E 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'F' and resid 21 through 22 removed outlier: 6.478A pdb=" N ASP F 21 " --> pdb=" O ALA F 461 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY F 300 " --> pdb=" O LEU F 462 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP F 295 " --> pdb=" O ASN F 336 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ALA F 418 " --> pdb=" O ASP F 335 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS F 337 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N TYR F 420 " --> pdb=" O CYS F 337 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE F 339 " --> pdb=" O TYR F 420 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL F 422 " --> pdb=" O PHE F 339 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS F 341 " --> pdb=" O VAL F 422 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 141 through 143 removed outlier: 6.797A pdb=" N VAL F 67 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE F 109 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE F 69 " --> pdb=" O ILE F 109 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR F 68 " --> pdb=" O ILE F 177 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE F 179 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL F 70 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N HIS F 181 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA F 176 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N CYS F 252 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU F 178 " --> pdb=" O CYS F 252 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA F 254 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY F 180 " --> pdb=" O ALA F 254 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU F 256 " --> pdb=" O GLY F 180 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR F 182 " --> pdb=" O LEU F 256 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU F 264 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 152 through 157 removed outlier: 5.800A pdb=" N VAL F 164 " --> pdb=" O LEU F 155 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 184 through 185 Processing sheet with id=AE1, first strand: chain 'F' and resid 286 through 290 removed outlier: 6.155A pdb=" N VAL F 287 " --> pdb=" O MET F 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 10 through 14 removed outlier: 12.841A pdb=" N ASP C 4 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N PHE C 299 " --> pdb=" O ASP C 4 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLU C 6 " --> pdb=" O PHE C 299 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY C 300 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP C 21 " --> pdb=" O ALA C 461 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 10 through 14 removed outlier: 12.841A pdb=" N ASP C 4 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N PHE C 299 " --> pdb=" O ASP C 4 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLU C 6 " --> pdb=" O PHE C 299 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP C 295 " --> pdb=" O ASN C 336 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALA C 418 " --> pdb=" O ASP C 335 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N CYS C 337 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N TYR C 420 " --> pdb=" O CYS C 337 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE C 339 " --> pdb=" O TYR C 420 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL C 422 " --> pdb=" O PHE C 339 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N CYS C 341 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 141 through 143 removed outlier: 8.206A pdb=" N ILE C 142 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU C 108 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR C 68 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE C 179 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL C 70 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N HIS C 181 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA C 176 " --> pdb=" O PHE C 250 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N CYS C 252 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU C 178 " --> pdb=" O CYS C 252 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA C 254 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY C 180 " --> pdb=" O ALA C 254 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU C 256 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR C 182 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU C 264 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 152 through 157 removed outlier: 5.633A pdb=" N VAL C 164 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 286 through 290 removed outlier: 6.155A pdb=" N VAL C 287 " --> pdb=" O MET C 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'G' and resid 10 through 14 removed outlier: 12.853A pdb=" N ASP G 4 " --> pdb=" O ILE G 297 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N PHE G 299 " --> pdb=" O ASP G 4 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU G 6 " --> pdb=" O PHE G 299 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY G 300 " --> pdb=" O LEU G 462 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP G 21 " --> pdb=" O ALA G 461 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 10 through 14 removed outlier: 12.853A pdb=" N ASP G 4 " --> pdb=" O ILE G 297 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N PHE G 299 " --> pdb=" O ASP G 4 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU G 6 " --> pdb=" O PHE G 299 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP G 295 " --> pdb=" O ASN G 336 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA G 418 " --> pdb=" O ASP G 335 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N CYS G 337 " --> pdb=" O ALA G 418 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N TYR G 420 " --> pdb=" O CYS G 337 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE G 339 " --> pdb=" O TYR G 420 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL G 422 " --> pdb=" O PHE G 339 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS G 341 " --> pdb=" O VAL G 422 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 25 through 26 removed outlier: 3.536A pdb=" N GLY G 26 " --> pdb=" O VAL G 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'G' and resid 141 through 143 removed outlier: 6.761A pdb=" N VAL G 67 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE G 109 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE G 69 " --> pdb=" O ILE G 109 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU G 264 " --> pdb=" O VAL G 255 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 152 through 157 removed outlier: 5.764A pdb=" N VAL G 164 " --> pdb=" O LEU G 155 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 184 through 185 Processing sheet with id=AF4, first strand: chain 'G' and resid 286 through 290 removed outlier: 6.137A pdb=" N VAL G 287 " --> pdb=" O MET G 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 1296 hydrogen bonds defined for protein. 3669 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: 8.46 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5539 1.32 - 1.45: 7989 1.45 - 1.57: 17193 1.57 - 1.70: 32 1.70 - 1.82: 357 Bond restraints: 31110 Sorted by residual: bond pdb=" C3R 4EY F 502 " pdb=" C4R 4EY F 502 " ideal model delta sigma weight residual 1.533 1.343 0.190 2.00e-02 2.50e+03 9.02e+01 bond pdb=" C3R 4EY E 502 " pdb=" C4R 4EY E 502 " ideal model delta sigma weight residual 1.533 1.343 0.190 2.00e-02 2.50e+03 9.02e+01 bond pdb=" C3R 4EY H 502 " pdb=" C4R 4EY H 502 " ideal model delta sigma weight residual 1.533 1.344 0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C3R 4EY G 502 " pdb=" C4R 4EY G 502 " ideal model delta sigma weight residual 1.533 1.344 0.189 2.00e-02 2.50e+03 8.95e+01 bond pdb=" C3R 4EY B 502 " pdb=" C4R 4EY B 502 " ideal model delta sigma weight residual 1.533 1.344 0.189 2.00e-02 2.50e+03 8.93e+01 ... (remaining 31105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 41442 2.12 - 4.24: 542 4.24 - 6.36: 124 6.36 - 8.48: 32 8.48 - 10.60: 12 Bond angle restraints: 42152 Sorted by residual: angle pdb=" C3 4EY D 502 " pdb=" C7 4EY D 502 " pdb=" S7 4EY D 502 " ideal model delta sigma weight residual 125.53 114.93 10.60 3.00e+00 1.11e-01 1.25e+01 angle pdb=" C3 4EY C 502 " pdb=" C7 4EY C 502 " pdb=" S7 4EY C 502 " ideal model delta sigma weight residual 125.53 115.23 10.30 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C3 4EY A 502 " pdb=" C7 4EY A 502 " pdb=" S7 4EY A 502 " ideal model delta sigma weight residual 125.53 115.25 10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" C3 4EY B 502 " pdb=" C7 4EY B 502 " pdb=" S7 4EY B 502 " ideal model delta sigma weight residual 125.53 115.44 10.09 3.00e+00 1.11e-01 1.13e+01 angle pdb=" C3 4EY F 502 " pdb=" C7 4EY F 502 " pdb=" S7 4EY F 502 " ideal model delta sigma weight residual 125.53 115.65 9.88 3.00e+00 1.11e-01 1.08e+01 ... (remaining 42147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.44: 17326 27.44 - 54.88: 1191 54.88 - 82.32: 173 82.32 - 109.76: 12 109.76 - 137.19: 8 Dihedral angle restraints: 18710 sinusoidal: 7610 harmonic: 11100 Sorted by residual: dihedral pdb=" C4R 4EY C 502 " pdb=" C5R 4EY C 502 " pdb=" O5R 4EY C 502 " pdb=" P 4EY C 502 " ideal model delta sinusoidal sigma weight residual 102.17 -120.64 -137.19 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C4R 4EY E 502 " pdb=" C5R 4EY E 502 " pdb=" O5R 4EY E 502 " pdb=" P 4EY E 502 " ideal model delta sinusoidal sigma weight residual 102.17 -121.45 -136.38 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" C4R 4EY G 502 " pdb=" C5R 4EY G 502 " pdb=" O5R 4EY G 502 " pdb=" P 4EY G 502 " ideal model delta sinusoidal sigma weight residual 102.17 -121.51 -136.32 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 18707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3557 0.049 - 0.098: 744 0.098 - 0.147: 214 0.147 - 0.196: 1 0.196 - 0.245: 8 Chirality restraints: 4524 Sorted by residual: chirality pdb=" C3R 4EY D 502 " pdb=" C2R 4EY D 502 " pdb=" C4R 4EY D 502 " pdb=" O3R 4EY D 502 " both_signs ideal model delta sigma weight residual False -2.72 -2.48 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C3R 4EY C 502 " pdb=" C2R 4EY C 502 " pdb=" C4R 4EY C 502 " pdb=" O3R 4EY C 502 " both_signs ideal model delta sigma weight residual False -2.72 -2.48 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C3R 4EY B 502 " pdb=" C2R 4EY B 502 " pdb=" C4R 4EY B 502 " pdb=" O3R 4EY B 502 " both_signs ideal model delta sigma weight residual False -2.72 -2.48 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 4521 not shown) Planarity restraints: 5470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 336 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.73e+00 pdb=" C ASN G 336 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN G 336 " -0.017 2.00e-02 2.50e+03 pdb=" N CYS G 337 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 212 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO A 213 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 213 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 213 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 336 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C ASN F 336 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN F 336 " -0.016 2.00e-02 2.50e+03 pdb=" N CYS F 337 " -0.014 2.00e-02 2.50e+03 ... (remaining 5467 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 435 2.56 - 3.15: 25044 3.15 - 3.73: 57627 3.73 - 4.32: 82529 4.32 - 4.90: 128361 Nonbonded interactions: 293996 Sorted by model distance: nonbonded pdb=" NE2 HIS H 211 " pdb="NI NI H 501 " model vdw 1.978 2.260 nonbonded pdb=" NE2 HIS G 211 " pdb="NI NI G 501 " model vdw 1.980 2.260 nonbonded pdb=" NE2 HIS E 211 " pdb="NI NI E 501 " model vdw 1.981 2.260 nonbonded pdb=" NE2 HIS F 211 " pdb="NI NI F 501 " model vdw 1.983 2.260 nonbonded pdb=" NE2 HIS C 211 " pdb="NI NI C 501 " model vdw 1.990 2.260 ... (remaining 293991 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 2 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 72 or (resid 73 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 74 through 216 or (res \ id 217 and (name N or name CA or name C or name O or name CB )) or resid 218 thr \ ough 277 or (resid 278 through 280 and (name N or name CA or name C or name O or \ name CB )) or resid 281 through 336 or resid 338 through 475 or (resid 476 and \ (name N or name CA or name C or name O or name CB )) or resid 477 through 502)) selection = (chain 'B' and (resid 2 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 74 through 120 or (resid 121 and (n \ ame N or name CA or name C or name O or name CB )) or resid 122 through 216 or ( \ resid 217 and (name N or name CA or name C or name O or name CB )) or resid 218 \ through 279 or (resid 280 and (name N or name CA or name C or name O or name CB \ )) or resid 281 through 336 or resid 338 through 475 or (resid 476 and (name N o \ r name CA or name C or name O or name CB )) or resid 477 through 502)) selection = (chain 'C' and (resid 2 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 72 or (resid 73 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 74 through 216 or (res \ id 217 and (name N or name CA or name C or name O or name CB )) or resid 218 thr \ ough 277 or (resid 278 through 280 and (name N or name CA or name C or name O or \ name CB )) or resid 281 through 336 or resid 338 through 475 or (resid 476 and \ (name N or name CA or name C or name O or name CB )) or resid 477 through 502)) selection = (chain 'D' and (resid 2 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 72 or (resid 73 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 74 through 120 or (res \ id 121 and (name N or name CA or name C or name O or name CB )) or resid 122 thr \ ough 277 or (resid 278 through 280 and (name N or name CA or name C or name O or \ name CB )) or resid 281 or (resid 282 through 283 and (name N or name CA or nam \ e C or name O or name CB )) or resid 284 through 336 or resid 338 through 502)) selection = (chain 'E' and (resid 2 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 72 or (resid 73 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 74 through 101 or (res \ id 102 and (name N or name CA or name C or name O or name CB )) or resid 103 thr \ ough 120 or (resid 121 and (name N or name CA or name C or name O or name CB )) \ or resid 122 through 216 or (resid 217 and (name N or name CA or name C or name \ O or name CB )) or resid 218 through 277 or (resid 278 through 280 and (name N o \ r name CA or name C or name O or name CB )) or resid 281 or (resid 282 through 2 \ 83 and (name N or name CA or name C or name O or name CB )) or resid 284 through \ 336 or resid 338 through 475 or (resid 476 and (name N or name CA or name C or \ name O or name CB )) or resid 477 through 502)) selection = (chain 'F' and (resid 2 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 72 or (resid 73 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 74 through 101 or (res \ id 102 and (name N or name CA or name C or name O or name CB )) or resid 103 thr \ ough 120 or (resid 121 and (name N or name CA or name C or name O or name CB )) \ or resid 122 through 216 or (resid 217 and (name N or name CA or name C or name \ O or name CB )) or resid 218 through 277 or (resid 278 through 280 and (name N o \ r name CA or name C or name O or name CB )) or resid 281 or (resid 282 through 2 \ 83 and (name N or name CA or name C or name O or name CB )) or resid 284 through \ 336 or resid 338 through 475 or (resid 476 and (name N or name CA or name C or \ name O or name CB )) or resid 477 through 502)) selection = (chain 'G' and (resid 2 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 101 or (resid 102 and (name N or na \ me CA or name C or name O or name CB )) or resid 103 through 120 or (resid 121 a \ nd (name N or name CA or name C or name O or name CB )) or resid 122 through 216 \ or (resid 217 and (name N or name CA or name C or name O or name CB )) or resid \ 218 through 277 or (resid 278 through 280 and (name N or name CA or name C or n \ ame O or name CB )) or resid 281 or (resid 282 through 283 and (name N or name C \ A or name C or name O or name CB )) or resid 284 through 336 or resid 338 throug \ h 475 or (resid 476 and (name N or name CA or name C or name O or name CB )) or \ resid 477 through 502)) selection = (chain 'H' and (resid 2 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 72 or (resid 73 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 74 through 101 or (res \ id 102 and (name N or name CA or name C or name O or name CB )) or resid 103 thr \ ough 120 or (resid 121 and (name N or name CA or name C or name O or name CB )) \ or resid 122 through 216 or (resid 217 and (name N or name CA or name C or name \ O or name CB )) or resid 218 through 277 or (resid 278 through 280 and (name N o \ r name CA or name C or name O or name CB )) or resid 281 or (resid 282 through 2 \ 83 and (name N or name CA or name C or name O or name CB )) or resid 284 through \ 336 or resid 338 through 475 or (resid 476 and (name N or name CA or name C or \ name O or name CB )) or resid 477 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.18 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: 0.010 Normalize map: mean=0, sd=1: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 36.940 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 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 : 0.006 0.190 31118 Z= 0.317 Angle : 0.661 10.600 42152 Z= 0.321 Chirality : 0.044 0.245 4524 Planarity : 0.005 0.061 5470 Dihedral : 18.293 137.195 11628 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.15 % Allowed : 23.14 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.22 (0.14), residues: 3829 helix: 0.32 (0.13), residues: 1512 sheet: -0.12 (0.23), residues: 501 loop : 0.27 (0.16), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 284 TYR 0.015 0.001 TYR H 169 PHE 0.023 0.002 PHE E 403 TRP 0.006 0.001 TRP A 278 HIS 0.007 0.001 HIS E 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.32 (31110) covalent geometry : angle 0.66102 / 0.32 (42152) hydrogen bonds : bond 0.14279 / 9.74 ( 1248) hydrogen bonds : angle 7.19214 / 5.11 ( 3669) Misc. bond : bond 0.00031 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 456 time to evaluate : 1.152 Fit side-chains REVERT: D 120 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7781 (mm-30) REVERT: A 366 LYS cc_start: 0.8565 (ttpt) cc_final: 0.8214 (mppt) REVERT: H 15 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.6555 (t0) REVERT: H 319 MET cc_start: 0.8990 (tpt) cc_final: 0.8741 (tpt) REVERT: E 99 VAL cc_start: 0.7439 (p) cc_final: 0.7035 (m) REVERT: E 271 ASP cc_start: 0.7315 (p0) cc_final: 0.7037 (p0) REVERT: E 475 MET cc_start: 0.7433 (mmm) cc_final: 0.7138 (mmm) REVERT: C 65 SER cc_start: 0.5557 (OUTLIER) cc_final: 0.5332 (t) REVERT: G 50 ASN cc_start: 0.8215 (m110) cc_final: 0.7898 (m110) REVERT: G 215 VAL cc_start: 0.6288 (t) cc_final: 0.6049 (t) outliers start: 37 outliers final: 26 residues processed: 489 average time/residue: 0.7097 time to fit residues: 406.9018 Evaluate side-chains 464 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 436 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 278 TRP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 471 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.0980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN D 196 HIS ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 HIS H 240 HIS H 262 GLN H 274 GLN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 458 ASN E 39 GLN E 112 ASN ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN ** E 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 ASN F 50 ASN ** F 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 GLN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 ASN ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN G 262 GLN G 274 GLN G 375 ASN ** G 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 455 GLN G 458 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.187584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.129577 restraints weight = 34744.649| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.84 r_work: 0.3235 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 31118 Z= 0.256 Angle : 0.652 12.330 42152 Z= 0.335 Chirality : 0.047 0.158 4524 Planarity : 0.005 0.059 5470 Dihedral : 9.904 147.538 4434 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.03 % Allowed : 20.37 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.35 (0.14), residues: 3829 helix: 0.37 (0.13), residues: 1528 sheet: -0.01 (0.24), residues: 445 loop : 0.37 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 389 TYR 0.019 0.002 TYR F 190 PHE 0.035 0.003 PHE G 403 TRP 0.006 0.002 TRP G 204 HIS 0.012 0.002 HIS E 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.26 (31110) covalent geometry : angle 0.65245 / 0.34 (42152) hydrogen bonds : bond 0.05001 / 3.38 ( 1248) hydrogen bonds : angle 6.23778 / 4.39 ( 3669) Misc. bond : bond 0.00139 / 0.07 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 474 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7054 (mtpm) REVERT: B 121 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7587 (tmtm) REVERT: B 266 ASN cc_start: 0.8053 (m-40) cc_final: 0.7801 (m110) REVERT: B 385 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7838 (mp0) REVERT: B 468 THR cc_start: 0.7282 (p) cc_final: 0.7007 (t) REVERT: A 207 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.8054 (mp) REVERT: A 447 ASP cc_start: 0.8640 (t70) cc_final: 0.8410 (t70) REVERT: H 15 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7188 (t0) REVERT: H 240 HIS cc_start: 0.8350 (t70) cc_final: 0.8081 (t-90) REVERT: H 319 MET cc_start: 0.9093 (tpt) cc_final: 0.8828 (tpt) REVERT: H 475 MET cc_start: 0.7778 (mmm) cc_final: 0.7572 (mmm) REVERT: E 33 GLU cc_start: 0.6585 (tp30) cc_final: 0.5655 (tm-30) REVERT: E 207 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8571 (mt) REVERT: E 272 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: E 475 MET cc_start: 0.7612 (mmm) cc_final: 0.7313 (mmm) REVERT: F 35 LEU cc_start: 0.7949 (mt) cc_final: 0.7676 (mt) REVERT: F 102 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7450 (mtpp) REVERT: F 157 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7879 (mttm) REVERT: F 272 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: F 280 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7825 (tp) REVERT: F 464 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7250 (mmtt) REVERT: F 475 MET cc_start: 0.7803 (mmm) cc_final: 0.7284 (mmm) REVERT: C 65 SER cc_start: 0.5348 (OUTLIER) cc_final: 0.5104 (t) REVERT: C 103 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7300 (tptm) REVERT: C 385 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7840 (mp0) REVERT: G 15 ASP cc_start: 0.7617 (t0) cc_final: 0.7302 (m-30) REVERT: G 50 ASN cc_start: 0.8248 (m110) cc_final: 0.7805 (m110) REVERT: G 54 MET cc_start: 0.7102 (mtp) cc_final: 0.6844 (mtm) REVERT: G 120 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8119 (mm-30) REVERT: G 336 ASN cc_start: 0.8066 (p0) cc_final: 0.7722 (p0) REVERT: G 475 MET cc_start: 0.7713 (mmm) cc_final: 0.7420 (mmm) outliers start: 97 outliers final: 42 residues processed: 547 average time/residue: 0.7238 time to fit residues: 464.1395 Evaluate side-chains 506 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 451 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 278 TRP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 284 ARG Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 464 LYS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 351 GLU Chi-restraints excluded: chain G residue 471 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 363 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 354 optimal weight: 8.9990 chunk 225 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 335 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 94 GLN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 GLN H 274 GLN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 458 ASN E 39 GLN ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 HIS E 240 HIS E 262 GLN E 274 GLN ** E 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 GLN E 458 ASN ** F 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 GLN F 375 ASN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 ASN ** F 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 GLN G 274 GLN ** G 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 458 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.184838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125387 restraints weight = 35256.717| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.90 r_work: 0.3194 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 31118 Z= 0.328 Angle : 0.703 14.162 42152 Z= 0.363 Chirality : 0.049 0.177 4524 Planarity : 0.006 0.058 5470 Dihedral : 9.967 149.116 4418 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.59 % Allowed : 19.59 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.20 (0.13), residues: 3829 helix: 0.21 (0.13), residues: 1528 sheet: 0.07 (0.25), residues: 349 loop : 0.26 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 431 TYR 0.023 0.003 TYR E 190 PHE 0.042 0.003 PHE H 403 TRP 0.009 0.002 TRP E 278 HIS 0.017 0.002 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.33 (31110) covalent geometry : angle 0.70308 / 0.36 (42152) hydrogen bonds : bond 0.05189 / 3.50 ( 1248) hydrogen bonds : angle 6.36882 / 4.47 ( 3669) Misc. bond : bond 0.00122 / 0.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 492 time to evaluate : 1.160 Fit side-chains REVERT: B 121 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7543 (tmtm) REVERT: B 385 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7905 (mp0) REVERT: D 103 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.6731 (tptp) REVERT: D 241 MET cc_start: 0.8300 (mtt) cc_final: 0.8012 (mtt) REVERT: D 385 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7954 (mp0) REVERT: A 191 SER cc_start: 0.5215 (OUTLIER) cc_final: 0.5005 (p) REVERT: H 15 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7247 (t0) REVERT: H 102 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7436 (mtpp) REVERT: H 240 HIS cc_start: 0.8527 (t70) cc_final: 0.8182 (t-90) REVERT: H 475 MET cc_start: 0.7875 (mmm) cc_final: 0.7404 (mmm) REVERT: E 235 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6155 (m-30) REVERT: E 240 HIS cc_start: 0.8477 (t70) cc_final: 0.8214 (t-90) REVERT: E 272 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: E 475 MET cc_start: 0.7656 (mmm) cc_final: 0.7427 (mmm) REVERT: F 35 LEU cc_start: 0.7977 (mt) cc_final: 0.7728 (mt) REVERT: F 102 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7455 (mtpp) REVERT: F 157 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8105 (mttm) REVERT: F 272 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: F 280 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7885 (tp) REVERT: F 464 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7572 (mtpt) REVERT: F 475 MET cc_start: 0.7877 (mmm) cc_final: 0.7434 (mmm) REVERT: C 103 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7364 (tptm) REVERT: C 385 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7934 (mp0) REVERT: G 15 ASP cc_start: 0.7789 (t0) cc_final: 0.7464 (m-30) REVERT: G 54 MET cc_start: 0.7155 (mtp) cc_final: 0.6859 (mtm) REVERT: G 235 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.6063 (m-30) REVERT: G 351 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: G 475 MET cc_start: 0.7771 (mmm) cc_final: 0.7431 (mmm) outliers start: 115 outliers final: 49 residues processed: 570 average time/residue: 0.6767 time to fit residues: 452.4729 Evaluate side-chains 526 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 462 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 278 TRP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 284 ARG Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 464 LYS Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 351 GLU Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 471 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 199 optimal weight: 4.9990 chunk 224 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 281 optimal weight: 0.5980 chunk 372 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 364 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 GLN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 GLN H 274 GLN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 458 ASN E 39 GLN ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN E 274 GLN ** E 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 ASN ** F 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 HIS F 262 GLN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 ASN ** F 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 ASN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 HIS G 226 ASN G 262 GLN G 274 GLN ** G 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 458 ASN ** G 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.190660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.133675 restraints weight = 41144.607| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.11 r_work: 0.3276 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31118 Z= 0.143 Angle : 0.580 10.533 42152 Z= 0.299 Chirality : 0.043 0.135 4524 Planarity : 0.005 0.059 5470 Dihedral : 9.637 146.584 4415 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.21 % Allowed : 20.27 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.17 (0.14), residues: 3829 helix: 0.33 (0.13), residues: 1528 sheet: -0.52 (0.23), residues: 445 loop : 0.29 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 331 TYR 0.017 0.002 TYR G 132 PHE 0.028 0.002 PHE G 403 TRP 0.006 0.001 TRP E 278 HIS 0.012 0.002 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (31110) covalent geometry : angle 0.57977 / 0.30 (42152) hydrogen bonds : bond 0.03892 / 2.63 ( 1248) hydrogen bonds : angle 5.94798 / 4.18 ( 3669) Misc. bond : bond 0.00046 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 498 time to evaluate : 1.197 Fit side-chains REVERT: B 103 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7273 (tptm) REVERT: B 121 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7532 (tmtm) REVERT: B 130 ASP cc_start: 0.7360 (t0) cc_final: 0.7073 (m-30) REVERT: B 447 ASP cc_start: 0.8634 (t70) cc_final: 0.8388 (t70) REVERT: B 468 THR cc_start: 0.7246 (p) cc_final: 0.6906 (t) REVERT: D 289 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7511 (t80) REVERT: D 317 MET cc_start: 0.9083 (mmm) cc_final: 0.8818 (mmm) REVERT: D 447 ASP cc_start: 0.8694 (t70) cc_final: 0.8486 (t70) REVERT: A 157 LYS cc_start: 0.7874 (mptp) cc_final: 0.7525 (mptp) REVERT: A 191 SER cc_start: 0.5180 (OUTLIER) cc_final: 0.4969 (p) REVERT: A 317 MET cc_start: 0.9130 (mmm) cc_final: 0.8880 (mmm) REVERT: A 447 ASP cc_start: 0.8605 (t70) cc_final: 0.8395 (t70) REVERT: H 102 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7468 (mtpp) REVERT: H 240 HIS cc_start: 0.8501 (t70) cc_final: 0.8189 (t-90) REVERT: H 351 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: H 425 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8422 (mt-10) REVERT: H 475 MET cc_start: 0.7900 (mmm) cc_final: 0.7610 (mmm) REVERT: E 207 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8381 (mt) REVERT: E 235 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6099 (m-30) REVERT: E 240 HIS cc_start: 0.8414 (t70) cc_final: 0.8180 (t-90) REVERT: E 272 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: E 425 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8393 (mt-10) REVERT: E 475 MET cc_start: 0.7638 (mmm) cc_final: 0.7369 (mmm) REVERT: F 35 LEU cc_start: 0.7906 (mt) cc_final: 0.7656 (mt) REVERT: F 39 GLN cc_start: 0.6640 (tp40) cc_final: 0.6430 (tp-100) REVERT: F 157 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8025 (mttm) REVERT: F 272 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: F 351 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: F 475 MET cc_start: 0.7822 (mmm) cc_final: 0.7447 (mmm) REVERT: C 317 MET cc_start: 0.9111 (mmm) cc_final: 0.8878 (mmm) REVERT: G 15 ASP cc_start: 0.7504 (t0) cc_final: 0.7224 (m-30) REVERT: G 50 ASN cc_start: 0.8305 (m110) cc_final: 0.7883 (m110) REVERT: G 82 THR cc_start: 0.8244 (t) cc_final: 0.7881 (m) REVERT: G 235 ASP cc_start: 0.6731 (OUTLIER) cc_final: 0.5942 (m-30) REVERT: G 259 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7471 (mmtt) REVERT: G 336 ASN cc_start: 0.7978 (p0) cc_final: 0.7619 (p0) REVERT: G 351 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: G 475 MET cc_start: 0.7818 (mmm) cc_final: 0.7324 (mmm) outliers start: 103 outliers final: 39 residues processed: 572 average time/residue: 0.7080 time to fit residues: 475.3247 Evaluate side-chains 507 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 451 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 278 TRP Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 284 ARG Chi-restraints excluded: chain H residue 289 PHE Chi-restraints excluded: chain H residue 351 GLU Chi-restraints excluded: chain H residue 425 GLU Chi-restraints excluded: chain E residue 12 MET Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 289 PHE Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 351 GLU Chi-restraints excluded: chain G residue 471 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 98 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 268 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 344 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 381 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 GLN H 274 GLN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 458 ASN E 39 GLN ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 GLN ** E 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 GLN E 458 ASN ** F 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 GLN F 274 GLN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 GLN F 458 ASN ** F 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 ASN C 375 ASN ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 GLN G 274 GLN ** G 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 455 GLN G 458 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.186911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127357 restraints weight = 35406.688| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.88 r_work: 0.3216 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31118 Z= 0.246 Angle : 0.639 12.582 42152 Z= 0.329 Chirality : 0.046 0.162 4524 Planarity : 0.005 0.059 5470 Dihedral : 9.681 147.220 4408 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.15 % Allowed : 20.77 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.16 (0.14), residues: 3829 helix: 0.29 (0.13), residues: 1528 sheet: -0.50 (0.23), residues: 445 loop : 0.31 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 389 TYR 0.022 0.002 TYR D 132 PHE 0.036 0.003 PHE F 403 TRP 0.008 0.002 TRP E 278 HIS 0.017 0.002 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.25 (31110) covalent geometry : angle 0.63944 / 0.33 (42152) hydrogen bonds : bond 0.04484 / 3.02 ( 1248) hydrogen bonds : angle 6.10433 / 4.28 ( 3669) Misc. bond : bond 0.00062 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 486 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7050 (mtpm) REVERT: B 52 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7286 (mt) REVERT: B 121 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7536 (tmtm) REVERT: B 130 ASP cc_start: 0.7352 (t0) cc_final: 0.7084 (m-30) REVERT: B 385 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7935 (mp0) REVERT: D 109 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8446 (mm) REVERT: D 241 MET cc_start: 0.8226 (mtt) cc_final: 0.7954 (mtt) REVERT: A 157 LYS cc_start: 0.7981 (mptp) cc_final: 0.7663 (mptp) REVERT: A 207 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8015 (mp) REVERT: A 447 ASP cc_start: 0.8725 (t70) cc_final: 0.8517 (t70) REVERT: A 468 THR cc_start: 0.7271 (p) cc_final: 0.6998 (t) REVERT: H 102 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7452 (mtpp) REVERT: H 240 HIS cc_start: 0.8494 (t70) cc_final: 0.8203 (t-90) REVERT: H 475 MET cc_start: 0.7864 (mmm) cc_final: 0.7414 (mmm) REVERT: E 33 GLU cc_start: 0.6559 (tp30) cc_final: 0.5651 (tm-30) REVERT: E 207 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8365 (mt) REVERT: E 235 ASP cc_start: 0.6897 (OUTLIER) cc_final: 0.6111 (m-30) REVERT: E 240 HIS cc_start: 0.8474 (t70) cc_final: 0.8181 (t-90) REVERT: E 272 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: F 35 LEU cc_start: 0.7946 (mt) cc_final: 0.7731 (mt) REVERT: F 102 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7440 (mtpp) REVERT: F 157 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8088 (mttm) REVERT: F 272 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: F 280 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7846 (tp) REVERT: F 475 MET cc_start: 0.7866 (mmm) cc_final: 0.7475 (mmm) REVERT: C 271 ASP cc_start: 0.6632 (OUTLIER) cc_final: 0.6212 (t0) REVERT: G 15 ASP cc_start: 0.7614 (t0) cc_final: 0.7324 (m-30) REVERT: G 50 ASN cc_start: 0.8333 (m110) cc_final: 0.7866 (m110) REVERT: G 82 THR cc_start: 0.8300 (t) cc_final: 0.7933 (m) REVERT: G 235 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6140 (m-30) REVERT: G 259 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7693 (mtmt) REVERT: G 475 MET cc_start: 0.7827 (mmm) cc_final: 0.7480 (mmm) outliers start: 101 outliers final: 50 residues processed: 554 average time/residue: 0.7151 time to fit residues: 465.6627 Evaluate side-chains 527 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 461 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 278 TRP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 284 ARG Chi-restraints excluded: chain H residue 289 PHE Chi-restraints excluded: chain E residue 12 MET Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 351 GLU Chi-restraints excluded: chain G residue 471 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 191 optimal weight: 5.9990 chunk 304 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 337 optimal weight: 0.0070 chunk 111 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 271 optimal weight: 2.9990 chunk 277 optimal weight: 0.7980 chunk 214 optimal weight: 10.0000 chunk 336 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 GLN H 274 GLN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 458 ASN ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN E 274 GLN ** E 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 GLN E 458 ASN ** F 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 HIS F 274 GLN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 GLN F 458 ASN ** F 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 ASN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 GLN G 274 GLN ** G 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 458 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.189015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.130426 restraints weight = 34981.727| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.89 r_work: 0.3269 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31118 Z= 0.179 Angle : 0.597 11.534 42152 Z= 0.308 Chirality : 0.044 0.150 4524 Planarity : 0.005 0.060 5470 Dihedral : 9.566 147.091 4406 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.24 % Allowed : 20.99 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.13 (0.14), residues: 3829 helix: 0.30 (0.13), residues: 1528 sheet: -0.63 (0.23), residues: 445 loop : 0.30 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 331 TYR 0.028 0.002 TYR D 132 PHE 0.031 0.002 PHE B 403 TRP 0.008 0.001 TRP E 278 HIS 0.016 0.002 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (31110) covalent geometry : angle 0.59680 / 0.31 (42152) hydrogen bonds : bond 0.04049 / 2.72 ( 1248) hydrogen bonds : angle 5.97508 / 4.19 ( 3669) Misc. bond : bond 0.00045 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 474 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: B 52 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7258 (mt) REVERT: B 103 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7437 (tptm) REVERT: B 120 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7392 (mm-30) REVERT: B 121 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7505 (tmtm) REVERT: B 130 ASP cc_start: 0.7301 (t0) cc_final: 0.7082 (m-30) REVERT: B 385 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7917 (mp0) REVERT: B 443 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8102 (mt-10) REVERT: D 109 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8414 (mm) REVERT: A 157 LYS cc_start: 0.7913 (mptp) cc_final: 0.7569 (mptp) REVERT: A 207 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7979 (mp) REVERT: A 447 ASP cc_start: 0.8652 (t70) cc_final: 0.8428 (t70) REVERT: H 102 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7471 (mtpp) REVERT: H 240 HIS cc_start: 0.8511 (t70) cc_final: 0.8199 (t-90) REVERT: H 475 MET cc_start: 0.7891 (mmm) cc_final: 0.7454 (mmm) REVERT: E 33 GLU cc_start: 0.6568 (tp30) cc_final: 0.5724 (tm-30) REVERT: E 207 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8411 (mt) REVERT: E 235 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.6137 (m-30) REVERT: E 240 HIS cc_start: 0.8435 (t70) cc_final: 0.8152 (t-90) REVERT: E 425 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8343 (mt-10) REVERT: F 35 LEU cc_start: 0.7974 (mt) cc_final: 0.7709 (mt) REVERT: F 102 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7437 (mtpp) REVERT: F 157 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8056 (mttm) REVERT: F 272 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: F 280 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7727 (tp) REVERT: F 425 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8308 (mt-10) REVERT: F 475 MET cc_start: 0.7863 (mmm) cc_final: 0.7493 (mmm) REVERT: C 41 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7093 (mt-10) REVERT: C 109 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8346 (mm) REVERT: G 15 ASP cc_start: 0.7452 (t0) cc_final: 0.7152 (m-30) REVERT: G 50 ASN cc_start: 0.8310 (m110) cc_final: 0.7875 (m110) REVERT: G 82 THR cc_start: 0.8246 (t) cc_final: 0.7893 (m) REVERT: G 235 ASP cc_start: 0.6804 (OUTLIER) cc_final: 0.6026 (m-30) REVERT: G 259 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7526 (mmtt) REVERT: G 336 ASN cc_start: 0.7927 (p0) cc_final: 0.7610 (p0) REVERT: G 475 MET cc_start: 0.7821 (mmm) cc_final: 0.7478 (mmm) outliers start: 104 outliers final: 52 residues processed: 551 average time/residue: 0.6940 time to fit residues: 449.2256 Evaluate side-chains 524 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 454 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 278 TRP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 284 ARG Chi-restraints excluded: chain H residue 289 PHE Chi-restraints excluded: chain E residue 12 MET Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 343 SER Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 425 GLU Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 351 GLU Chi-restraints excluded: chain G residue 471 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 326 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 chunk 355 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 281 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 293 optimal weight: 0.0010 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 GLN H 274 GLN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 455 GLN H 458 ASN E 39 GLN ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 GLN ** E 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 GLN E 458 ASN ** F 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 GLN F 274 GLN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 GLN F 458 ASN ** F 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 ASN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 GLN G 274 GLN ** G 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 458 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.187229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132072 restraints weight = 35410.013| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.01 r_work: 0.3257 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 31118 Z= 0.235 Angle : 0.635 12.510 42152 Z= 0.327 Chirality : 0.045 0.161 4524 Planarity : 0.005 0.060 5470 Dihedral : 9.645 148.463 4406 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.28 % Allowed : 20.87 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.13 (0.14), residues: 3829 helix: 0.24 (0.13), residues: 1528 sheet: -0.64 (0.24), residues: 397 loop : 0.32 (0.15), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 389 TYR 0.033 0.002 TYR D 132 PHE 0.036 0.003 PHE A 403 TRP 0.009 0.002 TRP E 278 HIS 0.017 0.002 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.24 (31110) covalent geometry : angle 0.63511 / 0.33 (42152) hydrogen bonds : bond 0.04394 / 2.95 ( 1248) hydrogen bonds : angle 6.08232 / 4.27 ( 3669) Misc. bond : bond 0.00054 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 485 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: B 52 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7277 (mt) REVERT: B 73 ASP cc_start: 0.8420 (p0) cc_final: 0.8210 (p0) REVERT: B 103 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7408 (tptm) REVERT: B 120 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7409 (tp30) REVERT: B 121 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7497 (tmtm) REVERT: B 130 ASP cc_start: 0.7277 (t0) cc_final: 0.7055 (m-30) REVERT: B 385 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7942 (mp0) REVERT: B 443 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8080 (mt-10) REVERT: D 109 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8423 (mm) REVERT: D 241 MET cc_start: 0.8315 (mtt) cc_final: 0.8077 (mtt) REVERT: D 335 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6336 (t0) REVERT: A 157 LYS cc_start: 0.7967 (mptp) cc_final: 0.7607 (mptp) REVERT: A 207 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.8015 (mp) REVERT: A 447 ASP cc_start: 0.8644 (t70) cc_final: 0.8441 (t70) REVERT: H 102 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7485 (mtpp) REVERT: H 475 MET cc_start: 0.7836 (mmm) cc_final: 0.7382 (mmm) REVERT: E 33 GLU cc_start: 0.6646 (tp30) cc_final: 0.5802 (tm-30) REVERT: E 207 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8479 (mt) REVERT: E 235 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6143 (m-30) REVERT: E 240 HIS cc_start: 0.8472 (t70) cc_final: 0.8142 (t-90) REVERT: E 272 GLU cc_start: 0.7346 (mp0) cc_final: 0.7092 (mp0) REVERT: E 475 MET cc_start: 0.7705 (mmm) cc_final: 0.7355 (mmm) REVERT: F 35 LEU cc_start: 0.7964 (mt) cc_final: 0.7699 (mt) REVERT: F 102 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7473 (mtpp) REVERT: F 157 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8097 (mttm) REVERT: F 271 ASP cc_start: 0.7372 (p0) cc_final: 0.7170 (p0) REVERT: F 272 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: F 280 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7782 (tp) REVERT: F 425 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8307 (mt-10) REVERT: F 475 MET cc_start: 0.7843 (mmm) cc_final: 0.7445 (mmm) REVERT: C 2 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6999 (mtpm) REVERT: C 41 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7077 (mt-10) REVERT: C 109 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8388 (mm) REVERT: C 162 ASP cc_start: 0.6663 (m-30) cc_final: 0.6442 (m-30) REVERT: G 50 ASN cc_start: 0.8299 (m110) cc_final: 0.7825 (m110) REVERT: G 82 THR cc_start: 0.8266 (t) cc_final: 0.7939 (m) REVERT: G 235 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6127 (m-30) REVERT: G 259 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7565 (mmtt) REVERT: G 475 MET cc_start: 0.7804 (mmm) cc_final: 0.7425 (mmm) outliers start: 105 outliers final: 58 residues processed: 560 average time/residue: 0.7253 time to fit residues: 476.4465 Evaluate side-chains 542 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 465 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 278 TRP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 284 ARG Chi-restraints excluded: chain H residue 351 GLU Chi-restraints excluded: chain H residue 367 GLU Chi-restraints excluded: chain E residue 12 MET Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 343 SER Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 425 GLU Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 351 GLU Chi-restraints excluded: chain G residue 471 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 136 optimal weight: 0.6980 chunk 226 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 363 optimal weight: 10.0000 chunk 216 optimal weight: 0.0470 chunk 160 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 GLN H 274 GLN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 458 ASN ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 GLN ** E 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 GLN E 458 ASN F 274 GLN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 GLN F 458 ASN ** F 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 ASN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 GLN G 274 GLN ** G 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 458 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.189891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132882 restraints weight = 41299.179| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.18 r_work: 0.3257 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31118 Z= 0.162 Angle : 0.591 11.294 42152 Z= 0.304 Chirality : 0.044 0.145 4524 Planarity : 0.005 0.060 5470 Dihedral : 9.534 147.024 4406 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.12 % Allowed : 21.09 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.09 (0.14), residues: 3829 helix: 0.27 (0.13), residues: 1528 sheet: -0.73 (0.23), residues: 445 loop : 0.28 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 331 TYR 0.034 0.002 TYR D 132 PHE 0.029 0.002 PHE H 403 TRP 0.007 0.001 TRP E 278 HIS 0.015 0.002 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (31110) covalent geometry : angle 0.59082 / 0.30 (42152) hydrogen bonds : bond 0.03927 / 2.65 ( 1248) hydrogen bonds : angle 5.93500 / 4.16 ( 3669) Misc. bond : bond 0.00046 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 469 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: B 52 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7241 (mt) REVERT: B 103 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7364 (tptm) REVERT: B 121 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7522 (tmtm) REVERT: B 443 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8086 (mt-10) REVERT: B 447 ASP cc_start: 0.8615 (t70) cc_final: 0.8350 (t70) REVERT: B 468 THR cc_start: 0.7226 (p) cc_final: 0.6891 (t) REVERT: D 109 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8360 (mm) REVERT: D 335 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.6344 (t0) REVERT: A 157 LYS cc_start: 0.7875 (mptp) cc_final: 0.7521 (mptp) REVERT: A 207 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7896 (mp) REVERT: A 447 ASP cc_start: 0.8655 (t70) cc_final: 0.8422 (t70) REVERT: H 102 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7464 (mtpp) REVERT: H 475 MET cc_start: 0.7826 (mmm) cc_final: 0.7375 (mmm) REVERT: E 207 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8418 (mt) REVERT: E 235 ASP cc_start: 0.6881 (OUTLIER) cc_final: 0.6090 (m-30) REVERT: E 240 HIS cc_start: 0.8416 (t70) cc_final: 0.8114 (t-90) REVERT: E 272 GLU cc_start: 0.7350 (mp0) cc_final: 0.7118 (mp0) REVERT: E 425 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8356 (mt-10) REVERT: E 475 MET cc_start: 0.7691 (mmm) cc_final: 0.7408 (mmm) REVERT: F 35 LEU cc_start: 0.7919 (mt) cc_final: 0.7667 (mt) REVERT: F 50 ASN cc_start: 0.8310 (m-40) cc_final: 0.7944 (m110) REVERT: F 102 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7406 (mtpp) REVERT: F 271 ASP cc_start: 0.7415 (p0) cc_final: 0.7203 (p0) REVERT: F 272 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: F 280 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7674 (tp) REVERT: F 284 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7699 (tmt170) REVERT: F 425 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: F 475 MET cc_start: 0.7797 (mmm) cc_final: 0.7392 (mmm) REVERT: C 41 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7092 (mt-10) REVERT: G 15 ASP cc_start: 0.7558 (t0) cc_final: 0.7312 (m-30) REVERT: G 50 ASN cc_start: 0.8312 (m110) cc_final: 0.7901 (m110) REVERT: G 82 THR cc_start: 0.8203 (t) cc_final: 0.7890 (m) REVERT: G 235 ASP cc_start: 0.6769 (OUTLIER) cc_final: 0.5972 (m-30) REVERT: G 259 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7557 (mmtt) REVERT: G 475 MET cc_start: 0.7793 (mmm) cc_final: 0.7348 (mmm) outliers start: 100 outliers final: 53 residues processed: 542 average time/residue: 0.7187 time to fit residues: 457.5818 Evaluate side-chains 522 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 451 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 278 TRP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 284 ARG Chi-restraints excluded: chain H residue 289 PHE Chi-restraints excluded: chain E residue 12 MET Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 284 ARG Chi-restraints excluded: chain F residue 343 SER Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 425 GLU Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 289 PHE Chi-restraints excluded: chain G residue 351 GLU Chi-restraints excluded: chain G residue 471 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 340 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 281 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 GLN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 455 GLN H 458 ASN E 39 GLN ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 GLN ** E 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 GLN E 458 ASN F 39 GLN F 274 GLN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 GLN F 458 ASN ** F 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 ASN ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 GLN G 274 GLN G 336 ASN ** G 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 455 GLN G 458 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.185766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124659 restraints weight = 32064.870| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.57 r_work: 0.3238 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 31118 Z= 0.297 Angle : 0.683 13.511 42152 Z= 0.353 Chirality : 0.048 0.182 4524 Planarity : 0.005 0.060 5470 Dihedral : 9.726 148.628 4406 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.78 % Allowed : 21.71 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.07 (0.14), residues: 3829 helix: 0.16 (0.13), residues: 1520 sheet: -0.61 (0.24), residues: 397 loop : 0.30 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 389 TYR 0.034 0.003 TYR D 132 PHE 0.042 0.003 PHE E 403 TRP 0.009 0.002 TRP E 278 HIS 0.021 0.002 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.30 (31110) covalent geometry : angle 0.68302 / 0.35 (42152) hydrogen bonds : bond 0.04751 / 3.19 ( 1248) hydrogen bonds : angle 6.22534 / 4.37 ( 3669) Misc. bond : bond 0.00077 / 0.04 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 477 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: B 103 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7451 (tptm) REVERT: B 121 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7489 (tmtm) REVERT: B 385 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7990 (mp0) REVERT: D 385 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7970 (mp0) REVERT: A 207 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8079 (mp) REVERT: H 102 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7489 (mtpp) REVERT: H 475 MET cc_start: 0.7860 (mmm) cc_final: 0.7392 (mmm) REVERT: E 35 LEU cc_start: 0.8091 (mt) cc_final: 0.7828 (mt) REVERT: E 235 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6164 (m-30) REVERT: E 272 GLU cc_start: 0.7359 (mp0) cc_final: 0.7128 (mp0) REVERT: E 475 MET cc_start: 0.7851 (mmm) cc_final: 0.7448 (mmm) REVERT: F 35 LEU cc_start: 0.7983 (mt) cc_final: 0.7709 (mt) REVERT: F 102 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7500 (mtpp) REVERT: F 272 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: F 280 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7845 (tp) REVERT: F 475 MET cc_start: 0.7884 (mmm) cc_final: 0.7451 (mmm) REVERT: C 41 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: G 15 ASP cc_start: 0.7581 (t0) cc_final: 0.7334 (m-30) REVERT: G 50 ASN cc_start: 0.8317 (m110) cc_final: 0.7830 (m110) REVERT: G 82 THR cc_start: 0.8314 (t) cc_final: 0.8001 (m) REVERT: G 235 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6130 (m-30) REVERT: G 259 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7770 (mtmt) REVERT: G 446 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7649 (mp0) REVERT: G 475 MET cc_start: 0.7839 (mmm) cc_final: 0.7417 (mmm) outliers start: 89 outliers final: 53 residues processed: 542 average time/residue: 0.7280 time to fit residues: 462.2272 Evaluate side-chains 523 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 459 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 278 TRP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 284 ARG Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain E residue 12 MET Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 351 GLU Chi-restraints excluded: chain G residue 471 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 41 optimal weight: 0.7980 chunk 326 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 195 optimal weight: 10.0000 chunk 175 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 276 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 323 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN A 266 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 GLN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 458 ASN E 39 GLN ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN E 274 GLN ** E 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 ASN F 274 GLN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 ASN ** F 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 ASN C 375 ASN ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 GLN G 274 GLN ** G 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.190929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.134211 restraints weight = 33749.591| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.88 r_work: 0.3314 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31118 Z= 0.151 Angle : 0.592 11.228 42152 Z= 0.306 Chirality : 0.044 0.137 4524 Planarity : 0.005 0.059 5470 Dihedral : 9.526 146.648 4406 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.28 % Allowed : 22.30 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.02 (0.14), residues: 3829 helix: 0.21 (0.13), residues: 1528 sheet: -0.76 (0.23), residues: 445 loop : 0.25 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 331 TYR 0.027 0.002 TYR A 132 PHE 0.027 0.002 PHE B 403 TRP 0.007 0.001 TRP E 278 HIS 0.015 0.002 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (31110) covalent geometry : angle 0.59247 / 0.31 (42152) hydrogen bonds : bond 0.03824 / 2.58 ( 1248) hydrogen bonds : angle 5.93048 / 4.17 ( 3669) Misc. bond : bond 0.00056 / 0.03 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7658 Ramachandran restraints generated. 3829 Oldfield, 0 Emsley, 3829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 464 time to evaluate : 1.196 Fit side-chains REVERT: B 121 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7456 (tmtm) REVERT: B 157 LYS cc_start: 0.7804 (mptp) cc_final: 0.7563 (mptp) REVERT: B 447 ASP cc_start: 0.8613 (t70) cc_final: 0.8374 (t70) REVERT: B 468 THR cc_start: 0.7238 (p) cc_final: 0.6918 (t) REVERT: A 447 ASP cc_start: 0.8638 (t70) cc_final: 0.8401 (t70) REVERT: H 102 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7473 (mtpp) REVERT: H 475 MET cc_start: 0.7885 (mmm) cc_final: 0.7511 (mmm) REVERT: E 35 LEU cc_start: 0.8003 (mt) cc_final: 0.7690 (mt) REVERT: E 235 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6168 (m-30) REVERT: E 240 HIS cc_start: 0.8422 (t70) cc_final: 0.8111 (t-90) REVERT: E 272 GLU cc_start: 0.7331 (mp0) cc_final: 0.7112 (mp0) REVERT: E 475 MET cc_start: 0.7778 (mmm) cc_final: 0.7407 (mmm) REVERT: F 35 LEU cc_start: 0.7957 (mt) cc_final: 0.7690 (mt) REVERT: F 50 ASN cc_start: 0.8308 (m-40) cc_final: 0.7952 (m110) REVERT: F 271 ASP cc_start: 0.7423 (p0) cc_final: 0.7211 (p0) REVERT: F 272 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: F 280 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7677 (tp) REVERT: F 425 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8258 (mt-10) REVERT: F 475 MET cc_start: 0.7871 (mmm) cc_final: 0.7470 (mmm) REVERT: C 41 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7073 (mt-10) REVERT: G 15 ASP cc_start: 0.7452 (t0) cc_final: 0.7222 (m-30) REVERT: G 50 ASN cc_start: 0.8304 (m110) cc_final: 0.7903 (m110) REVERT: G 82 THR cc_start: 0.8193 (t) cc_final: 0.7890 (m) REVERT: G 235 ASP cc_start: 0.6799 (OUTLIER) cc_final: 0.6027 (m-30) REVERT: G 259 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7542 (mmtt) REVERT: G 351 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7484 (tm-30) REVERT: G 475 MET cc_start: 0.7881 (mmm) cc_final: 0.7455 (mmm) outliers start: 73 outliers final: 49 residues processed: 521 average time/residue: 0.7181 time to fit residues: 439.9712 Evaluate side-chains 501 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 443 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 278 TRP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 284 ARG Chi-restraints excluded: chain E residue 12 MET Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 425 GLU Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 351 GLU Chi-restraints excluded: chain G residue 471 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 75 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 206 optimal weight: 0.7980 chunk 50 optimal weight: 0.0070 chunk 315 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 300 optimal weight: 6.9990 chunk 329 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN A 266 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 GLN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 455 GLN H 458 ASN ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN E 274 GLN ** E 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 GLN E 458 ASN F 39 GLN F 274 GLN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 GLN F 458 ASN ** F 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 HIS ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 ASN G 39 GLN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 GLN G 274 GLN ** G 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 455 GLN G 458 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.189945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132616 restraints weight = 35053.023| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.00 r_work: 0.3282 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31118 Z= 0.181 Angle : 0.609 11.267 42152 Z= 0.314 Chirality : 0.044 0.148 4524 Planarity : 0.005 0.058 5470 Dihedral : 9.528 147.228 4406 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.18 % Allowed : 22.68 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.03 (0.14), residues: 3829 helix: 0.20 (0.13), residues: 1528 sheet: -0.72 (0.23), residues: 445 loop : 0.26 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 331 TYR 0.030 0.002 TYR C 132 PHE 0.032 0.002 PHE C 403 TRP 0.007 0.001 TRP E 278 HIS 0.016 0.002 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (31110) covalent geometry : angle 0.60901 / 0.31 (42152) hydrogen bonds : bond 0.03985 / 2.68 ( 1248) hydrogen bonds : angle 5.94787 / 4.17 ( 3669) Misc. bond : bond 0.00041 / 0.02 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17452.41 seconds wall clock time: 297 minutes 55.31 seconds (17875.31 seconds total)