Starting phenix.real_space_refine on Sun Jul 5 22:55:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q3k_72200/07_2026/9q3k_72200.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q3k_72200/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9q3k_72200/07_2026/9q3k_72200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q3k_72200/07_2026/9q3k_72200.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q3k_72200/07_2026/9q3k_72200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q3k_72200/07_2026/9q3k_72200.map" } 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-dev-6108/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, 24 Ad-hoc single atom residues: {' NI': 1} Unusual residues: {'4EY': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Ad-hoc single atom residues: {' NI': 1} Unusual residues: {'4EY': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Ad-hoc single atom residues: {' NI': 1} Unusual residues: {'4EY': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Ad-hoc single atom residues: {' NI': 1} Unusual residues: {'4EY': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Ad-hoc single atom residues: {' NI': 1} Unusual residues: {'4EY': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Ad-hoc single atom residues: {' NI': 1} Unusual residues: {'4EY': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Ad-hoc single atom residues: {' NI': 1} Unusual residues: {'4EY': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Ad-hoc single atom residues: {' NI': 1} Unusual residues: {'4EY': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 9.51, per 1000 atoms: 0.31 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: 2.71 Conformation dependent library (CDL) restraints added in 2.0 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: 1.21 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: 6.51 Time building geometry restraints manager: 3.59 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 3.000 nonbonded pdb=" NE2 HIS G 211 " pdb="NI NI G 501 " model vdw 1.980 3.000 nonbonded pdb=" NE2 HIS E 211 " pdb="NI NI E 501 " model vdw 1.981 3.000 nonbonded pdb=" NE2 HIS F 211 " pdb="NI NI F 501 " model vdw 1.983 3.000 nonbonded pdb=" NE2 HIS C 211 " pdb="NI NI C 501 " model vdw 1.990 3.000 ... (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: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 32.780 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.370 ------------------------------------------------------------------------------- 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 : 1.148 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: 0.6947 time to fit residues: 398.2714 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 : 1.082 ------------------------------------------------------------------------------- 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: 0.7980 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: 1.5184 ------------------------------------------------------------------------------- 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 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 ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 HIS H 240 HIS 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 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 ASN ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN ** 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.190519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129809 restraints weight = 34854.553| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.65 r_work: 0.3303 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.0888 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= 0.190 Angle : 0.603 11.004 42152 Z= 0.311 Chirality : 0.045 0.141 4524 Planarity : 0.005 0.058 5470 Dihedral : 9.898 145.377 4434 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.78 % Allowed : 20.71 % 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: 0.38 (0.14), residues: 3829 helix: 0.43 (0.13), residues: 1528 sheet: -0.01 (0.24), residues: 445 loop : 0.36 (0.16), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 431 TYR 0.017 0.002 TYR E 132 PHE 0.032 0.002 PHE G 403 TRP 0.005 0.001 TRP G 204 HIS 0.011 0.002 HIS E 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (31110) covalent geometry : angle 0.60333 / 0.31 (42152) hydrogen bonds : bond 0.04458 / 3.01 ( 1248) hydrogen bonds : angle 6.05523 / 4.26 ( 3669) Misc. bond : bond 0.00043 / 0.02 ( 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 553 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 464 time to evaluate : 0.965 Fit side-chains REVERT: B 121 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7556 (tmtm) REVERT: B 266 ASN cc_start: 0.8015 (m-40) cc_final: 0.7790 (m110) REVERT: B 447 ASP cc_start: 0.8626 (t70) cc_final: 0.8379 (t70) REVERT: D 335 ASP cc_start: 0.7187 (OUTLIER) cc_final: 0.6286 (t0) REVERT: D 447 ASP cc_start: 0.8604 (t70) cc_final: 0.8371 (t70) REVERT: A 207 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8049 (mp) REVERT: A 447 ASP cc_start: 0.8633 (t70) cc_final: 0.8404 (t70) REVERT: H 15 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.7025 (t0) REVERT: H 240 HIS cc_start: 0.8270 (t70) cc_final: 0.8059 (t-90) REVERT: H 319 MET cc_start: 0.9041 (tpt) cc_final: 0.8784 (tpt) REVERT: E 207 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8607 (mt) REVERT: E 272 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: E 475 MET cc_start: 0.7543 (mmm) cc_final: 0.7232 (mmm) REVERT: F 35 LEU cc_start: 0.7947 (mt) cc_final: 0.7678 (mt) REVERT: F 102 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7574 (mtpp) REVERT: F 272 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: F 280 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7745 (tp) REVERT: F 475 MET cc_start: 0.7853 (mmm) cc_final: 0.7381 (mmm) REVERT: C 335 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.6517 (t0) REVERT: C 447 ASP cc_start: 0.8603 (t70) cc_final: 0.8352 (t70) REVERT: G 15 ASP cc_start: 0.7562 (t0) cc_final: 0.7271 (m-30) REVERT: G 50 ASN cc_start: 0.8232 (m110) cc_final: 0.7862 (m110) REVERT: G 120 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8028 (mm-30) REVERT: G 336 ASN cc_start: 0.8010 (p0) cc_final: 0.7681 (p0) REVERT: G 351 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: G 475 MET cc_start: 0.7711 (mmm) cc_final: 0.7421 (mmm) outliers start: 89 outliers final: 38 residues processed: 528 average time/residue: 0.6576 time to fit residues: 408.5657 Evaluate side-chains 490 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 441 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 372 VAL Chi-restraints excluded: chain B residue 411 LEU 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 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 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 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 160 GLN Chi-restraints excluded: chain C residue 202 THR 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 335 ASP 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: 7.9990 chunk 90 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 363 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 354 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 135 optimal weight: 0.4980 chunk 335 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- 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 303 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 240 HIS E 262 GLN E 274 GLN ** E 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 GLN 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 375 ASN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 ASN ** C 118 ASN ** 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 375 ASN ** G 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 455 GLN G 458 ASN ** G 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.183696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123434 restraints weight = 35196.237| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.84 r_work: 0.3181 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.113 31118 Z= 0.429 Angle : 0.778 15.533 42152 Z= 0.402 Chirality : 0.052 0.191 4524 Planarity : 0.006 0.059 5470 Dihedral : 10.071 147.320 4415 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.46 % Allowed : 19.68 % Favored : 76.86 % 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: 0.15 (0.13), residues: 3829 helix: 0.17 (0.13), residues: 1512 sheet: 0.18 (0.25), residues: 349 loop : 0.20 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 431 TYR 0.028 0.003 TYR F 190 PHE 0.044 0.004 PHE E 403 TRP 0.011 0.003 TRP E 278 HIS 0.017 0.003 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00944 / 0.43 (31110) covalent geometry : angle 0.77796 / 0.40 (42152) hydrogen bonds : bond 0.05717 / 3.86 ( 1248) hydrogen bonds : angle 6.54937 / 4.60 ( 3669) Misc. bond : bond 0.00164 / 0.08 ( 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 597 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 486 time to evaluate : 1.228 Fit side-chains REVERT: B 121 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7550 (tmtm) REVERT: B 385 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7958 (mp0) REVERT: D 103 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.6733 (tptp) REVERT: D 121 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7611 (tmtm) REVERT: D 385 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7975 (mp0) REVERT: A 319 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8731 (tpp) REVERT: A 385 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7981 (mp0) REVERT: H 15 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7333 (t0) REVERT: H 46 ASP cc_start: 0.7422 (t70) cc_final: 0.7114 (m-30) REVERT: E 235 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6169 (m-30) REVERT: E 240 HIS cc_start: 0.8512 (t70) cc_final: 0.8203 (t-90) REVERT: E 272 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: F 35 LEU cc_start: 0.7983 (mt) cc_final: 0.7740 (mt) REVERT: F 157 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8119 (mttm) REVERT: F 272 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: F 280 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7927 (tp) REVERT: F 464 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7627 (mtpt) REVERT: F 475 MET cc_start: 0.7877 (mmm) cc_final: 0.7432 (mmm) REVERT: C 385 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7965 (mp0) REVERT: G 235 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6126 (m-30) REVERT: G 446 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7666 (mp0) REVERT: G 464 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7593 (mmtm) REVERT: G 475 MET cc_start: 0.7791 (mmm) cc_final: 0.7443 (mmm) outliers start: 111 outliers final: 42 residues processed: 558 average time/residue: 0.7274 time to fit residues: 472.1518 Evaluate side-chains 511 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 456 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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 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 D residue 103 LYS 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 174 ASP 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 319 MET 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 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 99 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 237 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 F residue 99 VAL 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 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 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 411 LEU Chi-restraints excluded: chain G residue 464 LYS 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: 0.9990 chunk 224 optimal weight: 0.7980 chunk 193 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 281 optimal weight: 0.6980 chunk 372 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 364 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 183 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 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 HIS 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 ** C 118 ASN ** 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 ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.189891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132556 restraints weight = 41182.541| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.09 r_work: 0.3257 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 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 = 0.3115 r_free = 0.3115 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: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31118 Z= 0.152 Angle : 0.592 11.050 42152 Z= 0.305 Chirality : 0.044 0.135 4524 Planarity : 0.005 0.060 5470 Dihedral : 9.717 144.897 4409 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.03 % Allowed : 20.59 % Favored : 76.39 % 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: -0.49 (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 H 85 TYR 0.017 0.002 TYR E 169 PHE 0.030 0.002 PHE F 403 TRP 0.006 0.001 TRP G 278 HIS 0.014 0.002 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (31110) covalent geometry : angle 0.59222 / 0.31 (42152) hydrogen bonds : bond 0.04005 / 2.71 ( 1248) hydrogen bonds : angle 5.99358 / 4.21 ( 3669) Misc. bond : bond 0.00038 / 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 598 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 501 time to evaluate : 1.192 Fit side-chains REVERT: B 121 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7538 (tmtm) REVERT: B 130 ASP cc_start: 0.7373 (t0) cc_final: 0.7096 (m-30) REVERT: B 447 ASP cc_start: 0.8646 (t70) cc_final: 0.8406 (t70) REVERT: D 109 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8320 (mm) REVERT: D 289 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7532 (t80) REVERT: D 447 ASP cc_start: 0.8686 (t70) cc_final: 0.8483 (t70) REVERT: A 157 LYS cc_start: 0.7967 (mptp) cc_final: 0.7613 (mptp) REVERT: A 191 SER cc_start: 0.5106 (OUTLIER) cc_final: 0.4876 (p) REVERT: A 319 MET cc_start: 0.8998 (mmm) cc_final: 0.8792 (tpt) REVERT: A 385 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7924 (mp0) REVERT: H 240 HIS cc_start: 0.8464 (t70) cc_final: 0.8194 (t-90) REVERT: H 475 MET cc_start: 0.7726 (mmm) cc_final: 0.7412 (mmm) REVERT: E 240 HIS cc_start: 0.8409 (t70) cc_final: 0.8163 (t-90) REVERT: E 272 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: E 425 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8403 (mt-10) REVERT: E 475 MET cc_start: 0.7632 (mmm) cc_final: 0.7351 (mmm) REVERT: F 35 LEU cc_start: 0.7904 (mt) cc_final: 0.7663 (mt) REVERT: F 157 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8051 (mttm) REVERT: F 271 ASP cc_start: 0.7416 (p0) cc_final: 0.7215 (p0) REVERT: F 272 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: F 475 MET cc_start: 0.7831 (mmm) cc_final: 0.7376 (mmm) REVERT: C 41 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7092 (mt-10) REVERT: C 317 MET cc_start: 0.9100 (mmm) cc_final: 0.8816 (mmm) REVERT: C 385 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7942 (mp0) REVERT: G 50 ASN cc_start: 0.8340 (m110) cc_final: 0.7924 (m110) REVERT: G 82 THR cc_start: 0.8253 (t) cc_final: 0.7898 (m) REVERT: G 259 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7652 (mtmt) REVERT: G 336 ASN cc_start: 0.8089 (p0) cc_final: 0.7721 (p0) REVERT: G 446 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7427 (tp30) REVERT: G 475 MET cc_start: 0.7774 (mmm) cc_final: 0.7283 (mmm) outliers start: 97 outliers final: 44 residues processed: 565 average time/residue: 0.7261 time to fit residues: 480.2184 Evaluate side-chains 506 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 452 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 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 224 VAL Chi-restraints excluded: chain D residue 278 TRP Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 289 PHE 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 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 82 THR 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 301 MET 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 272 GLU 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 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 411 LEU Chi-restraints excluded: chain C residue 41 GLU 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 259 LYS 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: 4.9990 chunk 196 optimal weight: 8.9990 chunk 268 optimal weight: 10.0000 chunk 282 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 344 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 381 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** 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 ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 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 262 GLN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 GLN F 458 ASN ** C 118 ASN ** 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 ** 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 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 458 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.184104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.124365 restraints weight = 34907.702| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.92 r_work: 0.3185 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 31118 Z= 0.360 Angle : 0.721 14.655 42152 Z= 0.371 Chirality : 0.049 0.189 4524 Planarity : 0.006 0.060 5470 Dihedral : 9.872 147.209 4407 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.21 % Allowed : 20.80 % Favored : 75.98 % 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: 0.15 (0.13), residues: 3829 helix: 0.18 (0.13), residues: 1520 sheet: -0.08 (0.25), residues: 349 loop : 0.24 (0.15), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 389 TYR 0.025 0.003 TYR C 132 PHE 0.043 0.003 PHE E 403 TRP 0.011 0.003 TRP E 278 HIS 0.019 0.003 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00797 / 0.36 (31110) covalent geometry : angle 0.72075 / 0.37 (42152) hydrogen bonds : bond 0.05162 / 3.48 ( 1248) hydrogen bonds : angle 6.35343 / 4.46 ( 3669) Misc. bond : bond 0.00117 / 0.06 ( 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 589 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 486 time to evaluate : 1.210 Fit side-chains REVERT: B 120 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7832 (mm-30) REVERT: B 121 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7558 (tmtm) REVERT: B 130 ASP cc_start: 0.7396 (t0) cc_final: 0.7104 (m-30) REVERT: B 385 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7974 (mp0) REVERT: D 121 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7565 (tmtm) REVERT: D 259 LYS cc_start: 0.7496 (mtmt) cc_final: 0.7226 (mttp) REVERT: D 385 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7966 (mp0) REVERT: A 191 SER cc_start: 0.5331 (OUTLIER) cc_final: 0.5107 (p) REVERT: A 259 LYS cc_start: 0.7554 (mttt) cc_final: 0.7274 (mttp) REVERT: A 385 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7946 (mp0) REVERT: H 475 MET cc_start: 0.7711 (mmm) cc_final: 0.7470 (mmm) REVERT: E 235 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6191 (m-30) REVERT: E 272 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: E 475 MET cc_start: 0.7728 (mmm) cc_final: 0.7452 (mmm) REVERT: F 35 LEU cc_start: 0.7928 (mt) cc_final: 0.7643 (mt) REVERT: F 157 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8164 (mttm) REVERT: F 272 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: F 280 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7833 (tp) REVERT: F 446 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7689 (mp0) REVERT: F 475 MET cc_start: 0.7839 (mmm) cc_final: 0.7471 (mmm) REVERT: C 41 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7086 (mt-10) REVERT: C 385 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7938 (mp0) REVERT: G 15 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7575 (t0) REVERT: G 82 THR cc_start: 0.8368 (t) cc_final: 0.8021 (m) REVERT: G 235 ASP cc_start: 0.6863 (OUTLIER) cc_final: 0.6088 (m-30) REVERT: G 259 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7736 (mtmt) REVERT: G 280 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7945 (tp) REVERT: G 475 MET cc_start: 0.7788 (mmm) cc_final: 0.7427 (mmm) outliers start: 103 outliers final: 48 residues processed: 553 average time/residue: 0.7464 time to fit residues: 481.4850 Evaluate side-chains 533 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 472 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 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 D residue 38 ASP 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 191 SER Chi-restraints excluded: chain A residue 202 THR 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 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 E residue 12 MET Chi-restraints excluded: chain E residue 66 LYS 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 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 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 272 GLU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain C residue 41 GLU 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 15 ASP 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 259 LYS Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 411 LEU 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: 5.9990 chunk 123 optimal weight: 9.9990 chunk 337 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 271 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 chunk 336 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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** ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 262 GLN F 274 GLN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 ASN ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 HIS ** 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 262 GLN G 274 GLN ** G 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.187864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.129847 restraints weight = 34667.879| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.85 r_work: 0.3250 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 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 = 0.3120 r_free = 0.3120 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: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31118 Z= 0.184 Angle : 0.612 12.061 42152 Z= 0.316 Chirality : 0.044 0.144 4524 Planarity : 0.005 0.060 5470 Dihedral : 9.704 145.853 4407 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.09 % Allowed : 21.05 % 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: 0.14 (0.14), residues: 3829 helix: 0.25 (0.13), residues: 1528 sheet: -0.63 (0.23), residues: 397 loop : 0.31 (0.15), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.027 0.002 TYR B 132 PHE 0.031 0.002 PHE H 403 TRP 0.008 0.001 TRP E 278 HIS 0.014 0.002 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (31110) covalent geometry : angle 0.61232 / 0.32 (42152) hydrogen bonds : bond 0.04198 / 2.83 ( 1248) hydrogen bonds : angle 6.07745 / 4.26 ( 3669) Misc. bond : bond 0.00039 / 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 581 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 482 time to evaluate : 0.883 Fit side-chains REVERT: B 103 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7328 (tptm) REVERT: B 121 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7521 (tmtm) REVERT: B 130 ASP cc_start: 0.7328 (t0) cc_final: 0.7074 (m-30) REVERT: D 447 ASP cc_start: 0.8641 (t70) cc_final: 0.8417 (t70) REVERT: A 191 SER cc_start: 0.5297 (OUTLIER) cc_final: 0.5071 (p) REVERT: A 385 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7905 (mp0) REVERT: A 468 THR cc_start: 0.7322 (p) cc_final: 0.6999 (t) REVERT: H 102 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7440 (mtpp) REVERT: H 475 MET cc_start: 0.7726 (mmm) cc_final: 0.7475 (mmm) REVERT: E 207 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8455 (mt) REVERT: E 235 ASP cc_start: 0.6905 (OUTLIER) cc_final: 0.6115 (m-30) REVERT: E 240 HIS cc_start: 0.8442 (t70) cc_final: 0.8127 (t-90) REVERT: E 272 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: E 475 MET cc_start: 0.7611 (mmm) cc_final: 0.7337 (mmm) REVERT: F 35 LEU cc_start: 0.7909 (mt) cc_final: 0.7641 (mt) REVERT: F 157 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8127 (mttm) REVERT: F 271 ASP cc_start: 0.7401 (p0) cc_final: 0.7191 (p0) REVERT: F 272 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: F 280 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7711 (tp) REVERT: F 284 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7687 (tmt170) REVERT: F 475 MET cc_start: 0.7853 (mmm) cc_final: 0.7414 (mmm) REVERT: C 41 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: C 385 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7950 (mp0) REVERT: G 15 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7427 (t0) REVERT: G 50 ASN cc_start: 0.8337 (m110) cc_final: 0.7877 (m110) REVERT: G 82 THR cc_start: 0.8274 (t) cc_final: 0.7952 (m) REVERT: G 235 ASP cc_start: 0.6833 (OUTLIER) cc_final: 0.6019 (m-30) REVERT: G 259 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7655 (mtmt) REVERT: G 475 MET cc_start: 0.7791 (mmm) cc_final: 0.7472 (mmm) outliers start: 99 outliers final: 45 residues processed: 550 average time/residue: 0.6617 time to fit residues: 426.9837 Evaluate side-chains 519 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 459 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 411 LEU Chi-restraints excluded: chain D residue 471 VAL 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 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 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 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 284 ARG Chi-restraints excluded: chain F residue 289 PHE 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 224 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain G residue 15 ASP 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 259 LYS 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: 3.9990 chunk 213 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 253 optimal weight: 0.0060 chunk 355 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 chunk 281 optimal weight: 0.8980 chunk 191 optimal weight: 0.0370 chunk 277 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 293 optimal weight: 0.9980 overall best weight: 0.5674 ------------------------------------------------------------------------------- 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 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 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 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 GLN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 ASN ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.192042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132703 restraints weight = 35778.252| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.65 r_work: 0.3345 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31118 Z= 0.134 Angle : 0.571 10.861 42152 Z= 0.293 Chirality : 0.043 0.135 4524 Planarity : 0.005 0.060 5470 Dihedral : 9.494 146.073 4407 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.50 % Allowed : 21.71 % 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: 0.12 (0.14), residues: 3829 helix: 0.35 (0.13), residues: 1528 sheet: -0.73 (0.23), residues: 445 loop : 0.25 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 231 TYR 0.022 0.002 TYR C 132 PHE 0.026 0.002 PHE E 403 TRP 0.007 0.001 TRP E 278 HIS 0.012 0.002 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (31110) covalent geometry : angle 0.57103 / 0.29 (42152) hydrogen bonds : bond 0.03671 / 2.48 ( 1248) hydrogen bonds : angle 5.81402 / 4.08 ( 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 561 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 481 time to evaluate : 1.050 Fit side-chains REVERT: B 103 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7332 (tptm) REVERT: B 120 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7371 (mm-30) REVERT: B 121 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7492 (tmtm) REVERT: B 157 LYS cc_start: 0.7842 (mptp) cc_final: 0.7576 (mptp) REVERT: B 447 ASP cc_start: 0.8622 (t70) cc_final: 0.8388 (t70) REVERT: B 468 THR cc_start: 0.7202 (p) cc_final: 0.6882 (t) REVERT: D 447 ASP cc_start: 0.8649 (t70) cc_final: 0.8412 (t70) REVERT: A 191 SER cc_start: 0.5254 (OUTLIER) cc_final: 0.5038 (p) REVERT: A 443 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8111 (mt-10) REVERT: H 102 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7437 (mtpp) REVERT: H 240 HIS cc_start: 0.8501 (t70) cc_final: 0.8211 (t-90) REVERT: H 351 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: H 475 MET cc_start: 0.7770 (mmm) cc_final: 0.7519 (mmm) REVERT: E 207 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8421 (mt) REVERT: E 235 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6151 (m-30) REVERT: E 240 HIS cc_start: 0.8399 (t70) cc_final: 0.8154 (t-90) REVERT: E 272 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: E 351 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: F 35 LEU cc_start: 0.7981 (mt) cc_final: 0.7732 (mt) REVERT: F 271 ASP cc_start: 0.7443 (p0) cc_final: 0.7231 (p0) REVERT: F 272 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: F 280 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7705 (tp) REVERT: F 336 ASN cc_start: 0.7937 (p0) cc_final: 0.7639 (p0) REVERT: F 351 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: F 475 MET cc_start: 0.7868 (mmm) cc_final: 0.7525 (mmm) REVERT: C 41 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7044 (mt-10) REVERT: C 233 LYS cc_start: 0.6296 (mttp) cc_final: 0.5911 (mmmt) REVERT: C 447 ASP cc_start: 0.8585 (t70) cc_final: 0.8348 (t70) REVERT: G 15 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7366 (t0) REVERT: G 50 ASN cc_start: 0.8354 (m110) cc_final: 0.7978 (m110) REVERT: G 82 THR cc_start: 0.8152 (t) cc_final: 0.7827 (m) REVERT: G 259 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7536 (mmtt) REVERT: G 351 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7557 (mp0) REVERT: G 475 MET cc_start: 0.7845 (mmm) cc_final: 0.7517 (mmm) outliers start: 80 outliers final: 38 residues processed: 540 average time/residue: 0.6480 time to fit residues: 410.6777 Evaluate side-chains 503 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 450 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 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 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 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 215 VAL Chi-restraints excluded: chain H residue 280 LEU 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 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 289 PHE 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 121 LYS Chi-restraints excluded: chain F residue 126 VAL 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 289 PHE Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 259 LYS 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: 2.9990 chunk 226 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 202 optimal weight: 9.9990 chunk 363 optimal weight: 0.7980 chunk 216 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 178 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ** 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 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 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 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 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 ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.191460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130658 restraints weight = 41343.510| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.08 r_work: 0.3288 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 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 = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31118 Z= 0.148 Angle : 0.577 11.031 42152 Z= 0.296 Chirality : 0.043 0.138 4524 Planarity : 0.005 0.060 5470 Dihedral : 9.423 146.118 4404 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.31 % Allowed : 22.36 % Favored : 75.33 % 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: 0.10 (0.14), residues: 3829 helix: 0.34 (0.13), residues: 1528 sheet: -0.44 (0.25), residues: 373 loop : 0.12 (0.15), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 231 TYR 0.025 0.002 TYR B 132 PHE 0.028 0.002 PHE C 403 TRP 0.007 0.001 TRP E 278 HIS 0.012 0.002 HIS F 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (31110) covalent geometry : angle 0.57708 / 0.30 (42152) hydrogen bonds : bond 0.03738 / 2.51 ( 1248) hydrogen bonds : angle 5.80724 / 4.08 ( 3669) Misc. bond : bond 0.00047 / 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 536 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 462 time to evaluate : 1.185 Fit side-chains REVERT: B 103 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7332 (tptm) REVERT: B 121 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7478 (tmtm) REVERT: B 447 ASP cc_start: 0.8662 (t70) cc_final: 0.8419 (t70) REVERT: D 447 ASP cc_start: 0.8687 (t70) cc_final: 0.8446 (t70) REVERT: A 443 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8177 (mt-10) REVERT: H 240 HIS cc_start: 0.8471 (t70) cc_final: 0.8174 (t-90) REVERT: H 351 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: H 475 MET cc_start: 0.7703 (mmm) cc_final: 0.7498 (mmm) REVERT: E 207 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8381 (mt) REVERT: E 235 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6096 (m-30) REVERT: E 240 HIS cc_start: 0.8379 (t70) cc_final: 0.8128 (t-90) REVERT: E 351 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: F 35 LEU cc_start: 0.8004 (mt) cc_final: 0.7758 (mt) REVERT: F 46 ASP cc_start: 0.7626 (t70) cc_final: 0.7354 (t70) REVERT: F 50 ASN cc_start: 0.8292 (m-40) cc_final: 0.7950 (m110) REVERT: F 102 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7430 (mtpp) REVERT: F 271 ASP cc_start: 0.7364 (p0) cc_final: 0.7163 (p0) REVERT: F 272 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: F 280 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7642 (tp) REVERT: F 351 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: F 425 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8251 (mt-10) REVERT: F 475 MET cc_start: 0.7810 (mmm) cc_final: 0.7428 (mmm) REVERT: C 41 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7044 (mt-10) REVERT: C 233 LYS cc_start: 0.6160 (mttp) cc_final: 0.5788 (mmmt) REVERT: G 15 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7303 (t0) REVERT: G 50 ASN cc_start: 0.8290 (m110) cc_final: 0.7893 (m110) REVERT: G 82 THR cc_start: 0.8126 (t) cc_final: 0.7797 (m) REVERT: G 351 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7559 (mp0) REVERT: G 366 LYS cc_start: 0.8322 (ptpp) cc_final: 0.8112 (ptpp) REVERT: G 475 MET cc_start: 0.7813 (mmm) cc_final: 0.7386 (mmm) outliers start: 74 outliers final: 40 residues processed: 516 average time/residue: 0.6698 time to fit residues: 405.3860 Evaluate side-chains 489 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 436 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 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 A residue 38 ASP 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 H residue 82 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 ARG Chi-restraints excluded: chain H residue 351 GLU 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 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 191 SER Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 289 PHE Chi-restraints excluded: chain F residue 351 GLU 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 224 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 289 PHE 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: 8.9990 chunk 81 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 281 optimal weight: 0.2980 chunk 99 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 209 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 247 optimal weight: 5.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** 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 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 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 GLN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 GLN F 458 ASN ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN ** C 375 ASN ** 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 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 = 0.4105 r_free = 0.4105 target = 0.186057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124883 restraints weight = 31855.379| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.57 r_work: 0.3238 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1652 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= 0.294 Angle : 0.682 13.846 42152 Z= 0.352 Chirality : 0.048 0.183 4524 Planarity : 0.005 0.060 5470 Dihedral : 9.691 148.372 4404 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.37 % Allowed : 22.33 % Favored : 75.30 % 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: 0.17 (0.13), residues: 1520 sheet: -0.60 (0.24), residues: 397 loop : 0.31 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 389 TYR 0.032 0.003 TYR D 132 PHE 0.042 0.003 PHE E 403 TRP 0.009 0.002 TRP A 204 HIS 0.016 0.002 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.29 (31110) covalent geometry : angle 0.68236 / 0.35 (42152) hydrogen bonds : bond 0.04698 / 3.15 ( 1248) hydrogen bonds : angle 6.18719 / 4.34 ( 3669) Misc. bond : bond 0.00068 / 0.03 ( 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 544 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 468 time to evaluate : 1.178 Fit side-chains REVERT: B 52 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7258 (mt) REVERT: B 103 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7388 (tptm) REVERT: B 121 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7490 (tmtm) REVERT: D 385 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7971 (mp0) REVERT: A 385 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7895 (mp0) REVERT: A 468 THR cc_start: 0.7347 (p) cc_final: 0.7041 (t) REVERT: E 235 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6170 (m-30) REVERT: E 272 GLU cc_start: 0.7371 (mp0) cc_final: 0.7123 (mp0) REVERT: F 35 LEU cc_start: 0.8038 (mt) cc_final: 0.7791 (mt) REVERT: F 102 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7483 (mtpp) REVERT: F 272 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: F 280 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7795 (tp) REVERT: F 475 MET cc_start: 0.7884 (mmm) cc_final: 0.7457 (mmm) REVERT: C 41 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7086 (mt-10) REVERT: C 385 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7943 (mp0) REVERT: G 82 THR cc_start: 0.8304 (t) cc_final: 0.7993 (m) REVERT: G 259 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7638 (mmtt) REVERT: G 475 MET cc_start: 0.7851 (mmm) cc_final: 0.7432 (mmm) outliers start: 76 outliers final: 45 residues processed: 523 average time/residue: 0.7278 time to fit residues: 444.9671 Evaluate side-chains 504 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 450 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 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 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 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 99 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 284 ARG Chi-restraints excluded: chain H residue 351 GLU 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 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 191 SER Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 41 GLU 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 259 LYS Chi-restraints excluded: chain G residue 411 LEU 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: 0.9990 chunk 326 optimal weight: 0.6980 chunk 275 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 195 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 276 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 323 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 410 HIS ** 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 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 458 ASN 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 ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 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 458 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.190881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131357 restraints weight = 33763.673| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.61 r_work: 0.3319 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31118 Z= 0.144 Angle : 0.593 11.551 42152 Z= 0.305 Chirality : 0.044 0.137 4524 Planarity : 0.005 0.060 5470 Dihedral : 9.516 146.322 4404 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.78 % Allowed : 23.02 % Favored : 75.20 % 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: 0.22 (0.13), residues: 1528 sheet: -0.72 (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 F 331 TYR 0.030 0.002 TYR C 132 PHE 0.028 0.002 PHE H 403 TRP 0.007 0.001 TRP E 278 HIS 0.012 0.002 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (31110) covalent geometry : angle 0.59299 / 0.30 (42152) hydrogen bonds : bond 0.03795 / 2.56 ( 1248) hydrogen bonds : angle 5.91809 / 4.16 ( 3669) Misc. bond : bond 0.00050 / 0.02 ( 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 517 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 460 time to evaluate : 1.197 Fit side-chains REVERT: B 52 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7211 (mt) REVERT: B 103 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7264 (tptm) REVERT: B 447 ASP cc_start: 0.8625 (t70) cc_final: 0.8390 (t70) REVERT: B 468 THR cc_start: 0.7248 (p) cc_final: 0.6934 (t) REVERT: D 447 ASP cc_start: 0.8660 (t70) cc_final: 0.8427 (t70) REVERT: E 235 ASP cc_start: 0.6822 (OUTLIER) cc_final: 0.6103 (m-30) REVERT: E 240 HIS cc_start: 0.8413 (t70) cc_final: 0.8126 (t-90) REVERT: F 35 LEU cc_start: 0.8006 (mt) cc_final: 0.7766 (mt) REVERT: F 66 LYS cc_start: 0.7966 (mttp) cc_final: 0.7541 (mtmt) REVERT: F 271 ASP cc_start: 0.7428 (p0) cc_final: 0.7219 (p0) REVERT: F 272 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: F 280 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7679 (tp) REVERT: F 475 MET cc_start: 0.7881 (mmm) cc_final: 0.7500 (mmm) REVERT: C 41 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7014 (mt-10) REVERT: C 233 LYS cc_start: 0.6328 (mttp) cc_final: 0.5962 (mmmt) REVERT: C 241 MET cc_start: 0.8503 (mtt) cc_final: 0.8252 (mtp) REVERT: G 15 ASP cc_start: 0.7295 (t0) cc_final: 0.7074 (m-30) REVERT: G 50 ASN cc_start: 0.8346 (m110) cc_final: 0.7954 (m110) REVERT: G 82 THR cc_start: 0.8202 (t) cc_final: 0.7913 (m) REVERT: G 259 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7602 (mmtt) REVERT: G 351 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7566 (mp0) REVERT: G 475 MET cc_start: 0.7873 (mmm) cc_final: 0.7434 (mmm) outliers start: 57 outliers final: 40 residues processed: 502 average time/residue: 0.6902 time to fit residues: 406.6314 Evaluate side-chains 491 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 444 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 216 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 GLU 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 A residue 38 ASP 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 99 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 230 MET 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 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 191 SER Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 41 GLU 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 259 LYS Chi-restraints excluded: chain G residue 289 PHE 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: 0.5980 chunk 50 optimal weight: 0.0770 chunk 315 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 300 optimal weight: 5.9990 chunk 329 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.9342 ------------------------------------------------------------------------------- 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 ** 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** ** 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 274 GLN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 GLN F 458 ASN ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** 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 455 GLN G 458 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.187762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.130767 restraints weight = 35049.285| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.82 r_work: 0.3241 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- 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 = 0.37 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 = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 31118 Z= 0.219 Angle : 0.633 12.885 42152 Z= 0.326 Chirality : 0.045 0.160 4524 Planarity : 0.005 0.060 5470 Dihedral : 9.567 146.649 4404 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.93 % Allowed : 23.27 % Favored : 74.80 % 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: 0.04 (0.14), residues: 3829 helix: 0.18 (0.13), residues: 1528 sheet: -0.65 (0.23), residues: 445 loop : 0.28 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 389 TYR 0.031 0.002 TYR C 132 PHE 0.035 0.003 PHE A 403 TRP 0.008 0.002 TRP E 278 HIS 0.018 0.002 HIS G 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 (31110) covalent geometry : angle 0.63294 / 0.33 (42152) hydrogen bonds : bond 0.04231 / 2.84 ( 1248) hydrogen bonds : angle 6.02524 / 4.23 ( 3669) Misc. bond : bond 0.00042 / 0.02 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16904.39 seconds wall clock time: 288 minutes 23.14 seconds (17303.14 seconds total)