Starting phenix.real_space_refine on Fri Mar 6 19:21:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o81_0649/03_2026/6o81_0649_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o81_0649/03_2026/6o81_0649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6o81_0649/03_2026/6o81_0649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o81_0649/03_2026/6o81_0649.map" model { file = "/net/cci-nas-00/data/ceres_data/6o81_0649/03_2026/6o81_0649_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o81_0649/03_2026/6o81_0649_neut.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 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: 5 Type Number sf(0) Gaussians S 128 5.16 5 Cl 4 4.86 5 C 21225 2.51 5 N 6093 2.21 5 O 6243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33693 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4055 Classifications: {'peptide': 590} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 177} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 832 Unresolved non-hydrogen dihedrals: 539 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLU:plan': 23, 'ARG:plan': 10, 'ASN:plan1': 10, 'GLN:plan1': 16, 'ASP:plan': 11, 'PHE:plan': 9, 'TYR:plan': 5, 'HIS:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 391 Chain: "B" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4055 Classifications: {'peptide': 590} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 177} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 832 Unresolved non-hydrogen dihedrals: 539 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLU:plan': 23, 'ARG:plan': 10, 'ASN:plan1': 10, 'GLN:plan1': 16, 'ASP:plan': 11, 'PHE:plan': 9, 'TYR:plan': 5, 'HIS:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 391 Chain: "C" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2462 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2472 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2775 Classifications: {'peptide': 357} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2776 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2051 Classifications: {'peptide': 285} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 50} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 71 Chain: "H" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2051 Classifications: {'peptide': 285} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 50} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 71 Chain: "I" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1634 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 8, 'ASP:plan': 12, 'GLN:plan1': 2, 'GLU:plan': 7, 'PHE:plan': 2, 'TYR:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 164 Chain: "J" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1634 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 8, 'ASP:plan': 12, 'GLN:plan1': 2, 'GLU:plan': 7, 'PHE:plan': 2, 'TYR:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 164 Chain: "L" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1651 Classifications: {'peptide': 275} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 168} Link IDs: {'PTRANS': 9, 'TRANS': 265} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 740 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ARG:plan': 18, 'GLU:plan': 25, 'ASP:plan': 13, 'ASN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 296 Chain: "M" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1651 Classifications: {'peptide': 275} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 168} Link IDs: {'PTRANS': 9, 'TRANS': 265} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 740 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ARG:plan': 18, 'GLU:plan': 25, 'ASP:plan': 13, 'ASN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 296 Chain: "S" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2113 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 328} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1054 Unresolved non-hydrogen angles: 1342 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 143 Planarities with less than four sites: {'ASP:plan': 14, 'HIS:plan': 9, 'GLU:plan': 26, 'ARG:plan': 12, 'GLN:plan1': 13, 'ASN:plan1': 14, 'PHE:plan': 6, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 423 Chain: "T" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2113 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 328} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1054 Unresolved non-hydrogen angles: 1342 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 143 Planarities with less than four sites: {'ASP:plan': 14, 'HIS:plan': 9, 'GLU:plan': 26, 'ARG:plan': 12, 'GLN:plan1': 13, 'ASN:plan1': 14, 'PHE:plan': 6, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 423 Chain: "d" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "e" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 60 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 30 Unusual residues: {'C7B': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 30 Unusual residues: {'C7B': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C09AC7B C 401 " occ=0.50 ... (58 atoms not shown) pdb="CL2 BC7B C 401 " occ=0.50 Time building chain proxies: 7.68, per 1000 atoms: 0.23 Number of scatterers: 33693 At special positions: 0 Unit cell: (261.396, 189.06, 124.122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 128 16.00 O 6243 8.00 N 6093 7.00 C 21225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.4 seconds 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9404 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 52 sheets defined 43.8% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.834A pdb=" N GLN A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.685A pdb=" N GLN A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 279 removed outlier: 3.568A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.576A pdb=" N GLN A 333 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 334 " --> pdb=" O THR A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 334' Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 550 through 567 Processing helix chain 'A' and resid 570 through 586 Processing helix chain 'A' and resid 588 through 607 Proline residue: A 604 - end of helix Processing helix chain 'A' and resid 613 through 628 removed outlier: 3.956A pdb=" N TYR A 617 " --> pdb=" O ASP A 613 " (cutoff:3.500A) Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 638 through 656 Processing helix chain 'A' and resid 657 through 661 removed outlier: 5.200A pdb=" N ILE A 661 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 671 removed outlier: 3.555A pdb=" N LEU A 667 " --> pdb=" O MET A 663 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 687 Processing helix chain 'A' and resid 693 through 699 Processing helix chain 'A' and resid 700 through 715 Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.833A pdb=" N GLN B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.684A pdb=" N GLN B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 3.568A pdb=" N PHE B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.576A pdb=" N GLN B 333 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER B 334 " --> pdb=" O THR B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 334' Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 550 through 567 Processing helix chain 'B' and resid 570 through 586 Processing helix chain 'B' and resid 588 through 607 Proline residue: B 604 - end of helix Processing helix chain 'B' and resid 613 through 628 removed outlier: 3.956A pdb=" N TYR B 617 " --> pdb=" O ASP B 613 " (cutoff:3.500A) Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 628 through 636 Processing helix chain 'B' and resid 638 through 656 Processing helix chain 'B' and resid 657 through 661 removed outlier: 5.199A pdb=" N ILE B 661 " --> pdb=" O ALA B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 671 removed outlier: 3.554A pdb=" N LEU B 667 " --> pdb=" O MET B 663 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 687 Processing helix chain 'B' and resid 693 through 699 Processing helix chain 'B' and resid 700 through 715 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 48 removed outlier: 3.590A pdb=" N MET C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP C 48 " --> pdb=" O GLN C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.884A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 98 Processing helix chain 'C' and resid 128 through 146 removed outlier: 3.560A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 199 through 208 removed outlier: 3.882A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.735A pdb=" N LYS C 273 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 274 " --> pdb=" O MET C 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 270 through 274' Processing helix chain 'C' and resid 300 through 304 removed outlier: 3.624A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU C 304 " --> pdb=" O ASP C 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 300 through 304' Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.677A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR C 344 " --> pdb=" O MET C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.807A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL C 350 " --> pdb=" O ASP C 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 removed outlier: 3.518A pdb=" N GLY D 25 " --> pdb=" O THR D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 48 removed outlier: 3.598A pdb=" N ASP D 48 " --> pdb=" O GLN D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.702A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 98 removed outlier: 3.502A pdb=" N GLY D 98 " --> pdb=" O GLY D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 146 removed outlier: 3.550A pdb=" N GLN D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'D' and resid 155 through 158 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 208 removed outlier: 4.037A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 227 removed outlier: 4.063A pdb=" N SER D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.901A pdb=" N GLU D 293 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.697A pdb=" N LEU D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU D 304 " --> pdb=" O ASP D 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 300 through 304' Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 335 through 344 removed outlier: 3.646A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.770A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 181 removed outlier: 3.850A pdb=" N SER E 181 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 removed outlier: 3.812A pdb=" N GLN E 194 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET E 196 " --> pdb=" O THR E 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 191 through 196' Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 239 Processing helix chain 'E' and resid 247 through 267 removed outlier: 4.763A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 325 removed outlier: 5.518A pdb=" N ALA E 315 " --> pdb=" O LYS E 311 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN E 325 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 353 removed outlier: 3.545A pdb=" N GLY E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 378 removed outlier: 3.680A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 420 through 430 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 459 through 463 removed outlier: 3.946A pdb=" N LEU E 463 " --> pdb=" O PRO E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 508 through 510 No H-bonds generated for 'chain 'E' and resid 508 through 510' Processing helix chain 'E' and resid 511 through 518 removed outlier: 3.791A pdb=" N LEU E 516 " --> pdb=" O VAL E 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 181 removed outlier: 3.865A pdb=" N SER F 181 " --> pdb=" O SER F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 removed outlier: 3.865A pdb=" N GLN F 194 " --> pdb=" O SER F 191 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET F 196 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 216 Processing helix chain 'F' and resid 221 through 239 Processing helix chain 'F' and resid 247 through 267 removed outlier: 3.519A pdb=" N ASP F 251 " --> pdb=" O GLU F 247 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 286 removed outlier: 3.511A pdb=" N SER F 286 " --> pdb=" O LYS F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 325 removed outlier: 5.462A pdb=" N ALA F 315 " --> pdb=" O LYS F 311 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN F 325 " --> pdb=" O ARG F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 352 Processing helix chain 'F' and resid 368 through 378 removed outlier: 3.898A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 420 through 430 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 459 through 463 removed outlier: 3.967A pdb=" N LEU F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 510 No H-bonds generated for 'chain 'F' and resid 508 through 510' Processing helix chain 'F' and resid 511 through 518 removed outlier: 3.770A pdb=" N LEU F 516 " --> pdb=" O VAL F 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 16 Processing helix chain 'G' and resid 21 through 38 removed outlier: 3.788A pdb=" N ALA G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 60 WARNING: missing atoms! Processing helix chain 'G' and resid 62 through 83 removed outlier: 4.018A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 106 removed outlier: 3.587A pdb=" N CYS G 89 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS G 91 " --> pdb=" O SER G 87 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU G 106 " --> pdb=" O ARG G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 116 removed outlier: 3.705A pdb=" N HIS G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 160 through 170 removed outlier: 3.740A pdb=" N HIS G 170 " --> pdb=" O LYS G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 222 removed outlier: 4.056A pdb=" N MET G 215 " --> pdb=" O GLY G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 235 removed outlier: 3.584A pdb=" N LYS G 234 " --> pdb=" O GLU G 231 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE G 235 " --> pdb=" O SER G 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 231 through 235' Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 294 through 304 removed outlier: 3.788A pdb=" N ASP G 298 " --> pdb=" O SER G 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 16 Processing helix chain 'H' and resid 21 through 38 removed outlier: 3.788A pdb=" N ALA H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS H 38 " --> pdb=" O LEU H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 60 WARNING: missing atoms! Processing helix chain 'H' and resid 62 through 83 removed outlier: 4.016A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 106 removed outlier: 3.587A pdb=" N CYS H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS H 91 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU H 106 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 116 removed outlier: 3.705A pdb=" N HIS H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 160 through 170 removed outlier: 3.739A pdb=" N HIS H 170 " --> pdb=" O LYS H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 222 removed outlier: 4.056A pdb=" N MET H 215 " --> pdb=" O GLY H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 235 removed outlier: 3.584A pdb=" N LYS H 234 " --> pdb=" O GLU H 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE H 235 " --> pdb=" O SER H 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 231 through 235' Processing helix chain 'H' and resid 277 through 281 Processing helix chain 'H' and resid 294 through 304 removed outlier: 3.789A pdb=" N ASP H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 46 removed outlier: 4.201A pdb=" N VAL I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 68 removed outlier: 4.005A pdb=" N GLU I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 93 removed outlier: 3.545A pdb=" N ILE I 93 " --> pdb=" O SER I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 97 removed outlier: 3.592A pdb=" N LEU I 97 " --> pdb=" O TYR I 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 94 through 97' Processing helix chain 'I' and resid 114 through 124 removed outlier: 3.607A pdb=" N VAL I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 208 through 218 Processing helix chain 'I' and resid 223 through 228 Processing helix chain 'I' and resid 229 through 236 Processing helix chain 'I' and resid 281 through 292 removed outlier: 4.303A pdb=" N CYS I 285 " --> pdb=" O CYS I 281 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG I 286 " --> pdb=" O TRP I 282 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TRP I 290 " --> pdb=" O ARG I 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 46 removed outlier: 4.201A pdb=" N VAL J 46 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 68 removed outlier: 4.006A pdb=" N GLU J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 93 removed outlier: 3.545A pdb=" N ILE J 93 " --> pdb=" O SER J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 97 removed outlier: 3.591A pdb=" N LEU J 97 " --> pdb=" O TYR J 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 94 through 97' Processing helix chain 'J' and resid 114 through 124 removed outlier: 3.607A pdb=" N VAL J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR J 124 " --> pdb=" O LEU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 208 through 218 Processing helix chain 'J' and resid 223 through 228 Processing helix chain 'J' and resid 229 through 236 Processing helix chain 'J' and resid 281 through 292 removed outlier: 4.303A pdb=" N CYS J 285 " --> pdb=" O CYS J 281 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG J 286 " --> pdb=" O TRP J 282 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TRP J 290 " --> pdb=" O ARG J 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 61 removed outlier: 3.523A pdb=" N LYS L 60 " --> pdb=" O SER L 57 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU L 61 " --> pdb=" O ILE L 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 57 through 61' Processing helix chain 'L' and resid 90 through 119 Processing helix chain 'L' and resid 122 through 134 Processing helix chain 'L' and resid 134 through 142 Processing helix chain 'L' and resid 145 through 158 removed outlier: 3.770A pdb=" N SER L 157 " --> pdb=" O LYS L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 165 removed outlier: 3.563A pdb=" N SER L 164 " --> pdb=" O ILE L 161 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU L 165 " --> pdb=" O LEU L 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 161 through 165' Processing helix chain 'L' and resid 168 through 183 removed outlier: 3.775A pdb=" N ARG L 172 " --> pdb=" O ASN L 168 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU L 173 " --> pdb=" O GLU L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 217 Processing helix chain 'L' and resid 242 through 264 removed outlier: 3.842A pdb=" N SER L 248 " --> pdb=" O THR L 244 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS L 264 " --> pdb=" O LYS L 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 61 removed outlier: 3.523A pdb=" N LYS M 60 " --> pdb=" O SER M 57 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU M 61 " --> pdb=" O ILE M 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 57 through 61' Processing helix chain 'M' and resid 90 through 119 Processing helix chain 'M' and resid 122 through 134 Processing helix chain 'M' and resid 134 through 142 Processing helix chain 'M' and resid 145 through 158 removed outlier: 3.769A pdb=" N SER M 157 " --> pdb=" O LYS M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 165 removed outlier: 3.562A pdb=" N SER M 164 " --> pdb=" O ILE M 161 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU M 165 " --> pdb=" O LEU M 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 161 through 165' Processing helix chain 'M' and resid 168 through 183 removed outlier: 3.775A pdb=" N ARG M 172 " --> pdb=" O ASN M 168 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU M 173 " --> pdb=" O GLU M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 202 through 217 Processing helix chain 'M' and resid 242 through 264 removed outlier: 3.842A pdb=" N SER M 248 " --> pdb=" O THR M 244 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS M 264 " --> pdb=" O LYS M 260 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 62 Processing helix chain 'S' and resid 137 through 146 removed outlier: 3.810A pdb=" N LEU S 141 " --> pdb=" O GLY S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 179 removed outlier: 3.844A pdb=" N GLN S 169 " --> pdb=" O CYS S 165 " (cutoff:3.500A) Processing helix chain 'S' and resid 195 through 217 Processing helix chain 'S' and resid 229 through 243 Processing helix chain 'T' and resid 53 through 62 Processing helix chain 'T' and resid 137 through 146 removed outlier: 3.809A pdb=" N LEU T 141 " --> pdb=" O GLY T 137 " (cutoff:3.500A) Processing helix chain 'T' and resid 165 through 179 removed outlier: 3.844A pdb=" N GLN T 169 " --> pdb=" O CYS T 165 " (cutoff:3.500A) Processing helix chain 'T' and resid 195 through 217 Processing helix chain 'T' and resid 229 through 243 Processing helix chain 'd' and resid 4 through 16 Processing helix chain 'e' and resid 4 through 16 Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 124 removed outlier: 7.570A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA A 45 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N PHE A 94 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 47 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLN A 44 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL A 151 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL A 46 " --> pdb=" O VAL A 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 246 Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 246 removed outlier: 4.645A pdb=" N ILE A 287 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE I 157 " --> pdb=" O MET I 170 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N MET I 170 " --> pdb=" O PHE I 157 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY I 159 " --> pdb=" O LEU I 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.374A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 367 through 368 removed outlier: 6.631A pdb=" N VAL A 367 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N HIS A 384 " --> pdb=" O VAL A 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.356A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU A 412 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 418 through 419 removed outlier: 7.764A pdb=" N GLU A 418 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 122 through 124 removed outlier: 7.571A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA B 45 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N PHE B 94 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU B 47 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLN B 44 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL B 151 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL B 46 " --> pdb=" O VAL B 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AB4, first strand: chain 'B' and resid 244 through 246 Processing sheet with id=AB5, first strand: chain 'B' and resid 244 through 246 removed outlier: 4.645A pdb=" N ILE B 287 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 238 " --> pdb=" O PHE J 195 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE J 157 " --> pdb=" O MET J 170 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET J 170 " --> pdb=" O PHE J 157 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY J 159 " --> pdb=" O LEU J 168 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AB7, first strand: chain 'B' and resid 336 through 337 Processing sheet with id=AB8, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.374A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE B 373 " --> pdb=" O LEU B 391 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 367 through 368 removed outlier: 6.631A pdb=" N VAL B 367 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N HIS B 384 " --> pdb=" O VAL B 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 395 through 396 removed outlier: 6.356A pdb=" N TYR B 395 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU B 412 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 430 " --> pdb=" O ILE B 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 418 through 419 removed outlier: 7.764A pdb=" N GLU B 418 " --> pdb=" O VAL B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.207A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AC5, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.117A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL D 189 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N MET D 217 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL D 191 " --> pdb=" O MET D 217 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR D 214 " --> pdb=" O ARG E 483 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AC7, first strand: chain 'D' and resid 306 through 308 removed outlier: 6.466A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL E 332 " --> pdb=" O LYS E 400 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU E 402 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU E 334 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLY E 404 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N TYR E 336 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 407 through 408 removed outlier: 3.606A pdb=" N ASP E 490 " --> pdb=" O SER E 416 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 383 through 387 removed outlier: 6.615A pdb=" N VAL F 358 " --> pdb=" O SER F 384 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU F 386 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL F 360 " --> pdb=" O LEU F 386 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE F 333 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL F 361 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL F 335 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL F 332 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU F 402 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU F 334 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLY F 404 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N TYR F 336 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 407 through 408 Processing sheet with id=AD2, first strand: chain 'G' and resid 175 through 178 removed outlier: 8.306A pdb=" N THR G 176 " --> pdb=" O PHE G 148 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N THR G 124 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE G 194 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU G 126 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLY G 196 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL G 229 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL G 195 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU G 283 " --> pdb=" O PHE G 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 199 through 200 removed outlier: 3.683A pdb=" N ASN G 208 " --> pdb=" O ASP G 274 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 175 through 178 removed outlier: 8.306A pdb=" N THR H 176 " --> pdb=" O PHE H 148 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL H 150 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL H 178 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL H 152 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N THR H 124 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE H 194 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU H 126 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLY H 196 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL H 229 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL H 195 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU H 283 " --> pdb=" O PHE H 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 199 through 200 removed outlier: 3.684A pdb=" N ASN H 208 " --> pdb=" O ASP H 274 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 75 through 78 removed outlier: 3.568A pdb=" N ILE I 78 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE I 52 " --> pdb=" O PHE I 3 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA I 5 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL I 54 " --> pdb=" O ALA I 5 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL I 7 " --> pdb=" O VAL I 54 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLN I 4 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU I 104 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL I 6 " --> pdb=" O LEU I 104 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 200 through 201 removed outlier: 6.360A pdb=" N LEU I 128 " --> pdb=" O TYR I 264 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N PHE I 266 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET I 130 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LYS I 268 " --> pdb=" O MET I 130 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N MET I 132 " --> pdb=" O LYS I 268 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 75 through 78 removed outlier: 3.567A pdb=" N ILE J 78 " --> pdb=" O VAL J 53 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE J 52 " --> pdb=" O PHE J 3 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA J 5 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL J 54 " --> pdb=" O ALA J 5 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL J 7 " --> pdb=" O VAL J 54 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLN J 4 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU J 104 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL J 6 " --> pdb=" O LEU J 104 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 200 through 201 removed outlier: 6.360A pdb=" N LEU J 128 " --> pdb=" O TYR J 264 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N PHE J 266 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET J 130 " --> pdb=" O PHE J 266 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LYS J 268 " --> pdb=" O MET J 130 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N MET J 132 " --> pdb=" O LYS J 268 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 18 through 26 removed outlier: 6.829A pdb=" N TYR L 32 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE L 26 " --> pdb=" O GLY L 30 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY L 30 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLU L 42 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N LEU L 84 " --> pdb=" O GLU L 42 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N MET L 44 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG L 74 " --> pdb=" O ASP L 83 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER L 85 " --> pdb=" O VAL L 72 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL L 72 " --> pdb=" O SER L 85 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 224 through 227 Processing sheet with id=AE3, first strand: chain 'L' and resid 224 through 227 Processing sheet with id=AE4, first strand: chain 'M' and resid 18 through 26 removed outlier: 6.829A pdb=" N TYR M 32 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE M 26 " --> pdb=" O GLY M 30 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY M 30 " --> pdb=" O ILE M 26 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLU M 42 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N LEU M 84 " --> pdb=" O GLU M 42 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N MET M 44 " --> pdb=" O LEU M 84 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG M 74 " --> pdb=" O ASP M 83 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER M 85 " --> pdb=" O VAL M 72 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL M 72 " --> pdb=" O SER M 85 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 224 through 227 Processing sheet with id=AE6, first strand: chain 'M' and resid 224 through 227 Processing sheet with id=AE7, first strand: chain 'S' and resid 42 through 46 removed outlier: 4.407A pdb=" N VAL S 127 " --> pdb=" O ILE S 88 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE S 88 " --> pdb=" O VAL S 127 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS S 129 " --> pdb=" O ALA S 86 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA S 86 " --> pdb=" O HIS S 129 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER S 131 " --> pdb=" O ALA S 84 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ALA S 84 " --> pdb=" O SER S 131 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL S 133 " --> pdb=" O GLY S 82 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY S 82 " --> pdb=" O VAL S 133 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 155 through 159 removed outlier: 6.988A pdb=" N ALA S 155 " --> pdb=" O LEU S 186 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU S 188 " --> pdb=" O ALA S 155 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU S 157 " --> pdb=" O LEU S 188 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'S' and resid 256 through 258 removed outlier: 3.600A pdb=" N SER S 316 " --> pdb=" O ILE S 294 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 300 through 302 Processing sheet with id=AF2, first strand: chain 'S' and resid 376 through 377 removed outlier: 3.538A pdb=" N PHE S 376 " --> pdb=" O TRP S 456 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU S 443 " --> pdb=" O ILE S 454 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP S 456 " --> pdb=" O ILE S 441 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE S 441 " --> pdb=" O TRP S 456 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA S 442 " --> pdb=" O ASN S 407 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN S 407 " --> pdb=" O ALA S 442 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG S 446 " --> pdb=" O VAL S 403 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N VAL S 403 " --> pdb=" O ARG S 446 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N SER S 412 " --> pdb=" O PRO S 432 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLY S 414 " --> pdb=" O THR S 430 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS S 426 " --> pdb=" O SER S 418 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL S 420 " --> pdb=" O LEU S 424 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU S 424 " --> pdb=" O VAL S 420 " (cutoff:3.500A) removed outlier: 9.639A pdb=" N ILE S 427 " --> pdb=" O SER S 374 " (cutoff:3.500A) removed outlier: 10.174A pdb=" N SER S 374 " --> pdb=" O ILE S 427 " (cutoff:3.500A) removed outlier: 11.191A pdb=" N LEU S 429 " --> pdb=" O GLU S 372 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N GLU S 372 " --> pdb=" O LEU S 429 " (cutoff:3.500A) removed outlier: 11.242A pdb=" N ASN S 431 " --> pdb=" O GLU S 370 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU S 370 " --> pdb=" O ASN S 431 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE S 367 " --> pdb=" O ILE S 465 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL S 463 " --> pdb=" O THR S 369 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU S 371 " --> pdb=" O ARG S 461 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG S 461 " --> pdb=" O LEU S 371 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE S 373 " --> pdb=" O ILE S 459 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE S 459 " --> pdb=" O ILE S 373 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 42 through 46 removed outlier: 4.407A pdb=" N VAL T 127 " --> pdb=" O ILE T 88 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE T 88 " --> pdb=" O VAL T 127 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS T 129 " --> pdb=" O ALA T 86 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA T 86 " --> pdb=" O HIS T 129 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER T 131 " --> pdb=" O ALA T 84 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ALA T 84 " --> pdb=" O SER T 131 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL T 133 " --> pdb=" O GLY T 82 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY T 82 " --> pdb=" O VAL T 133 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'T' and resid 155 through 159 removed outlier: 6.988A pdb=" N ALA T 155 " --> pdb=" O LEU T 186 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU T 188 " --> pdb=" O ALA T 155 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU T 157 " --> pdb=" O LEU T 188 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'T' and resid 256 through 258 removed outlier: 3.599A pdb=" N SER T 316 " --> pdb=" O ILE T 294 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'T' and resid 300 through 302 Processing sheet with id=AF7, first strand: chain 'T' and resid 376 through 377 removed outlier: 3.538A pdb=" N PHE T 376 " --> pdb=" O TRP T 456 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU T 443 " --> pdb=" O ILE T 454 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TRP T 456 " --> pdb=" O ILE T 441 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE T 441 " --> pdb=" O TRP T 456 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA T 442 " --> pdb=" O ASN T 407 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN T 407 " --> pdb=" O ALA T 442 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG T 446 " --> pdb=" O VAL T 403 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N VAL T 403 " --> pdb=" O ARG T 446 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N SER T 412 " --> pdb=" O PRO T 432 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY T 414 " --> pdb=" O THR T 430 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS T 426 " --> pdb=" O SER T 418 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL T 420 " --> pdb=" O LEU T 424 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU T 424 " --> pdb=" O VAL T 420 " (cutoff:3.500A) removed outlier: 9.639A pdb=" N ILE T 427 " --> pdb=" O SER T 374 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N SER T 374 " --> pdb=" O ILE T 427 " (cutoff:3.500A) removed outlier: 11.191A pdb=" N LEU T 429 " --> pdb=" O GLU T 372 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N GLU T 372 " --> pdb=" O LEU T 429 " (cutoff:3.500A) removed outlier: 11.243A pdb=" N ASN T 431 " --> pdb=" O GLU T 370 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU T 370 " --> pdb=" O ASN T 431 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE T 367 " --> pdb=" O ILE T 465 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL T 463 " --> pdb=" O THR T 369 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU T 371 " --> pdb=" O ARG T 461 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG T 461 " --> pdb=" O LEU T 371 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE T 373 " --> pdb=" O ILE T 459 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE T 459 " --> pdb=" O ILE T 373 " (cutoff:3.500A) 1660 hydrogen bonds defined for protein. 4749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.45 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5769 1.31 - 1.44: 8466 1.44 - 1.56: 19758 1.56 - 1.69: 1 1.69 - 1.82: 200 Bond restraints: 34194 Sorted by residual: bond pdb=" C16AC7B C 401 " pdb=" N08AC7B C 401 " ideal model delta sigma weight residual 1.341 1.464 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C16BC7B C 401 " pdb=" N08BC7B C 401 " ideal model delta sigma weight residual 1.341 1.463 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C15AC7B C 401 " pdb=" N07AC7B C 401 " ideal model delta sigma weight residual 1.341 1.454 -0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" C15BC7B C 401 " pdb=" N07BC7B C 401 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" CD2 TRP M 135 " pdb=" CE2 TRP M 135 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.70e-02 3.46e+03 1.91e+01 ... (remaining 34189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 46407 3.40 - 6.81: 221 6.81 - 10.21: 42 10.21 - 13.61: 5 13.61 - 17.01: 2 Bond angle restraints: 46677 Sorted by residual: angle pdb=" CD2 TRP L 135 " pdb=" CE3 TRP L 135 " pdb=" CZ3 TRP L 135 " ideal model delta sigma weight residual 118.60 129.48 -10.88 1.30e+00 5.92e-01 7.01e+01 angle pdb=" CD2 TRP M 135 " pdb=" CE3 TRP M 135 " pdb=" CZ3 TRP M 135 " ideal model delta sigma weight residual 118.60 129.41 -10.81 1.30e+00 5.92e-01 6.92e+01 angle pdb=" CE2 TRP M 135 " pdb=" CD2 TRP M 135 " pdb=" CE3 TRP M 135 " ideal model delta sigma weight residual 118.80 124.83 -6.03 1.00e+00 1.00e+00 3.63e+01 angle pdb=" CE2 TRP L 135 " pdb=" CD2 TRP L 135 " pdb=" CE3 TRP L 135 " ideal model delta sigma weight residual 118.80 124.76 -5.96 1.00e+00 1.00e+00 3.56e+01 angle pdb=" N ILE F 388 " pdb=" CA ILE F 388 " pdb=" C ILE F 388 " ideal model delta sigma weight residual 108.88 119.48 -10.60 2.16e+00 2.14e-01 2.41e+01 ... (remaining 46672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.83: 20006 29.83 - 59.66: 336 59.66 - 89.49: 29 89.49 - 119.32: 12 119.32 - 149.15: 2 Dihedral angle restraints: 20385 sinusoidal: 5946 harmonic: 14439 Sorted by residual: dihedral pdb=" CA LYS S 421 " pdb=" C LYS S 421 " pdb=" N ALA S 422 " pdb=" CA ALA S 422 " ideal model delta harmonic sigma weight residual 180.00 151.71 28.29 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LYS T 421 " pdb=" C LYS T 421 " pdb=" N ALA T 422 " pdb=" CA ALA T 422 " ideal model delta harmonic sigma weight residual 180.00 151.73 28.27 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LYS E 311 " pdb=" C LYS E 311 " pdb=" N ILE E 312 " pdb=" CA ILE E 312 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 20382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 5694 1.020 - 2.040: 0 2.040 - 3.059: 0 3.059 - 4.079: 0 4.079 - 5.099: 4 Chirality restraints: 5698 Sorted by residual: chirality pdb=" C09BC7B C 401 " pdb=" C13BC7B C 401 " pdb=" C14BC7B C 401 " pdb=" N07BC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.63 5.10 2.00e-01 2.50e+01 6.50e+02 chirality pdb=" C09AC7B C 401 " pdb=" C13AC7B C 401 " pdb=" C14AC7B C 401 " pdb=" N07AC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.61 5.08 2.00e-01 2.50e+01 6.45e+02 chirality pdb=" C10BC7B C 401 " pdb=" C11BC7B C 401 " pdb=" C12BC7B C 401 " pdb=" N08BC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.44 4.90 2.00e-01 2.50e+01 6.01e+02 ... (remaining 5695 not shown) Planarity restraints: 6130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 395 " -0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO F 396 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO F 396 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 396 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 395 " 0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO E 396 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO E 396 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 396 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS S 421 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C LYS S 421 " -0.043 2.00e-02 2.50e+03 pdb=" O LYS S 421 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA S 422 " 0.014 2.00e-02 2.50e+03 ... (remaining 6127 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9796 2.81 - 3.33: 28532 3.33 - 3.85: 55796 3.85 - 4.38: 59569 4.38 - 4.90: 105973 Nonbonded interactions: 259666 Sorted by model distance: nonbonded pdb=" OG SER A 411 " pdb=" OG SER A 429 " model vdw 2.285 3.040 nonbonded pdb=" OG SER B 411 " pdb=" OG SER B 429 " model vdw 2.286 3.040 nonbonded pdb=" O GLU H 202 " pdb=" OG SER H 297 " model vdw 2.289 3.040 nonbonded pdb=" O GLU G 202 " pdb=" OG SER G 297 " model vdw 2.290 3.040 nonbonded pdb=" OG SER B 130 " pdb=" O GLN B 267 " model vdw 2.302 3.040 ... (remaining 259661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 8 through 351) selection = (chain 'D' and (resid 8 through 98 or resid 126 through 351)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 166 through 521 or (resid 522 and (name N or name CA or na \ me C or name O )))) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'd' selection = chain 'e' } 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=0.50 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: 8.130 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: 0.760 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.370 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 34194 Z= 0.179 Angle : 0.714 17.013 46677 Z= 0.387 Chirality : 0.142 5.099 5698 Planarity : 0.006 0.080 6130 Dihedral : 12.344 149.152 10981 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.34 % Allowed : 4.86 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -4.06 (0.09), residues: 4881 helix: -2.63 (0.08), residues: 1898 sheet: -2.54 (0.17), residues: 746 loop : -2.70 (0.11), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 108 TYR 0.015 0.001 TYR B 395 PHE 0.033 0.001 PHE C 177 TRP 0.010 0.001 TRP H 272 HIS 0.003 0.001 HIS F 470 Details of bonding type rmsd covalent geometry : bond 0.00354 (34194) covalent geometry : angle 0.71368 (46677) hydrogen bonds : bond 0.14659 ( 1636) hydrogen bonds : angle 6.60285 ( 4749) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1017 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 LEU cc_start: 0.7085 (tp) cc_final: 0.6810 (tp) REVERT: A 264 PHE cc_start: 0.6197 (m-80) cc_final: 0.5955 (m-80) REVERT: A 310 CYS cc_start: 0.7566 (t) cc_final: 0.6968 (t) REVERT: B 218 THR cc_start: 0.6990 (p) cc_final: 0.5929 (m) REVERT: B 224 PHE cc_start: 0.7173 (m-80) cc_final: 0.6840 (m-80) REVERT: B 277 LEU cc_start: 0.8107 (mt) cc_final: 0.7808 (mt) REVERT: C 58 MET cc_start: 0.6717 (mtt) cc_final: 0.6495 (mtt) REVERT: C 129 LEU cc_start: 0.7882 (pt) cc_final: 0.7580 (tt) REVERT: D 134 ILE cc_start: 0.8529 (mm) cc_final: 0.8200 (tp) REVERT: D 138 ASN cc_start: 0.8678 (m-40) cc_final: 0.8462 (m110) REVERT: D 206 ASN cc_start: 0.7580 (m-40) cc_final: 0.7370 (m-40) REVERT: D 251 THR cc_start: 0.8415 (t) cc_final: 0.8065 (m) REVERT: F 260 MET cc_start: 0.7488 (mmp) cc_final: 0.5473 (ptp) REVERT: F 300 LEU cc_start: 0.7705 (mt) cc_final: 0.7308 (mt) REVERT: H 121 ASP cc_start: 0.5679 (t70) cc_final: 0.5419 (t70) REVERT: H 232 SER cc_start: 0.6514 (m) cc_final: 0.6230 (p) REVERT: I 46 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8381 (m) REVERT: I 78 ILE cc_start: 0.7953 (pt) cc_final: 0.7711 (mm) REVERT: I 131 LEU cc_start: 0.6940 (tp) cc_final: 0.6651 (tp) REVERT: J 210 TYR cc_start: 0.6309 (p90) cc_final: 0.4449 (t80) REVERT: M 36 LEU cc_start: 0.8054 (mt) cc_final: 0.7578 (mp) outliers start: 9 outliers final: 1 residues processed: 1020 average time/residue: 0.2260 time to fit residues: 363.2216 Evaluate side-chains 599 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 597 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain I residue 46 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.0370 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 50.0000 overall best weight: 2.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 337 HIS A 407 GLN B 72 ASN ** B 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS B 376 ASN C 158 HIS C 252 HIS ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS D 150 ASN D 158 HIS D 252 HIS D 261 HIS D 277 GLN D 331 ASN E 245 ASN ** E 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 HIS ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN F 254 ASN F 430 HIS F 475 ASN F 477 GLN G 244 GLN I 41 ASN I 115 HIS I 172 ASN J 172 ASN J 196 HIS ** L 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.123502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.095885 restraints weight = 82058.695| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.33 r_work: 0.3429 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 34194 Z= 0.298 Angle : 0.791 19.154 46677 Z= 0.412 Chirality : 0.051 0.346 5698 Planarity : 0.006 0.070 6130 Dihedral : 5.886 170.070 5261 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.87 % Allowed : 15.40 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.11), residues: 4881 helix: -0.42 (0.11), residues: 1935 sheet: -1.77 (0.19), residues: 645 loop : -2.14 (0.12), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 66 TYR 0.037 0.003 TYR L 146 PHE 0.040 0.003 PHE D 177 TRP 0.035 0.002 TRP A 97 HIS 0.039 0.002 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00606 (34194) covalent geometry : angle 0.79051 (46677) hydrogen bonds : bond 0.03994 ( 1636) hydrogen bonds : angle 4.46192 ( 4749) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 572 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8726 (m-10) cc_final: 0.8429 (m-80) REVERT: A 249 ILE cc_start: 0.8901 (pt) cc_final: 0.8668 (mt) REVERT: A 289 MET cc_start: 0.8979 (ttp) cc_final: 0.8713 (ttp) REVERT: B 303 LEU cc_start: 0.5237 (OUTLIER) cc_final: 0.4938 (pp) REVERT: D 93 TYR cc_start: 0.5259 (t80) cc_final: 0.4660 (t80) REVERT: D 138 ASN cc_start: 0.9191 (m-40) cc_final: 0.8944 (m110) REVERT: D 197 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7664 (p90) REVERT: D 202 GLU cc_start: 0.7768 (pm20) cc_final: 0.7552 (mp0) REVERT: E 173 TYR cc_start: 0.8665 (t80) cc_final: 0.7854 (t80) REVERT: F 210 LEU cc_start: 0.9161 (tp) cc_final: 0.8794 (tp) REVERT: F 214 TYR cc_start: 0.8879 (m-10) cc_final: 0.8375 (m-10) REVERT: F 282 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8535 (mtpt) REVERT: G 186 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8894 (mt) REVERT: G 188 GLU cc_start: 0.8881 (pt0) cc_final: 0.8673 (pt0) REVERT: G 213 ASN cc_start: 0.9013 (t0) cc_final: 0.8718 (t0) REVERT: H 72 PHE cc_start: 0.8837 (t80) cc_final: 0.8318 (t80) REVERT: H 75 PHE cc_start: 0.9166 (t80) cc_final: 0.7218 (m-80) REVERT: H 130 TYR cc_start: 0.8217 (t80) cc_final: 0.7922 (t80) REVERT: H 244 GLN cc_start: 0.8139 (pt0) cc_final: 0.7874 (pm20) REVERT: I 45 ARG cc_start: 0.8420 (mtm180) cc_final: 0.8105 (ttm110) REVERT: J 40 LEU cc_start: 0.8291 (mt) cc_final: 0.7584 (mt) REVERT: J 44 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6300 (mp0) REVERT: J 49 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7081 (pm20) REVERT: J 125 ASP cc_start: 0.7941 (t70) cc_final: 0.7640 (t0) REVERT: M 36 LEU cc_start: 0.8308 (mt) cc_final: 0.7782 (mp) REVERT: M 37 GLU cc_start: 0.8655 (pt0) cc_final: 0.7896 (pm20) outliers start: 157 outliers final: 78 residues processed: 686 average time/residue: 0.2043 time to fit residues: 230.3164 Evaluate side-chains 513 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 431 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 437 CYS Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 252 TYR Chi-restraints excluded: chain H residue 286 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 214 PHE Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain S residue 450 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 48 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 347 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 429 optimal weight: 40.0000 chunk 221 optimal weight: 0.8980 chunk 228 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 409 HIS B 407 GLN C 128 GLN C 230 ASN C 309 HIS ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN D 331 ASN E 265 GLN E 406 HIS E 431 ASN J 4 GLN L 22 ASN M 9 GLN M 40 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.118285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088837 restraints weight = 105839.841| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.46 r_work: 0.3299 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 34194 Z= 0.208 Angle : 0.628 11.160 46677 Z= 0.321 Chirality : 0.047 0.221 5698 Planarity : 0.004 0.059 6130 Dihedral : 5.540 179.090 5259 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.08 % Allowed : 19.18 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.12), residues: 4881 helix: 0.75 (0.12), residues: 1942 sheet: -1.68 (0.19), residues: 711 loop : -1.89 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 145 TYR 0.025 0.002 TYR B 296 PHE 0.028 0.002 PHE C 278 TRP 0.014 0.001 TRP I 37 HIS 0.008 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00481 (34194) covalent geometry : angle 0.62770 (46677) hydrogen bonds : bond 0.03510 ( 1636) hydrogen bonds : angle 4.00928 ( 4749) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 450 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8960 (ttp) cc_final: 0.8639 (ttp) REVERT: B 86 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8301 (m) REVERT: B 145 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7668 (mmm160) REVERT: C 180 GLU cc_start: 0.8098 (pp20) cc_final: 0.7843 (pp20) REVERT: D 93 TYR cc_start: 0.5281 (t80) cc_final: 0.4692 (t80) REVERT: D 138 ASN cc_start: 0.9290 (m-40) cc_final: 0.9085 (m110) REVERT: D 197 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7774 (p90) REVERT: D 202 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: D 319 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8591 (pm20) REVERT: E 173 TYR cc_start: 0.8694 (t80) cc_final: 0.8411 (t80) REVERT: F 282 LYS cc_start: 0.9040 (ttpt) cc_final: 0.8789 (ttpt) REVERT: G 186 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8967 (mt) REVERT: H 72 PHE cc_start: 0.8899 (t80) cc_final: 0.8538 (t80) REVERT: H 130 TYR cc_start: 0.8633 (t80) cc_final: 0.8308 (t80) REVERT: H 244 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8262 (pm20) REVERT: J 8 MET cc_start: 0.8535 (mmm) cc_final: 0.8311 (mmm) REVERT: J 49 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7251 (pm20) REVERT: J 125 ASP cc_start: 0.8628 (t70) cc_final: 0.8085 (t0) REVERT: J 210 TYR cc_start: 0.7694 (p90) cc_final: 0.4983 (t80) REVERT: L 54 ARG cc_start: 0.7277 (tpt170) cc_final: 0.6603 (tpt170) REVERT: L 76 ASP cc_start: 0.8631 (t0) cc_final: 0.8196 (t0) REVERT: M 36 LEU cc_start: 0.8383 (mt) cc_final: 0.8055 (mp) REVERT: M 56 ARG cc_start: 0.7710 (tpp-160) cc_final: 0.7369 (tpp-160) outliers start: 136 outliers final: 78 residues processed: 552 average time/residue: 0.1997 time to fit residues: 179.1587 Evaluate side-chains 454 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 370 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 244 GLN Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 214 PHE Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain S residue 450 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 464 optimal weight: 30.0000 chunk 51 optimal weight: 30.0000 chunk 360 optimal weight: 20.0000 chunk 424 optimal weight: 0.8980 chunk 427 optimal weight: 9.9990 chunk 279 optimal weight: 5.9990 chunk 440 optimal weight: 50.0000 chunk 114 optimal weight: 50.0000 chunk 417 optimal weight: 8.9990 chunk 285 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 337 HIS C 154 GLN C 261 HIS C 277 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 ASN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 213 ASN G 270 HIS I 190 HIS M 22 ASN M 40 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.110727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.080787 restraints weight = 110793.268| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.67 r_work: 0.3120 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.8551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.102 34194 Z= 0.369 Angle : 0.791 12.350 46677 Z= 0.409 Chirality : 0.052 0.367 5698 Planarity : 0.006 0.065 6130 Dihedral : 6.266 179.835 5259 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 7.07 % Allowed : 19.18 % Favored : 73.76 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.12), residues: 4881 helix: 0.75 (0.12), residues: 1950 sheet: -2.00 (0.17), residues: 756 loop : -1.77 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 54 TYR 0.032 0.002 TYR D 315 PHE 0.028 0.003 PHE D 177 TRP 0.017 0.002 TRP I 37 HIS 0.011 0.002 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00854 (34194) covalent geometry : angle 0.79146 (46677) hydrogen bonds : bond 0.04079 ( 1636) hydrogen bonds : angle 4.48880 ( 4749) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 371 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 VAL cc_start: 0.8566 (p) cc_final: 0.8348 (m) REVERT: C 91 GLU cc_start: 0.8447 (pp20) cc_final: 0.7908 (tp30) REVERT: C 97 HIS cc_start: 0.7807 (OUTLIER) cc_final: 0.7356 (m90) REVERT: C 143 GLU cc_start: 0.8604 (tp30) cc_final: 0.8381 (tt0) REVERT: C 219 ASP cc_start: 0.8466 (p0) cc_final: 0.8253 (p0) REVERT: D 72 GLN cc_start: 0.8445 (tp40) cc_final: 0.8182 (tp-100) REVERT: D 93 TYR cc_start: 0.6067 (t80) cc_final: 0.5292 (t80) REVERT: D 197 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8119 (p90) REVERT: D 202 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: F 418 VAL cc_start: 0.9024 (m) cc_final: 0.8750 (t) REVERT: G 186 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9157 (mt) REVERT: H 243 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8391 (mm110) REVERT: H 244 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8302 (pm20) REVERT: I 50 GLU cc_start: 0.8801 (tp30) cc_final: 0.8345 (tm-30) REVERT: I 210 TYR cc_start: 0.8329 (p90) cc_final: 0.6194 (t80) REVERT: J 8 MET cc_start: 0.8728 (mmm) cc_final: 0.8471 (mmm) REVERT: J 49 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7632 (pm20) REVERT: L 3 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6600 (tp) REVERT: L 54 ARG cc_start: 0.7473 (tpt170) cc_final: 0.7041 (tpt170) REVERT: L 76 ASP cc_start: 0.8721 (t0) cc_final: 0.8305 (t0) REVERT: L 86 LYS cc_start: 0.8799 (tptm) cc_final: 0.8567 (mmmm) REVERT: M 36 LEU cc_start: 0.8581 (mt) cc_final: 0.8252 (mt) REVERT: S 352 ARG cc_start: 0.7658 (mtp-110) cc_final: 0.7363 (mtp-110) REVERT: T 368 PHE cc_start: 0.6561 (OUTLIER) cc_final: 0.5491 (m-80) outliers start: 189 outliers final: 118 residues processed: 526 average time/residue: 0.1991 time to fit residues: 170.7053 Evaluate side-chains 451 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 326 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 437 CYS Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain F residue 484 LEU Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 244 GLN Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 214 PHE Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 22 ASN Chi-restraints excluded: chain S residue 450 HIS Chi-restraints excluded: chain T residue 368 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 142 optimal weight: 4.9990 chunk 393 optimal weight: 0.9980 chunk 344 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 315 optimal weight: 6.9990 chunk 276 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 chunk 362 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 392 optimal weight: 40.0000 chunk 64 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN C 49 HIS C 154 GLN C 261 HIS ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN M 22 ASN M 40 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.113763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.083578 restraints weight = 115869.858| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.58 r_work: 0.3193 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.8549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34194 Z= 0.144 Angle : 0.581 12.795 46677 Z= 0.296 Chirality : 0.045 0.204 5698 Planarity : 0.004 0.060 6130 Dihedral : 5.702 178.640 5259 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.30 % Allowed : 21.94 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -0.60 (0.12), residues: 4881 helix: 1.42 (0.12), residues: 1947 sheet: -1.84 (0.18), residues: 744 loop : -1.55 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 54 TYR 0.020 0.001 TYR G 86 PHE 0.020 0.001 PHE D 177 TRP 0.018 0.001 TRP I 37 HIS 0.006 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00327 (34194) covalent geometry : angle 0.58066 (46677) hydrogen bonds : bond 0.03105 ( 1636) hydrogen bonds : angle 4.00622 ( 4749) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 381 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: B 65 ARG cc_start: 0.8423 (ptp-170) cc_final: 0.8191 (ttm170) REVERT: B 119 VAL cc_start: 0.8368 (p) cc_final: 0.8155 (m) REVERT: B 324 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8273 (pm20) REVERT: C 91 GLU cc_start: 0.8391 (pp20) cc_final: 0.7924 (tp30) REVERT: C 143 GLU cc_start: 0.8522 (tp30) cc_final: 0.8270 (tt0) REVERT: C 219 ASP cc_start: 0.8383 (p0) cc_final: 0.8152 (p0) REVERT: D 72 GLN cc_start: 0.8368 (tp40) cc_final: 0.8064 (tp-100) REVERT: D 93 TYR cc_start: 0.6040 (t80) cc_final: 0.5400 (t80) REVERT: D 197 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7834 (p90) REVERT: D 202 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: D 319 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8622 (pm20) REVERT: E 324 TYR cc_start: 0.8224 (t80) cc_final: 0.7987 (t80) REVERT: G 186 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8918 (mt) REVERT: H 244 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8245 (pm20) REVERT: H 287 ASP cc_start: 0.7787 (p0) cc_final: 0.7387 (t70) REVERT: I 50 GLU cc_start: 0.8746 (tp30) cc_final: 0.8304 (tm-30) REVERT: I 210 TYR cc_start: 0.8149 (p90) cc_final: 0.6018 (t80) REVERT: J 50 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8618 (tm-30) REVERT: J 186 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7648 (mm) REVERT: J 210 TYR cc_start: 0.8175 (p90) cc_final: 0.5518 (t80) REVERT: L 3 LEU cc_start: 0.7148 (tt) cc_final: 0.6742 (tp) REVERT: L 54 ARG cc_start: 0.7391 (tpt170) cc_final: 0.6993 (tpt170) REVERT: L 76 ASP cc_start: 0.8724 (t0) cc_final: 0.8347 (t0) REVERT: L 86 LYS cc_start: 0.8747 (tptm) cc_final: 0.8523 (mmmm) REVERT: M 36 LEU cc_start: 0.8608 (mt) cc_final: 0.8306 (mt) REVERT: S 248 ARG cc_start: 0.6751 (mtt-85) cc_final: 0.6550 (mtt-85) REVERT: T 368 PHE cc_start: 0.6397 (OUTLIER) cc_final: 0.5433 (m-80) outliers start: 115 outliers final: 84 residues processed: 473 average time/residue: 0.1990 time to fit residues: 153.1896 Evaluate side-chains 445 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 353 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 244 GLN Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 214 PHE Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 22 ASN Chi-restraints excluded: chain S residue 450 HIS Chi-restraints excluded: chain T residue 368 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 49 optimal weight: 50.0000 chunk 130 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 257 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 400 optimal weight: 30.0000 chunk 394 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 306 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN H 213 ASN J 115 HIS M 22 ASN M 40 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.111550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.080917 restraints weight = 120778.185| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.88 r_work: 0.3118 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.8845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 34194 Z= 0.244 Angle : 0.630 14.538 46677 Z= 0.321 Chirality : 0.047 0.210 5698 Planarity : 0.004 0.062 6130 Dihedral : 5.751 179.620 5259 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.50 % Allowed : 20.97 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -0.47 (0.12), residues: 4881 helix: 1.53 (0.12), residues: 1959 sheet: -1.86 (0.18), residues: 720 loop : -1.49 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 14 TYR 0.020 0.002 TYR D 315 PHE 0.023 0.002 PHE D 177 TRP 0.015 0.001 TRP I 37 HIS 0.005 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00579 (34194) covalent geometry : angle 0.62959 (46677) hydrogen bonds : bond 0.03317 ( 1636) hydrogen bonds : angle 4.03173 ( 4749) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 347 time to evaluate : 1.168 Fit side-chains revert: symmetry clash REVERT: B 119 VAL cc_start: 0.8454 (p) cc_final: 0.8245 (m) REVERT: B 324 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8281 (pm20) REVERT: C 91 GLU cc_start: 0.8428 (pp20) cc_final: 0.7936 (tp30) REVERT: C 143 GLU cc_start: 0.8611 (tp30) cc_final: 0.8384 (tt0) REVERT: C 180 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8169 (tm-30) REVERT: C 246 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8212 (ptp-170) REVERT: D 93 TYR cc_start: 0.6439 (t80) cc_final: 0.5864 (t80) REVERT: D 197 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.7989 (p90) REVERT: D 202 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: G 186 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.9004 (mt) REVERT: H 103 ARG cc_start: 0.6995 (ttt180) cc_final: 0.6775 (ttt180) REVERT: H 244 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8152 (pm20) REVERT: H 287 ASP cc_start: 0.7819 (p0) cc_final: 0.7489 (t70) REVERT: I 50 GLU cc_start: 0.8787 (tp30) cc_final: 0.8330 (tm-30) REVERT: I 264 TYR cc_start: 0.9161 (m-80) cc_final: 0.8870 (m-80) REVERT: J 8 MET cc_start: 0.8866 (mmm) cc_final: 0.8515 (mmm) REVERT: L 3 LEU cc_start: 0.7457 (tt) cc_final: 0.6974 (tp) REVERT: L 54 ARG cc_start: 0.7413 (tpt170) cc_final: 0.6976 (tpt170) REVERT: L 76 ASP cc_start: 0.8747 (t0) cc_final: 0.8378 (t0) REVERT: L 86 LYS cc_start: 0.8753 (tptm) cc_final: 0.8539 (mmmm) REVERT: M 36 LEU cc_start: 0.8566 (mt) cc_final: 0.8240 (mt) REVERT: T 368 PHE cc_start: 0.6258 (OUTLIER) cc_final: 0.5470 (m-80) outliers start: 147 outliers final: 115 residues processed: 467 average time/residue: 0.1989 time to fit residues: 153.0548 Evaluate side-chains 454 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 332 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 244 GLN Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 214 PHE Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 22 ASN Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain S residue 450 HIS Chi-restraints excluded: chain T residue 368 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 397 optimal weight: 30.0000 chunk 290 optimal weight: 0.1980 chunk 473 optimal weight: 30.0000 chunk 197 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 334 optimal weight: 40.0000 chunk 110 optimal weight: 20.0000 chunk 281 optimal weight: 30.0000 chunk 151 optimal weight: 0.7980 chunk 408 optimal weight: 50.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN C 154 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 ASN M 40 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.112137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.081809 restraints weight = 104761.911| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.49 r_work: 0.3144 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.9050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 34194 Z= 0.202 Angle : 0.597 14.180 46677 Z= 0.305 Chirality : 0.046 0.203 5698 Planarity : 0.004 0.062 6130 Dihedral : 5.684 179.448 5259 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.57 % Allowed : 21.12 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -0.33 (0.12), residues: 4881 helix: 1.69 (0.12), residues: 1956 sheet: -1.84 (0.18), residues: 734 loop : -1.41 (0.13), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 54 TYR 0.021 0.001 TYR G 86 PHE 0.022 0.001 PHE D 177 TRP 0.015 0.001 TRP I 37 HIS 0.007 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00475 (34194) covalent geometry : angle 0.59749 (46677) hydrogen bonds : bond 0.03161 ( 1636) hydrogen bonds : angle 3.95171 ( 4749) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 349 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: B 324 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8265 (pm20) REVERT: C 91 GLU cc_start: 0.8421 (pp20) cc_final: 0.7942 (tp30) REVERT: C 143 GLU cc_start: 0.8615 (tp30) cc_final: 0.8369 (tt0) REVERT: C 180 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8114 (tm-30) REVERT: D 72 GLN cc_start: 0.8428 (tp40) cc_final: 0.8014 (tt0) REVERT: D 93 TYR cc_start: 0.6535 (t80) cc_final: 0.5981 (t80) REVERT: D 197 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.7949 (p90) REVERT: D 202 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: D 319 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8757 (pm20) REVERT: G 151 TYR cc_start: 0.8927 (m-80) cc_final: 0.8695 (m-80) REVERT: G 186 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.9005 (mt) REVERT: G 187 MET cc_start: 0.9402 (tpp) cc_final: 0.9187 (tpp) REVERT: H 103 ARG cc_start: 0.6925 (ttt180) cc_final: 0.6693 (ttt180) REVERT: H 130 TYR cc_start: 0.9168 (t80) cc_final: 0.8870 (t80) REVERT: H 244 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8151 (pm20) REVERT: I 50 GLU cc_start: 0.8756 (tp30) cc_final: 0.8327 (tm-30) REVERT: I 264 TYR cc_start: 0.9127 (m-80) cc_final: 0.8898 (m-80) REVERT: J 8 MET cc_start: 0.8938 (mmm) cc_final: 0.8593 (mmm) REVERT: L 3 LEU cc_start: 0.7427 (tt) cc_final: 0.7001 (tp) REVERT: L 42 GLU cc_start: 0.7554 (tp30) cc_final: 0.7259 (tp30) REVERT: L 56 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7354 (mmm160) REVERT: L 76 ASP cc_start: 0.8754 (t0) cc_final: 0.8405 (t0) REVERT: L 86 LYS cc_start: 0.8724 (tptm) cc_final: 0.8507 (mmmm) REVERT: M 36 LEU cc_start: 0.8529 (mt) cc_final: 0.8060 (mp) REVERT: T 368 PHE cc_start: 0.6216 (OUTLIER) cc_final: 0.5534 (m-80) outliers start: 149 outliers final: 119 residues processed: 471 average time/residue: 0.2069 time to fit residues: 160.4786 Evaluate side-chains 463 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 336 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 244 GLN Chi-restraints excluded: chain H residue 305 LEU Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 22 ASN Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain S residue 450 HIS Chi-restraints excluded: chain T residue 368 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 231 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 471 optimal weight: 40.0000 chunk 435 optimal weight: 50.0000 chunk 41 optimal weight: 0.0870 chunk 408 optimal weight: 50.0000 chunk 291 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 HIS M 22 ASN M 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.113726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.083601 restraints weight = 118039.273| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.71 r_work: 0.3170 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.9060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34194 Z= 0.123 Angle : 0.556 15.112 46677 Z= 0.281 Chirality : 0.044 0.189 5698 Planarity : 0.004 0.062 6130 Dihedral : 5.507 179.636 5259 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.60 % Allowed : 21.87 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -0.06 (0.13), residues: 4881 helix: 1.97 (0.12), residues: 1948 sheet: -1.70 (0.18), residues: 720 loop : -1.31 (0.13), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 14 TYR 0.026 0.001 TYR G 86 PHE 0.020 0.001 PHE D 177 TRP 0.014 0.001 TRP I 37 HIS 0.008 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00284 (34194) covalent geometry : angle 0.55627 (46677) hydrogen bonds : bond 0.02857 ( 1636) hydrogen bonds : angle 3.78987 ( 4749) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 370 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: A 86 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8791 (m) REVERT: B 65 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8077 (ttm170) REVERT: B 137 ASP cc_start: 0.8595 (m-30) cc_final: 0.8384 (m-30) REVERT: B 324 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8290 (pm20) REVERT: C 91 GLU cc_start: 0.8371 (pp20) cc_final: 0.7958 (tp30) REVERT: C 143 GLU cc_start: 0.8613 (tp30) cc_final: 0.8396 (tt0) REVERT: C 246 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8241 (ptm160) REVERT: D 68 MET cc_start: 0.8898 (mmm) cc_final: 0.8642 (mtp) REVERT: D 72 GLN cc_start: 0.8405 (tp40) cc_final: 0.8043 (tt0) REVERT: D 93 TYR cc_start: 0.6737 (t80) cc_final: 0.6229 (t80) REVERT: D 197 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7662 (p90) REVERT: D 202 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: D 319 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8726 (pm20) REVERT: E 348 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: G 186 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8953 (mt) REVERT: H 103 ARG cc_start: 0.7013 (ttt180) cc_final: 0.6767 (ttt180) REVERT: H 130 TYR cc_start: 0.9138 (t80) cc_final: 0.8857 (t80) REVERT: H 244 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8115 (pm20) REVERT: I 50 GLU cc_start: 0.8755 (tp30) cc_final: 0.8308 (tm-30) REVERT: L 3 LEU cc_start: 0.7539 (tt) cc_final: 0.7336 (tp) REVERT: L 42 GLU cc_start: 0.7602 (tp30) cc_final: 0.7260 (tp30) REVERT: L 49 GLU cc_start: 0.8043 (tp30) cc_final: 0.7784 (tp30) REVERT: L 56 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7361 (mmm160) REVERT: L 76 ASP cc_start: 0.8754 (t0) cc_final: 0.8339 (t0) REVERT: L 86 LYS cc_start: 0.8701 (tptm) cc_final: 0.8462 (mmmm) REVERT: M 36 LEU cc_start: 0.8496 (mt) cc_final: 0.8138 (mt) outliers start: 123 outliers final: 94 residues processed: 477 average time/residue: 0.2199 time to fit residues: 170.3714 Evaluate side-chains 449 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 344 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 244 GLN Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 22 ASN Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain S residue 450 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 351 optimal weight: 0.0050 chunk 206 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 chunk 314 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 307 optimal weight: 20.0000 chunk 403 optimal weight: 30.0000 chunk 95 optimal weight: 6.9990 chunk 369 optimal weight: 10.0000 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN C 154 GLN M 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.113600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083556 restraints weight = 99034.399| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.37 r_work: 0.3186 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.9126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34194 Z= 0.139 Angle : 0.567 15.496 46677 Z= 0.284 Chirality : 0.045 0.178 5698 Planarity : 0.004 0.061 6130 Dihedral : 5.466 179.805 5259 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.37 % Allowed : 22.28 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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 (0.13), residues: 4881 helix: 2.04 (0.12), residues: 1948 sheet: -1.70 (0.18), residues: 730 loop : -1.25 (0.13), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 354 TYR 0.027 0.001 TYR G 86 PHE 0.020 0.001 PHE D 177 TRP 0.013 0.001 TRP I 37 HIS 0.006 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00325 (34194) covalent geometry : angle 0.56678 (46677) hydrogen bonds : bond 0.02876 ( 1636) hydrogen bonds : angle 3.73993 ( 4749) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 346 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: A 86 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8809 (m) REVERT: B 65 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8165 (ttm170) REVERT: B 137 ASP cc_start: 0.8555 (m-30) cc_final: 0.8337 (m-30) REVERT: B 324 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8262 (pm20) REVERT: C 91 GLU cc_start: 0.8339 (pp20) cc_final: 0.7949 (tp30) REVERT: C 143 GLU cc_start: 0.8600 (tp30) cc_final: 0.8395 (tt0) REVERT: C 246 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8159 (ptm160) REVERT: D 68 MET cc_start: 0.8899 (mmm) cc_final: 0.8666 (mtp) REVERT: D 72 GLN cc_start: 0.8392 (tp40) cc_final: 0.8025 (tt0) REVERT: D 93 TYR cc_start: 0.6828 (t80) cc_final: 0.6347 (t80) REVERT: D 197 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7722 (p90) REVERT: D 202 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: D 319 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8708 (pm20) REVERT: G 186 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.9001 (mt) REVERT: H 103 ARG cc_start: 0.6903 (ttt180) cc_final: 0.6665 (ttt180) REVERT: H 130 TYR cc_start: 0.9131 (t80) cc_final: 0.8867 (t80) REVERT: H 244 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8137 (pm20) REVERT: I 44 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7748 (mm-30) REVERT: I 50 GLU cc_start: 0.8732 (tp30) cc_final: 0.8287 (tm-30) REVERT: L 3 LEU cc_start: 0.7583 (tt) cc_final: 0.7262 (tp) REVERT: L 42 GLU cc_start: 0.7568 (tp30) cc_final: 0.7235 (tp30) REVERT: L 49 GLU cc_start: 0.8055 (tp30) cc_final: 0.7775 (tp30) REVERT: L 56 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7404 (mmm160) REVERT: L 76 ASP cc_start: 0.8740 (t0) cc_final: 0.8340 (t0) REVERT: L 86 LYS cc_start: 0.8755 (tptm) cc_final: 0.8517 (mmmm) REVERT: M 36 LEU cc_start: 0.8505 (mt) cc_final: 0.8140 (mt) REVERT: T 368 PHE cc_start: 0.6248 (OUTLIER) cc_final: 0.5520 (m-80) outliers start: 117 outliers final: 95 residues processed: 450 average time/residue: 0.2141 time to fit residues: 157.4018 Evaluate side-chains 444 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 338 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain G residue 156 GLN Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 244 GLN Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 22 ASN Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain S residue 450 HIS Chi-restraints excluded: chain T residue 368 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 245 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 341 optimal weight: 8.9990 chunk 308 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 471 optimal weight: 40.0000 chunk 185 optimal weight: 6.9990 chunk 451 optimal weight: 50.0000 chunk 232 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN M 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.111735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081465 restraints weight = 112507.620| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.74 r_work: 0.3126 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.9336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 34194 Z= 0.222 Angle : 0.623 15.632 46677 Z= 0.314 Chirality : 0.046 0.210 5698 Planarity : 0.004 0.061 6130 Dihedral : 5.636 178.353 5259 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.41 % Allowed : 22.36 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -0.06 (0.13), residues: 4881 helix: 1.94 (0.12), residues: 1944 sheet: -1.76 (0.18), residues: 742 loop : -1.24 (0.13), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 54 TYR 0.025 0.002 TYR G 86 PHE 0.022 0.002 PHE D 177 TRP 0.012 0.001 TRP I 37 HIS 0.007 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00527 (34194) covalent geometry : angle 0.62297 (46677) hydrogen bonds : bond 0.03197 ( 1636) hydrogen bonds : angle 3.86267 ( 4749) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 334 time to evaluate : 1.452 Fit side-chains revert: symmetry clash REVERT: A 86 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8857 (m) REVERT: B 65 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8353 (ttm170) REVERT: B 137 ASP cc_start: 0.8589 (m-30) cc_final: 0.8356 (m-30) REVERT: B 324 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.8260 (pm20) REVERT: B 328 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8700 (p) REVERT: C 91 GLU cc_start: 0.8431 (pp20) cc_final: 0.7979 (tp30) REVERT: C 143 GLU cc_start: 0.8652 (tp30) cc_final: 0.8419 (tt0) REVERT: C 246 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8262 (ptp-170) REVERT: C 350 VAL cc_start: 0.9041 (m) cc_final: 0.8833 (p) REVERT: D 72 GLN cc_start: 0.8409 (tp40) cc_final: 0.7995 (tt0) REVERT: D 93 TYR cc_start: 0.7189 (t80) cc_final: 0.6722 (t80) REVERT: D 197 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.7899 (p90) REVERT: D 202 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: G 186 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9109 (mt) REVERT: H 103 ARG cc_start: 0.7036 (ttt180) cc_final: 0.6787 (ttt180) REVERT: H 130 TYR cc_start: 0.9134 (t80) cc_final: 0.8789 (t80) REVERT: H 244 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8168 (pm20) REVERT: I 50 GLU cc_start: 0.8767 (tp30) cc_final: 0.8309 (tm-30) REVERT: J 41 ASN cc_start: 0.8211 (t0) cc_final: 0.7618 (t0) REVERT: L 3 LEU cc_start: 0.7607 (tt) cc_final: 0.7405 (tp) REVERT: L 42 GLU cc_start: 0.7591 (tp30) cc_final: 0.7223 (tp30) REVERT: L 49 GLU cc_start: 0.8094 (tp30) cc_final: 0.7793 (tp30) REVERT: L 56 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7476 (mmm160) REVERT: L 76 ASP cc_start: 0.8752 (t0) cc_final: 0.8348 (t0) REVERT: L 86 LYS cc_start: 0.8765 (tptm) cc_final: 0.8519 (mmmm) REVERT: M 36 LEU cc_start: 0.8534 (mt) cc_final: 0.8017 (mp) REVERT: T 368 PHE cc_start: 0.6324 (OUTLIER) cc_final: 0.5584 (m-80) outliers start: 118 outliers final: 100 residues processed: 437 average time/residue: 0.2071 time to fit residues: 148.6889 Evaluate side-chains 442 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 331 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain G residue 156 GLN Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 244 GLN Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 22 ASN Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain S residue 450 HIS Chi-restraints excluded: chain T residue 368 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 42 optimal weight: 30.0000 chunk 63 optimal weight: 0.9990 chunk 225 optimal weight: 0.6980 chunk 463 optimal weight: 30.0000 chunk 450 optimal weight: 40.0000 chunk 184 optimal weight: 0.7980 chunk 274 optimal weight: 0.0670 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 239 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.114418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.084180 restraints weight = 107628.189| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.55 r_work: 0.3190 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.9315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34194 Z= 0.110 Angle : 0.560 15.689 46677 Z= 0.281 Chirality : 0.044 0.175 5698 Planarity : 0.004 0.061 6130 Dihedral : 5.463 179.739 5259 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.59 % Allowed : 23.36 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 4881 helix: 2.15 (0.12), residues: 1948 sheet: -1.65 (0.19), residues: 718 loop : -1.18 (0.13), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 54 TYR 0.026 0.001 TYR G 86 PHE 0.018 0.001 PHE D 177 TRP 0.014 0.001 TRP I 37 HIS 0.008 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00247 (34194) covalent geometry : angle 0.56029 (46677) hydrogen bonds : bond 0.02796 ( 1636) hydrogen bonds : angle 3.68547 ( 4749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11756.91 seconds wall clock time: 200 minutes 28.76 seconds (12028.76 seconds total)