Starting phenix.real_space_refine on Tue Aug 26 19:02:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3ja7_6324/08_2025/3ja7_6324.cif Found real_map, /net/cci-nas-00/data/ceres_data/3ja7_6324/08_2025/3ja7_6324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3ja7_6324/08_2025/3ja7_6324.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3ja7_6324/08_2025/3ja7_6324.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3ja7_6324/08_2025/3ja7_6324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3ja7_6324/08_2025/3ja7_6324.map" } resolution = 3.6 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 228 5.16 5 C 25968 2.51 5 N 7296 2.21 5 O 7788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41280 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "B" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "D" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "E" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "F" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "G" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "H" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "I" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "J" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "K" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "L" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 15, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 70 Time building chain proxies: 9.48, per 1000 atoms: 0.23 Number of scatterers: 41280 At special positions: 0 Unit cell: (185, 185, 137, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 228 16.00 O 7788 8.00 N 7296 7.00 C 25968 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=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9864 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 60 sheets defined 47.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 70 through 81 removed outlier: 3.602A pdb=" N ARG A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 100 removed outlier: 3.627A pdb=" N ILE A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 257 through 277 removed outlier: 3.632A pdb=" N LYS A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 266 " --> pdb=" O ASN A 262 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A 267 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 298 through 309 removed outlier: 3.691A pdb=" N HIS A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL A 304 " --> pdb=" O HIS A 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET A 305 " --> pdb=" O MET A 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 306 " --> pdb=" O GLN A 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 307 " --> pdb=" O HIS A 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 373 removed outlier: 3.946A pdb=" N GLN A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 411 removed outlier: 3.529A pdb=" N LEU A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 424 Proline residue: A 421 - end of helix removed outlier: 3.815A pdb=" N THR A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 441 " --> pdb=" O TRP A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 Processing helix chain 'A' and resid 482 through 490 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A 508 " --> pdb=" O GLN A 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 100 removed outlier: 3.628A pdb=" N ILE B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN B 124 " --> pdb=" O PRO B 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP B 132 " --> pdb=" O ASP B 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 257 through 277 removed outlier: 3.632A pdb=" N LYS B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 266 " --> pdb=" O ASN B 262 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 272 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 Processing helix chain 'B' and resid 298 through 309 removed outlier: 3.692A pdb=" N HIS B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B 304 " --> pdb=" O HIS B 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET B 305 " --> pdb=" O MET B 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 306 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 307 " --> pdb=" O HIS B 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 373 removed outlier: 3.946A pdb=" N GLN B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 411 removed outlier: 3.529A pdb=" N LEU B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 424 Proline residue: B 421 - end of helix removed outlier: 3.815A pdb=" N THR B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP B 439 " --> pdb=" O ASP B 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 440 " --> pdb=" O GLU B 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 441 " --> pdb=" O TRP B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 473 Processing helix chain 'B' and resid 482 through 490 Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU B 507 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 508 " --> pdb=" O GLN B 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER B 509 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 100 removed outlier: 3.628A pdb=" N ILE C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN C 124 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 257 through 277 removed outlier: 3.631A pdb=" N LYS C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 266 " --> pdb=" O ASN C 262 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 272 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 298 Processing helix chain 'C' and resid 298 through 309 removed outlier: 3.692A pdb=" N HIS C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL C 304 " --> pdb=" O HIS C 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET C 305 " --> pdb=" O MET C 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN C 306 " --> pdb=" O GLN C 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR C 307 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET C 308 " --> pdb=" O VAL C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 373 removed outlier: 3.945A pdb=" N GLN C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 411 removed outlier: 3.530A pdb=" N LEU C 401 " --> pdb=" O THR C 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C 405 " --> pdb=" O LEU C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 424 Proline residue: C 421 - end of helix removed outlier: 3.815A pdb=" N THR C 424 " --> pdb=" O ASP C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 Processing helix chain 'C' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP C 439 " --> pdb=" O ASP C 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU C 440 " --> pdb=" O GLU C 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 441 " --> pdb=" O TRP C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU C 456 " --> pdb=" O SER C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 473 Processing helix chain 'C' and resid 482 through 490 Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU C 506 " --> pdb=" O ALA C 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 508 " --> pdb=" O GLN C 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER C 509 " --> pdb=" O ILE C 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG D 80 " --> pdb=" O ILE D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 100 removed outlier: 3.627A pdb=" N ILE D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP D 98 " --> pdb=" O GLU D 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE D 100 " --> pdb=" O VAL D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN D 124 " --> pdb=" O PRO D 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP D 128 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP D 132 " --> pdb=" O ASP D 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS D 146 " --> pdb=" O LYS D 142 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 256 No H-bonds generated for 'chain 'D' and resid 254 through 256' Processing helix chain 'D' and resid 257 through 277 removed outlier: 3.632A pdb=" N LYS D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 266 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 Processing helix chain 'D' and resid 298 through 309 removed outlier: 3.691A pdb=" N HIS D 303 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL D 304 " --> pdb=" O HIS D 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET D 305 " --> pdb=" O MET D 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN D 306 " --> pdb=" O GLN D 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR D 307 " --> pdb=" O HIS D 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET D 308 " --> pdb=" O VAL D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 373 removed outlier: 3.946A pdb=" N GLN D 367 " --> pdb=" O ARG D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 411 removed outlier: 3.529A pdb=" N LEU D 401 " --> pdb=" O THR D 397 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 405 " --> pdb=" O LEU D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 424 Proline residue: D 421 - end of helix removed outlier: 3.815A pdb=" N THR D 424 " --> pdb=" O ASP D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 429 Processing helix chain 'D' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP D 439 " --> pdb=" O ASP D 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU D 440 " --> pdb=" O GLU D 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D 441 " --> pdb=" O TRP D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 473 Processing helix chain 'D' and resid 482 through 490 Processing helix chain 'D' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU D 506 " --> pdb=" O ALA D 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU D 507 " --> pdb=" O LYS D 503 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER D 509 " --> pdb=" O ILE D 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG E 80 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 100 removed outlier: 3.628A pdb=" N ILE E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE E 100 " --> pdb=" O VAL E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN E 124 " --> pdb=" O PRO E 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP E 128 " --> pdb=" O ASN E 124 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP E 132 " --> pdb=" O ASP E 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU E 137 " --> pdb=" O VAL E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER E 144 " --> pdb=" O GLN E 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP E 145 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS E 146 " --> pdb=" O LYS E 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG E 148 " --> pdb=" O SER E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 257 through 277 removed outlier: 3.632A pdb=" N LYS E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 266 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU E 267 " --> pdb=" O GLN E 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA E 270 " --> pdb=" O LEU E 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 272 " --> pdb=" O GLU E 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG E 275 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR E 277 " --> pdb=" O ILE E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 298 Processing helix chain 'E' and resid 298 through 309 removed outlier: 3.692A pdb=" N HIS E 303 " --> pdb=" O GLU E 299 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL E 304 " --> pdb=" O HIS E 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET E 305 " --> pdb=" O MET E 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN E 306 " --> pdb=" O GLN E 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR E 307 " --> pdb=" O HIS E 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET E 308 " --> pdb=" O VAL E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 373 removed outlier: 3.946A pdb=" N GLN E 367 " --> pdb=" O ARG E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 411 removed outlier: 3.529A pdb=" N LEU E 401 " --> pdb=" O THR E 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS E 405 " --> pdb=" O LEU E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 424 Proline residue: E 421 - end of helix removed outlier: 3.815A pdb=" N THR E 424 " --> pdb=" O ASP E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 429 Processing helix chain 'E' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP E 439 " --> pdb=" O ASP E 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU E 440 " --> pdb=" O GLU E 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE E 441 " --> pdb=" O TRP E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU E 456 " --> pdb=" O SER E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 473 Processing helix chain 'E' and resid 482 through 490 Processing helix chain 'E' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU E 506 " --> pdb=" O ALA E 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU E 507 " --> pdb=" O LYS E 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU E 508 " --> pdb=" O GLN E 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER E 509 " --> pdb=" O ILE E 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG F 80 " --> pdb=" O ILE F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 100 removed outlier: 3.628A pdb=" N ILE F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP F 98 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE F 100 " --> pdb=" O VAL F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN F 124 " --> pdb=" O PRO F 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP F 128 " --> pdb=" O ASN F 124 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP F 132 " --> pdb=" O ASP F 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN F 135 " --> pdb=" O SER F 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU F 137 " --> pdb=" O VAL F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER F 144 " --> pdb=" O GLN F 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP F 145 " --> pdb=" O ARG F 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS F 146 " --> pdb=" O LYS F 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG F 148 " --> pdb=" O SER F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 257 through 277 removed outlier: 3.631A pdb=" N LYS F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU F 266 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU F 267 " --> pdb=" O GLN F 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU F 268 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA F 270 " --> pdb=" O LEU F 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL F 272 " --> pdb=" O GLU F 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG F 275 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR F 277 " --> pdb=" O ILE F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 298 Processing helix chain 'F' and resid 298 through 309 removed outlier: 3.692A pdb=" N HIS F 303 " --> pdb=" O GLU F 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL F 304 " --> pdb=" O HIS F 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET F 305 " --> pdb=" O MET F 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN F 306 " --> pdb=" O GLN F 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR F 307 " --> pdb=" O HIS F 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET F 308 " --> pdb=" O VAL F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 373 removed outlier: 3.945A pdb=" N GLN F 367 " --> pdb=" O ARG F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 411 removed outlier: 3.530A pdb=" N LEU F 401 " --> pdb=" O THR F 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS F 405 " --> pdb=" O LEU F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 424 Proline residue: F 421 - end of helix removed outlier: 3.815A pdb=" N THR F 424 " --> pdb=" O ASP F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 429 Processing helix chain 'F' and resid 433 through 441 removed outlier: 5.021A pdb=" N ASP F 439 " --> pdb=" O ASP F 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU F 440 " --> pdb=" O GLU F 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE F 441 " --> pdb=" O TRP F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU F 456 " --> pdb=" O SER F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 473 Processing helix chain 'F' and resid 482 through 490 Processing helix chain 'F' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU F 506 " --> pdb=" O ALA F 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU F 507 " --> pdb=" O LYS F 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU F 508 " --> pdb=" O GLN F 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER F 509 " --> pdb=" O ILE F 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG G 80 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 100 removed outlier: 3.627A pdb=" N ILE G 95 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP G 98 " --> pdb=" O GLU G 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE G 100 " --> pdb=" O VAL G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN G 124 " --> pdb=" O PRO G 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU G 127 " --> pdb=" O LYS G 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP G 128 " --> pdb=" O ASN G 124 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP G 132 " --> pdb=" O ASP G 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN G 135 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU G 137 " --> pdb=" O VAL G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP G 145 " --> pdb=" O ARG G 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 256 No H-bonds generated for 'chain 'G' and resid 254 through 256' Processing helix chain 'G' and resid 257 through 277 removed outlier: 3.632A pdb=" N LYS G 265 " --> pdb=" O ALA G 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU G 266 " --> pdb=" O ASN G 262 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU G 267 " --> pdb=" O GLN G 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 268 " --> pdb=" O LEU G 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA G 270 " --> pdb=" O LEU G 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL G 272 " --> pdb=" O GLU G 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG G 275 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR G 277 " --> pdb=" O ILE G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 298 Processing helix chain 'G' and resid 298 through 309 removed outlier: 3.691A pdb=" N HIS G 303 " --> pdb=" O GLU G 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL G 304 " --> pdb=" O HIS G 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET G 305 " --> pdb=" O MET G 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN G 306 " --> pdb=" O GLN G 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR G 307 " --> pdb=" O HIS G 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET G 308 " --> pdb=" O VAL G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 373 removed outlier: 3.946A pdb=" N GLN G 367 " --> pdb=" O ARG G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 411 removed outlier: 3.529A pdb=" N LEU G 401 " --> pdb=" O THR G 397 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS G 405 " --> pdb=" O LEU G 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 424 Proline residue: G 421 - end of helix removed outlier: 3.815A pdb=" N THR G 424 " --> pdb=" O ASP G 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 429 Processing helix chain 'G' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP G 439 " --> pdb=" O ASP G 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU G 440 " --> pdb=" O GLU G 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE G 441 " --> pdb=" O TRP G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU G 456 " --> pdb=" O SER G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 473 Processing helix chain 'G' and resid 482 through 490 Processing helix chain 'G' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU G 506 " --> pdb=" O ALA G 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU G 507 " --> pdb=" O LYS G 503 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU G 508 " --> pdb=" O GLN G 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER G 509 " --> pdb=" O ILE G 505 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG H 80 " --> pdb=" O ILE H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 100 removed outlier: 3.628A pdb=" N ILE H 95 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP H 98 " --> pdb=" O GLU H 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE H 100 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN H 124 " --> pdb=" O PRO H 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU H 127 " --> pdb=" O LYS H 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP H 128 " --> pdb=" O ASN H 124 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP H 132 " --> pdb=" O ASP H 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU H 137 " --> pdb=" O VAL H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER H 144 " --> pdb=" O GLN H 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP H 145 " --> pdb=" O ARG H 141 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS H 146 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG H 148 " --> pdb=" O SER H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 256 No H-bonds generated for 'chain 'H' and resid 254 through 256' Processing helix chain 'H' and resid 257 through 277 removed outlier: 3.632A pdb=" N LYS H 265 " --> pdb=" O ALA H 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU H 266 " --> pdb=" O ASN H 262 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU H 267 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU H 268 " --> pdb=" O LEU H 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA H 270 " --> pdb=" O LEU H 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL H 272 " --> pdb=" O GLU H 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG H 275 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR H 277 " --> pdb=" O ILE H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 298 Processing helix chain 'H' and resid 298 through 309 removed outlier: 3.692A pdb=" N HIS H 303 " --> pdb=" O GLU H 299 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL H 304 " --> pdb=" O HIS H 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET H 305 " --> pdb=" O MET H 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN H 306 " --> pdb=" O GLN H 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR H 307 " --> pdb=" O HIS H 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET H 308 " --> pdb=" O VAL H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 361 through 373 removed outlier: 3.946A pdb=" N GLN H 367 " --> pdb=" O ARG H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 411 removed outlier: 3.529A pdb=" N LEU H 401 " --> pdb=" O THR H 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS H 405 " --> pdb=" O LEU H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 424 Proline residue: H 421 - end of helix removed outlier: 3.815A pdb=" N THR H 424 " --> pdb=" O ASP H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 424 through 429 Processing helix chain 'H' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP H 439 " --> pdb=" O ASP H 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU H 440 " --> pdb=" O GLU H 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE H 441 " --> pdb=" O TRP H 437 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU H 456 " --> pdb=" O SER H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 473 Processing helix chain 'H' and resid 482 through 490 Processing helix chain 'H' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU H 506 " --> pdb=" O ALA H 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU H 507 " --> pdb=" O LYS H 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU H 508 " --> pdb=" O GLN H 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER H 509 " --> pdb=" O ILE H 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG I 80 " --> pdb=" O ILE I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 100 removed outlier: 3.628A pdb=" N ILE I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP I 98 " --> pdb=" O GLU I 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE I 100 " --> pdb=" O VAL I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN I 124 " --> pdb=" O PRO I 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU I 127 " --> pdb=" O LYS I 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP I 128 " --> pdb=" O ASN I 124 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP I 132 " --> pdb=" O ASP I 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN I 135 " --> pdb=" O SER I 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU I 137 " --> pdb=" O VAL I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER I 144 " --> pdb=" O GLN I 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP I 145 " --> pdb=" O ARG I 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG I 148 " --> pdb=" O SER I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 256 No H-bonds generated for 'chain 'I' and resid 254 through 256' Processing helix chain 'I' and resid 257 through 277 removed outlier: 3.631A pdb=" N LYS I 265 " --> pdb=" O ALA I 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU I 266 " --> pdb=" O ASN I 262 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU I 267 " --> pdb=" O GLN I 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU I 268 " --> pdb=" O LEU I 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA I 270 " --> pdb=" O LEU I 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL I 272 " --> pdb=" O GLU I 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG I 275 " --> pdb=" O VAL I 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR I 277 " --> pdb=" O ILE I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 298 Processing helix chain 'I' and resid 298 through 309 removed outlier: 3.692A pdb=" N HIS I 303 " --> pdb=" O GLU I 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL I 304 " --> pdb=" O HIS I 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET I 305 " --> pdb=" O MET I 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN I 306 " --> pdb=" O GLN I 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR I 307 " --> pdb=" O HIS I 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET I 308 " --> pdb=" O VAL I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 373 removed outlier: 3.945A pdb=" N GLN I 367 " --> pdb=" O ARG I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 411 removed outlier: 3.530A pdb=" N LEU I 401 " --> pdb=" O THR I 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS I 405 " --> pdb=" O LEU I 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 424 Proline residue: I 421 - end of helix removed outlier: 3.815A pdb=" N THR I 424 " --> pdb=" O ASP I 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 424 through 429 Processing helix chain 'I' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP I 439 " --> pdb=" O ASP I 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU I 440 " --> pdb=" O GLU I 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE I 441 " --> pdb=" O TRP I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU I 456 " --> pdb=" O SER I 452 " (cutoff:3.500A) Processing helix chain 'I' and resid 460 through 473 Processing helix chain 'I' and resid 482 through 490 Processing helix chain 'I' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU I 506 " --> pdb=" O ALA I 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU I 507 " --> pdb=" O LYS I 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU I 508 " --> pdb=" O GLN I 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER I 509 " --> pdb=" O ILE I 505 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG J 80 " --> pdb=" O ILE J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 100 removed outlier: 3.627A pdb=" N ILE J 95 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP J 98 " --> pdb=" O GLU J 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE J 100 " --> pdb=" O VAL J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN J 124 " --> pdb=" O PRO J 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU J 127 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP J 128 " --> pdb=" O ASN J 124 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP J 132 " --> pdb=" O ASP J 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN J 135 " --> pdb=" O SER J 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU J 137 " --> pdb=" O VAL J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER J 144 " --> pdb=" O GLN J 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP J 145 " --> pdb=" O ARG J 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS J 146 " --> pdb=" O LYS J 142 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG J 148 " --> pdb=" O SER J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 256 No H-bonds generated for 'chain 'J' and resid 254 through 256' Processing helix chain 'J' and resid 257 through 277 removed outlier: 3.632A pdb=" N LYS J 265 " --> pdb=" O ALA J 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU J 266 " --> pdb=" O ASN J 262 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU J 267 " --> pdb=" O GLN J 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU J 268 " --> pdb=" O LEU J 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA J 270 " --> pdb=" O LEU J 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL J 272 " --> pdb=" O GLU J 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG J 275 " --> pdb=" O VAL J 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR J 277 " --> pdb=" O ILE J 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 298 Processing helix chain 'J' and resid 298 through 309 removed outlier: 3.691A pdb=" N HIS J 303 " --> pdb=" O GLU J 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL J 304 " --> pdb=" O HIS J 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET J 305 " --> pdb=" O MET J 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN J 306 " --> pdb=" O GLN J 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR J 307 " --> pdb=" O HIS J 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET J 308 " --> pdb=" O VAL J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 361 through 373 removed outlier: 3.946A pdb=" N GLN J 367 " --> pdb=" O ARG J 363 " (cutoff:3.500A) Processing helix chain 'J' and resid 397 through 411 removed outlier: 3.529A pdb=" N LEU J 401 " --> pdb=" O THR J 397 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS J 405 " --> pdb=" O LEU J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 415 through 424 Proline residue: J 421 - end of helix removed outlier: 3.815A pdb=" N THR J 424 " --> pdb=" O ASP J 420 " (cutoff:3.500A) Processing helix chain 'J' and resid 424 through 429 Processing helix chain 'J' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP J 439 " --> pdb=" O ASP J 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU J 440 " --> pdb=" O GLU J 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE J 441 " --> pdb=" O TRP J 437 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU J 456 " --> pdb=" O SER J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 460 through 473 Processing helix chain 'J' and resid 482 through 490 Processing helix chain 'J' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU J 506 " --> pdb=" O ALA J 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU J 507 " --> pdb=" O LYS J 503 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER J 509 " --> pdb=" O ILE J 505 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG K 80 " --> pdb=" O ILE K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 100 removed outlier: 3.628A pdb=" N ILE K 95 " --> pdb=" O ALA K 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP K 98 " --> pdb=" O GLU K 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE K 100 " --> pdb=" O VAL K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN K 124 " --> pdb=" O PRO K 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU K 127 " --> pdb=" O LYS K 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP K 128 " --> pdb=" O ASN K 124 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP K 132 " --> pdb=" O ASP K 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN K 135 " --> pdb=" O SER K 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU K 137 " --> pdb=" O VAL K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER K 144 " --> pdb=" O GLN K 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP K 145 " --> pdb=" O ARG K 141 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS K 146 " --> pdb=" O LYS K 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG K 148 " --> pdb=" O SER K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 256 No H-bonds generated for 'chain 'K' and resid 254 through 256' Processing helix chain 'K' and resid 257 through 277 removed outlier: 3.632A pdb=" N LYS K 265 " --> pdb=" O ALA K 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU K 266 " --> pdb=" O ASN K 262 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU K 267 " --> pdb=" O GLN K 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU K 268 " --> pdb=" O LEU K 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA K 270 " --> pdb=" O LEU K 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL K 272 " --> pdb=" O GLU K 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG K 275 " --> pdb=" O VAL K 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR K 277 " --> pdb=" O ILE K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 293 through 298 Processing helix chain 'K' and resid 298 through 309 removed outlier: 3.692A pdb=" N HIS K 303 " --> pdb=" O GLU K 299 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL K 304 " --> pdb=" O HIS K 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET K 305 " --> pdb=" O MET K 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN K 306 " --> pdb=" O GLN K 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR K 307 " --> pdb=" O HIS K 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET K 308 " --> pdb=" O VAL K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 373 removed outlier: 3.946A pdb=" N GLN K 367 " --> pdb=" O ARG K 363 " (cutoff:3.500A) Processing helix chain 'K' and resid 397 through 411 removed outlier: 3.529A pdb=" N LEU K 401 " --> pdb=" O THR K 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS K 405 " --> pdb=" O LEU K 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 415 through 424 Proline residue: K 421 - end of helix removed outlier: 3.815A pdb=" N THR K 424 " --> pdb=" O ASP K 420 " (cutoff:3.500A) Processing helix chain 'K' and resid 424 through 429 Processing helix chain 'K' and resid 433 through 441 removed outlier: 5.022A pdb=" N ASP K 439 " --> pdb=" O ASP K 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU K 440 " --> pdb=" O GLU K 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE K 441 " --> pdb=" O TRP K 437 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU K 456 " --> pdb=" O SER K 452 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 473 Processing helix chain 'K' and resid 482 through 490 Processing helix chain 'K' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU K 506 " --> pdb=" O ALA K 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU K 507 " --> pdb=" O LYS K 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU K 508 " --> pdb=" O GLN K 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER K 509 " --> pdb=" O ILE K 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 81 removed outlier: 3.602A pdb=" N ARG L 80 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 100 removed outlier: 3.628A pdb=" N ILE L 95 " --> pdb=" O ALA L 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP L 98 " --> pdb=" O GLU L 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE L 100 " --> pdb=" O VAL L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 138 removed outlier: 3.901A pdb=" N ASN L 124 " --> pdb=" O PRO L 120 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU L 127 " --> pdb=" O LYS L 123 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP L 128 " --> pdb=" O ASN L 124 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP L 132 " --> pdb=" O ASP L 128 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN L 135 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 154 removed outlier: 6.710A pdb=" N SER L 144 " --> pdb=" O GLN L 140 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP L 145 " --> pdb=" O ARG L 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS L 146 " --> pdb=" O LYS L 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG L 148 " --> pdb=" O SER L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 256 No H-bonds generated for 'chain 'L' and resid 254 through 256' Processing helix chain 'L' and resid 257 through 277 removed outlier: 3.631A pdb=" N LYS L 265 " --> pdb=" O ALA L 261 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU L 266 " --> pdb=" O ASN L 262 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU L 267 " --> pdb=" O GLN L 263 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA L 270 " --> pdb=" O LEU L 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL L 272 " --> pdb=" O GLU L 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG L 275 " --> pdb=" O VAL L 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR L 277 " --> pdb=" O ILE L 273 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 298 Processing helix chain 'L' and resid 298 through 309 removed outlier: 3.692A pdb=" N HIS L 303 " --> pdb=" O GLU L 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL L 304 " --> pdb=" O HIS L 300 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET L 305 " --> pdb=" O MET L 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN L 306 " --> pdb=" O GLN L 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR L 307 " --> pdb=" O HIS L 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET L 308 " --> pdb=" O VAL L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 361 through 373 removed outlier: 3.945A pdb=" N GLN L 367 " --> pdb=" O ARG L 363 " (cutoff:3.500A) Processing helix chain 'L' and resid 397 through 411 removed outlier: 3.530A pdb=" N LEU L 401 " --> pdb=" O THR L 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS L 405 " --> pdb=" O LEU L 401 " (cutoff:3.500A) Processing helix chain 'L' and resid 415 through 424 Proline residue: L 421 - end of helix removed outlier: 3.815A pdb=" N THR L 424 " --> pdb=" O ASP L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 424 through 429 Processing helix chain 'L' and resid 433 through 441 removed outlier: 5.021A pdb=" N ASP L 439 " --> pdb=" O ASP L 435 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU L 440 " --> pdb=" O GLU L 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE L 441 " --> pdb=" O TRP L 437 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 459 removed outlier: 3.666A pdb=" N GLU L 456 " --> pdb=" O SER L 452 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 473 Processing helix chain 'L' and resid 482 through 490 Processing helix chain 'L' and resid 494 through 509 removed outlier: 3.840A pdb=" N GLU L 506 " --> pdb=" O ALA L 502 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU L 507 " --> pdb=" O LYS L 503 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU L 508 " --> pdb=" O GLN L 504 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER L 509 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 110 through 111 Processing sheet with id=B, first strand: chain 'A' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE A 157 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=D, first strand: chain 'A' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG A 283 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'A' and resid 313 through 314 removed outlier: 3.730A pdb=" N TYR A 314 " --> pdb=" O MET B 328 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'A' and resid 328 through 329 removed outlier: 3.730A pdb=" N TYR L 314 " --> pdb=" O MET A 328 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'A' and resid 332 through 336 removed outlier: 6.776A pdb=" N GLU A 332 " --> pdb=" O ARG L 283 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N TRP L 285 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR A 334 " --> pdb=" O TRP L 285 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=I, first strand: chain 'B' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE B 157 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'B' and resid 182 through 183 Processing sheet with id=K, first strand: chain 'B' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG B 283 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'B' and resid 313 through 314 removed outlier: 3.731A pdb=" N TYR B 314 " --> pdb=" O MET C 328 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'C' and resid 110 through 111 Processing sheet with id=N, first strand: chain 'C' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE C 157 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'C' and resid 182 through 183 Processing sheet with id=P, first strand: chain 'C' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG C 283 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'C' and resid 313 through 314 removed outlier: 3.730A pdb=" N TYR C 314 " --> pdb=" O MET D 328 " (cutoff:3.500A) Processing sheet with id=R, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=S, first strand: chain 'D' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE D 157 " --> pdb=" O LEU D 177 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'D' and resid 182 through 183 Processing sheet with id=U, first strand: chain 'D' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG D 283 " --> pdb=" O GLU E 332 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'D' and resid 313 through 314 removed outlier: 3.730A pdb=" N TYR D 314 " --> pdb=" O MET E 328 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain 'E' and resid 110 through 111 Processing sheet with id=X, first strand: chain 'E' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE E 157 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'E' and resid 182 through 183 Processing sheet with id=Z, first strand: chain 'E' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG E 283 " --> pdb=" O GLU F 332 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'E' and resid 313 through 314 removed outlier: 3.731A pdb=" N TYR E 314 " --> pdb=" O MET F 328 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'F' and resid 110 through 111 Processing sheet with id=AC, first strand: chain 'F' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE F 157 " --> pdb=" O LEU F 177 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'F' and resid 182 through 183 Processing sheet with id=AE, first strand: chain 'F' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG F 283 " --> pdb=" O GLU G 332 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'F' and resid 313 through 314 removed outlier: 3.730A pdb=" N TYR F 314 " --> pdb=" O MET G 328 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'G' and resid 110 through 111 Processing sheet with id=AH, first strand: chain 'G' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE G 157 " --> pdb=" O LEU G 177 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'G' and resid 182 through 183 Processing sheet with id=AJ, first strand: chain 'G' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG G 283 " --> pdb=" O GLU H 332 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain 'G' and resid 313 through 314 removed outlier: 3.730A pdb=" N TYR G 314 " --> pdb=" O MET H 328 " (cutoff:3.500A) Processing sheet with id=AL, first strand: chain 'H' and resid 110 through 111 Processing sheet with id=AM, first strand: chain 'H' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE H 157 " --> pdb=" O LEU H 177 " (cutoff:3.500A) Processing sheet with id=AN, first strand: chain 'H' and resid 182 through 183 Processing sheet with id=AO, first strand: chain 'H' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG H 283 " --> pdb=" O GLU I 332 " (cutoff:3.500A) Processing sheet with id=AP, first strand: chain 'H' and resid 313 through 314 removed outlier: 3.731A pdb=" N TYR H 314 " --> pdb=" O MET I 328 " (cutoff:3.500A) Processing sheet with id=AQ, first strand: chain 'I' and resid 110 through 111 Processing sheet with id=AR, first strand: chain 'I' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE I 157 " --> pdb=" O LEU I 177 " (cutoff:3.500A) Processing sheet with id=AS, first strand: chain 'I' and resid 182 through 183 Processing sheet with id=AT, first strand: chain 'I' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG I 283 " --> pdb=" O GLU J 332 " (cutoff:3.500A) Processing sheet with id=AU, first strand: chain 'I' and resid 313 through 314 removed outlier: 3.730A pdb=" N TYR I 314 " --> pdb=" O MET J 328 " (cutoff:3.500A) Processing sheet with id=AV, first strand: chain 'J' and resid 110 through 111 Processing sheet with id=AW, first strand: chain 'J' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE J 157 " --> pdb=" O LEU J 177 " (cutoff:3.500A) Processing sheet with id=AX, first strand: chain 'J' and resid 182 through 183 Processing sheet with id=AY, first strand: chain 'J' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG J 283 " --> pdb=" O GLU K 332 " (cutoff:3.500A) Processing sheet with id=AZ, first strand: chain 'J' and resid 313 through 314 removed outlier: 3.730A pdb=" N TYR J 314 " --> pdb=" O MET K 328 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'K' and resid 110 through 111 Processing sheet with id=BB, first strand: chain 'K' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE K 157 " --> pdb=" O LEU K 177 " (cutoff:3.500A) Processing sheet with id=BC, first strand: chain 'K' and resid 182 through 183 Processing sheet with id=BD, first strand: chain 'K' and resid 346 through 349 removed outlier: 3.932A pdb=" N ARG K 283 " --> pdb=" O GLU L 332 " (cutoff:3.500A) Processing sheet with id=BE, first strand: chain 'K' and resid 313 through 314 removed outlier: 3.731A pdb=" N TYR K 314 " --> pdb=" O MET L 328 " (cutoff:3.500A) Processing sheet with id=BF, first strand: chain 'L' and resid 110 through 111 Processing sheet with id=BG, first strand: chain 'L' and resid 174 through 177 removed outlier: 4.520A pdb=" N PHE L 157 " --> pdb=" O LEU L 177 " (cutoff:3.500A) Processing sheet with id=BH, first strand: chain 'L' and resid 182 through 183 1414 hydrogen bonds defined for protein. 4026 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: 9.44 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13349 1.33 - 1.45: 6073 1.45 - 1.57: 22206 1.57 - 1.70: 0 1.70 - 1.82: 420 Bond restraints: 42048 Sorted by residual: bond pdb=" C ILE B 380 " pdb=" N PRO B 381 " ideal model delta sigma weight residual 1.336 1.395 -0.059 1.20e-02 6.94e+03 2.42e+01 bond pdb=" C ILE H 380 " pdb=" N PRO H 381 " ideal model delta sigma weight residual 1.336 1.395 -0.059 1.20e-02 6.94e+03 2.42e+01 bond pdb=" C ILE E 380 " pdb=" N PRO E 381 " ideal model delta sigma weight residual 1.336 1.395 -0.059 1.20e-02 6.94e+03 2.42e+01 bond pdb=" C ILE K 380 " pdb=" N PRO K 381 " ideal model delta sigma weight residual 1.336 1.395 -0.059 1.20e-02 6.94e+03 2.42e+01 bond pdb=" C ILE D 380 " pdb=" N PRO D 381 " ideal model delta sigma weight residual 1.336 1.395 -0.059 1.20e-02 6.94e+03 2.42e+01 ... (remaining 42043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 55218 3.86 - 7.72: 1338 7.72 - 11.57: 132 11.57 - 15.43: 60 15.43 - 19.29: 12 Bond angle restraints: 56760 Sorted by residual: angle pdb=" N ARG J 379 " pdb=" CA ARG J 379 " pdb=" C ARG J 379 " ideal model delta sigma weight residual 110.50 91.21 19.29 1.41e+00 5.03e-01 1.87e+02 angle pdb=" N ARG G 379 " pdb=" CA ARG G 379 " pdb=" C ARG G 379 " ideal model delta sigma weight residual 110.50 91.21 19.29 1.41e+00 5.03e-01 1.87e+02 angle pdb=" N ARG D 379 " pdb=" CA ARG D 379 " pdb=" C ARG D 379 " ideal model delta sigma weight residual 110.50 91.21 19.29 1.41e+00 5.03e-01 1.87e+02 angle pdb=" N ARG A 379 " pdb=" CA ARG A 379 " pdb=" C ARG A 379 " ideal model delta sigma weight residual 110.50 91.21 19.29 1.41e+00 5.03e-01 1.87e+02 angle pdb=" N ARG L 379 " pdb=" CA ARG L 379 " pdb=" C ARG L 379 " ideal model delta sigma weight residual 110.50 91.21 19.29 1.41e+00 5.03e-01 1.87e+02 ... (remaining 56755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.36: 21807 14.36 - 28.73: 2588 28.73 - 43.09: 817 43.09 - 57.45: 456 57.45 - 71.82: 72 Dihedral angle restraints: 25740 sinusoidal: 10596 harmonic: 15144 Sorted by residual: dihedral pdb=" CA GLY B 357 " pdb=" C GLY B 357 " pdb=" N ASN B 358 " pdb=" CA ASN B 358 " ideal model delta harmonic sigma weight residual 0.00 20.32 -20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLY E 357 " pdb=" C GLY E 357 " pdb=" N ASN E 358 " pdb=" CA ASN E 358 " ideal model delta harmonic sigma weight residual 0.00 20.32 -20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLY K 357 " pdb=" C GLY K 357 " pdb=" N ASN K 358 " pdb=" CA ASN K 358 " ideal model delta harmonic sigma weight residual 0.00 20.32 -20.32 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 25737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4804 0.073 - 0.145: 1244 0.145 - 0.218: 144 0.218 - 0.290: 24 0.290 - 0.363: 12 Chirality restraints: 6228 Sorted by residual: chirality pdb=" CA ARG L 379 " pdb=" N ARG L 379 " pdb=" C ARG L 379 " pdb=" CB ARG L 379 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA ARG C 379 " pdb=" N ARG C 379 " pdb=" C ARG C 379 " pdb=" CB ARG C 379 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA ARG F 379 " pdb=" N ARG F 379 " pdb=" C ARG F 379 " pdb=" CB ARG F 379 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 6225 not shown) Planarity restraints: 7404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 279 " -0.065 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO C 280 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 280 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 280 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 279 " 0.065 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO I 280 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO I 280 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO I 280 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 279 " 0.065 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO L 280 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO L 280 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO L 280 " 0.052 5.00e-02 4.00e+02 ... (remaining 7401 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 312 2.41 - 3.03: 26345 3.03 - 3.66: 59446 3.66 - 4.28: 90471 4.28 - 4.90: 142293 Nonbonded interactions: 318867 Sorted by model distance: nonbonded pdb=" O TYR J 86 " pdb=" CG GLU J 87 " model vdw 1.788 3.440 nonbonded pdb=" O TYR D 86 " pdb=" CG GLU D 87 " model vdw 1.788 3.440 nonbonded pdb=" O TYR G 86 " pdb=" CG GLU G 87 " model vdw 1.788 3.440 nonbonded pdb=" O TYR A 86 " pdb=" CG GLU A 87 " model vdw 1.788 3.440 nonbonded pdb=" O TYR B 86 " pdb=" CG GLU B 87 " model vdw 1.788 3.440 ... (remaining 318862 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.670 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 38.820 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.120 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.010 0.180 42072 Z= 0.656 Angle : 1.539 19.291 56760 Z= 0.992 Chirality : 0.064 0.363 6228 Planarity : 0.006 0.100 7404 Dihedral : 15.936 71.818 15876 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 38.28 Ramachandran Plot: Outliers : 2.12 % Allowed : 11.05 % Favored : 86.83 % Rotamer: Outliers : 10.44 % Allowed : 10.74 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % 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 aren not related in a simple way. whole: -4.92 (0.09), residues: 5088 helix: -3.99 (0.07), residues: 1980 sheet: -3.23 (0.16), residues: 624 loop : -2.53 (0.10), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 149 TYR 0.014 0.003 TYR B 102 PHE 0.019 0.003 PHE B 157 TRP 0.017 0.004 TRP I 150 HIS 0.007 0.001 HIS H 255 Details of bonding type rmsd covalent geometry : bond 0.00956 (42048) covalent geometry : angle 1.53865 (56760) hydrogen bonds : bond 0.30174 ( 1414) hydrogen bonds : angle 11.13411 ( 4026) Misc. bond : bond 0.14486 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1524 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 456 poor density : 1068 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8649 (mmm) cc_final: 0.8392 (tpp) REVERT: A 176 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7741 (ttt180) REVERT: A 221 MET cc_start: 0.5050 (tpt) cc_final: 0.4685 (mtp) REVERT: A 296 LYS cc_start: 0.7711 (ttmm) cc_final: 0.6925 (tmtt) REVERT: A 320 LYS cc_start: 0.7759 (mtmt) cc_final: 0.7491 (ptmt) REVERT: A 401 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8709 (tt) REVERT: A 420 ASP cc_start: 0.7738 (p0) cc_final: 0.7294 (t0) REVERT: A 468 ASN cc_start: 0.8584 (t0) cc_final: 0.8003 (t0) REVERT: A 507 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7723 (tp30) REVERT: B 92 VAL cc_start: 0.9506 (OUTLIER) cc_final: 0.9254 (t) REVERT: B 221 MET cc_start: 0.5023 (tpt) cc_final: 0.4626 (mtp) REVERT: B 296 LYS cc_start: 0.7654 (ttmm) cc_final: 0.6932 (tmtt) REVERT: B 320 LYS cc_start: 0.8000 (mtmt) cc_final: 0.7581 (ptmt) REVERT: B 361 ASP cc_start: 0.9022 (t0) cc_final: 0.8506 (t0) REVERT: B 371 MET cc_start: 0.8270 (mtp) cc_final: 0.7252 (mtp) REVERT: B 397 THR cc_start: 0.8924 (m) cc_final: 0.8673 (p) REVERT: B 457 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9209 (tt) REVERT: B 468 ASN cc_start: 0.8575 (t0) cc_final: 0.8014 (t0) REVERT: B 507 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7757 (tp30) REVERT: C 83 MET cc_start: 0.8605 (mmm) cc_final: 0.8279 (tpp) REVERT: C 86 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.6780 (t80) REVERT: C 176 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7540 (ttt180) REVERT: C 221 MET cc_start: 0.4642 (tpt) cc_final: 0.4329 (mtp) REVERT: C 275 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7444 (ttt180) REVERT: C 296 LYS cc_start: 0.7599 (ttmm) cc_final: 0.6923 (tmtt) REVERT: C 320 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7567 (ptmt) REVERT: C 361 ASP cc_start: 0.9006 (t0) cc_final: 0.8733 (t0) REVERT: C 369 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8835 (tp) REVERT: C 377 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8195 (mt) REVERT: C 397 THR cc_start: 0.9000 (m) cc_final: 0.8788 (p) REVERT: C 420 ASP cc_start: 0.7700 (p0) cc_final: 0.7314 (t0) REVERT: C 468 ASN cc_start: 0.8449 (t0) cc_final: 0.7875 (t0) REVERT: D 83 MET cc_start: 0.8645 (mmm) cc_final: 0.8388 (tpp) REVERT: D 176 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7738 (ttt180) REVERT: D 221 MET cc_start: 0.5053 (tpt) cc_final: 0.4690 (mtp) REVERT: D 296 LYS cc_start: 0.7709 (ttmm) cc_final: 0.6927 (tmtt) REVERT: D 320 LYS cc_start: 0.7757 (mtmt) cc_final: 0.7493 (ptmt) REVERT: D 401 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8706 (tt) REVERT: D 420 ASP cc_start: 0.7736 (p0) cc_final: 0.7292 (t0) REVERT: D 468 ASN cc_start: 0.8581 (t0) cc_final: 0.8004 (t0) REVERT: D 507 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: E 92 VAL cc_start: 0.9506 (OUTLIER) cc_final: 0.9253 (t) REVERT: E 221 MET cc_start: 0.5026 (tpt) cc_final: 0.4628 (mtp) REVERT: E 296 LYS cc_start: 0.7655 (ttmm) cc_final: 0.6932 (tmtt) REVERT: E 320 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7579 (ptmt) REVERT: E 361 ASP cc_start: 0.9022 (t0) cc_final: 0.8505 (t0) REVERT: E 371 MET cc_start: 0.8270 (mtp) cc_final: 0.7248 (mtp) REVERT: E 397 THR cc_start: 0.8928 (m) cc_final: 0.8676 (p) REVERT: E 457 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9209 (tt) REVERT: E 468 ASN cc_start: 0.8574 (t0) cc_final: 0.8010 (t0) REVERT: E 507 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7757 (tp30) REVERT: F 83 MET cc_start: 0.8605 (mmm) cc_final: 0.8282 (tpp) REVERT: F 86 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.6780 (t80) REVERT: F 176 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7540 (ttt180) REVERT: F 221 MET cc_start: 0.4636 (tpt) cc_final: 0.4325 (mtp) REVERT: F 275 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7438 (ttt180) REVERT: F 296 LYS cc_start: 0.7604 (ttmm) cc_final: 0.6928 (tmtt) REVERT: F 320 LYS cc_start: 0.7878 (mtmt) cc_final: 0.7571 (ptmt) REVERT: F 361 ASP cc_start: 0.9009 (t0) cc_final: 0.8733 (t0) REVERT: F 369 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8836 (tp) REVERT: F 377 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8191 (mt) REVERT: F 397 THR cc_start: 0.9002 (m) cc_final: 0.8790 (p) REVERT: F 420 ASP cc_start: 0.7698 (p0) cc_final: 0.7315 (t0) REVERT: F 468 ASN cc_start: 0.8453 (t0) cc_final: 0.7878 (t0) REVERT: G 83 MET cc_start: 0.8643 (mmm) cc_final: 0.8387 (tpp) REVERT: G 176 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7736 (ttt180) REVERT: G 221 MET cc_start: 0.5054 (tpt) cc_final: 0.4692 (mtp) REVERT: G 296 LYS cc_start: 0.7707 (ttmm) cc_final: 0.6925 (tmtt) REVERT: G 320 LYS cc_start: 0.7760 (mtmt) cc_final: 0.7495 (ptmt) REVERT: G 401 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8709 (tt) REVERT: G 420 ASP cc_start: 0.7732 (p0) cc_final: 0.7293 (t0) REVERT: G 468 ASN cc_start: 0.8586 (t0) cc_final: 0.8007 (t0) REVERT: G 507 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7729 (tp30) REVERT: H 92 VAL cc_start: 0.9508 (OUTLIER) cc_final: 0.9254 (t) REVERT: H 221 MET cc_start: 0.5026 (tpt) cc_final: 0.4626 (mtp) REVERT: H 296 LYS cc_start: 0.7661 (ttmm) cc_final: 0.6937 (tmtt) REVERT: H 320 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7579 (ptmt) REVERT: H 361 ASP cc_start: 0.9022 (t0) cc_final: 0.8504 (t0) REVERT: H 371 MET cc_start: 0.8270 (mtp) cc_final: 0.7223 (mtp) REVERT: H 397 THR cc_start: 0.8927 (m) cc_final: 0.8678 (p) REVERT: H 457 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9207 (tt) REVERT: H 468 ASN cc_start: 0.8572 (t0) cc_final: 0.8008 (t0) REVERT: H 507 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7753 (tp30) REVERT: I 83 MET cc_start: 0.8608 (mmm) cc_final: 0.8281 (tpp) REVERT: I 86 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.6706 (t80) REVERT: I 176 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7544 (ttt180) REVERT: I 221 MET cc_start: 0.4638 (tpt) cc_final: 0.4325 (mtp) REVERT: I 275 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7439 (ttt180) REVERT: I 296 LYS cc_start: 0.7602 (ttmm) cc_final: 0.6929 (tmtt) REVERT: I 320 LYS cc_start: 0.7873 (mtmt) cc_final: 0.7567 (ptmt) REVERT: I 361 ASP cc_start: 0.9008 (t0) cc_final: 0.8728 (t0) REVERT: I 369 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8834 (tp) REVERT: I 377 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8197 (mt) REVERT: I 397 THR cc_start: 0.9000 (m) cc_final: 0.8789 (p) REVERT: I 420 ASP cc_start: 0.7695 (p0) cc_final: 0.7310 (t0) REVERT: I 468 ASN cc_start: 0.8450 (t0) cc_final: 0.7877 (t0) REVERT: J 83 MET cc_start: 0.8648 (mmm) cc_final: 0.8394 (tpp) REVERT: J 176 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7734 (ttt180) REVERT: J 221 MET cc_start: 0.5052 (tpt) cc_final: 0.4691 (mtp) REVERT: J 296 LYS cc_start: 0.7708 (ttmm) cc_final: 0.6924 (tmtt) REVERT: J 320 LYS cc_start: 0.7759 (mtmt) cc_final: 0.7492 (ptmt) REVERT: J 401 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8712 (tt) REVERT: J 420 ASP cc_start: 0.7734 (p0) cc_final: 0.7294 (t0) REVERT: J 468 ASN cc_start: 0.8583 (t0) cc_final: 0.8006 (t0) REVERT: J 507 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7723 (tp30) REVERT: K 92 VAL cc_start: 0.9510 (OUTLIER) cc_final: 0.9256 (t) REVERT: K 221 MET cc_start: 0.5025 (tpt) cc_final: 0.4627 (mtp) REVERT: K 296 LYS cc_start: 0.7657 (ttmm) cc_final: 0.6931 (tmtt) REVERT: K 320 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7579 (ptmt) REVERT: K 361 ASP cc_start: 0.9023 (t0) cc_final: 0.8505 (t0) REVERT: K 371 MET cc_start: 0.8268 (mtp) cc_final: 0.7253 (mtp) REVERT: K 397 THR cc_start: 0.8927 (m) cc_final: 0.8677 (p) REVERT: K 457 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9207 (tt) REVERT: K 468 ASN cc_start: 0.8571 (t0) cc_final: 0.8010 (t0) REVERT: K 507 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7757 (tp30) REVERT: L 83 MET cc_start: 0.8607 (mmm) cc_final: 0.8281 (tpp) REVERT: L 86 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.6781 (t80) REVERT: L 176 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7543 (ttt180) REVERT: L 221 MET cc_start: 0.4640 (tpt) cc_final: 0.4325 (mtp) REVERT: L 275 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7437 (ttt180) REVERT: L 296 LYS cc_start: 0.7603 (ttmm) cc_final: 0.6924 (tmtt) REVERT: L 320 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7566 (ptmt) REVERT: L 361 ASP cc_start: 0.9009 (t0) cc_final: 0.8719 (t0) REVERT: L 369 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8839 (tp) REVERT: L 377 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8196 (mt) REVERT: L 397 THR cc_start: 0.9000 (m) cc_final: 0.8788 (p) REVERT: L 420 ASP cc_start: 0.7696 (p0) cc_final: 0.7313 (t0) REVERT: L 468 ASN cc_start: 0.8450 (t0) cc_final: 0.7877 (t0) outliers start: 456 outliers final: 100 residues processed: 1428 average time/residue: 0.3173 time to fit residues: 691.6849 Evaluate side-chains 852 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 708 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 513 ARG Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 507 GLU Chi-restraints excluded: chain D residue 513 ARG Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 507 GLU Chi-restraints excluded: chain E residue 513 ARG Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 176 ARG Chi-restraints excluded: chain F residue 275 ARG Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 513 ARG Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 467 ILE Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 507 GLU Chi-restraints excluded: chain G residue 513 ARG Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 283 ARG Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 457 LEU Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain H residue 507 GLU Chi-restraints excluded: chain H residue 513 ARG Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 176 ARG Chi-restraints excluded: chain I residue 275 ARG Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 399 ASP Chi-restraints excluded: chain I residue 401 LEU Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 513 ARG Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 176 ARG Chi-restraints excluded: chain J residue 254 LEU Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 467 ILE Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain J residue 507 GLU Chi-restraints excluded: chain J residue 513 ARG Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 283 ARG Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 377 LEU Chi-restraints excluded: chain K residue 399 ASP Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 494 THR Chi-restraints excluded: chain K residue 507 GLU Chi-restraints excluded: chain K residue 513 ARG Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 176 ARG Chi-restraints excluded: chain L residue 275 ARG Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain L residue 369 LEU Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 399 ASP Chi-restraints excluded: chain L residue 401 LEU Chi-restraints excluded: chain L residue 494 THR Chi-restraints excluded: chain L residue 513 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.9980 chunk 455 optimal weight: 0.6980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 494 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 146 HIS A 183 GLN A 355 ASN A 358 ASN B 90 ASN B 146 HIS B 355 ASN B 358 ASN C 146 HIS C 183 GLN C 255 HIS C 355 ASN C 358 ASN C 492 GLN D 84 ASN D 146 HIS D 183 GLN D 355 ASN D 358 ASN E 90 ASN E 146 HIS E 355 ASN E 358 ASN F 146 HIS F 183 GLN F 255 HIS F 355 ASN F 358 ASN F 492 GLN G 84 ASN G 146 HIS G 183 GLN G 355 ASN G 358 ASN H 90 ASN H 146 HIS H 355 ASN H 358 ASN I 146 HIS I 183 GLN I 255 HIS I 355 ASN I 358 ASN I 492 GLN J 84 ASN J 146 HIS J 183 GLN J 355 ASN J 358 ASN K 90 ASN K 146 HIS K 355 ASN K 358 ASN L 146 HIS L 183 GLN L 355 ASN L 358 ASN L 492 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.174540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135865 restraints weight = 54406.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134301 restraints weight = 52168.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.135725 restraints weight = 54145.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.136252 restraints weight = 40685.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.136560 restraints weight = 37438.511| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 42072 Z= 0.171 Angle : 0.801 9.631 56760 Z= 0.425 Chirality : 0.046 0.243 6228 Planarity : 0.005 0.054 7404 Dihedral : 8.871 57.492 5940 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.46 % Favored : 95.83 % Rotamer: Outliers : 4.88 % Allowed : 16.32 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % 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 aren not related in a simple way. whole: -3.56 (0.10), residues: 5088 helix: -2.55 (0.09), residues: 2244 sheet: -2.06 (0.21), residues: 384 loop : -2.12 (0.11), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 398 TYR 0.009 0.001 TYR L 237 PHE 0.012 0.002 PHE K 365 TRP 0.011 0.002 TRP F 150 HIS 0.003 0.001 HIS G 412 Details of bonding type rmsd covalent geometry : bond 0.00350 (42048) covalent geometry : angle 0.80147 (56760) hydrogen bonds : bond 0.04168 ( 1414) hydrogen bonds : angle 6.22201 ( 4026) Misc. bond : bond 0.00255 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 831 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8293 (mm) cc_final: 0.7976 (pt) REVERT: A 83 MET cc_start: 0.8165 (mmm) cc_final: 0.7915 (mmm) REVERT: A 87 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7000 (pt0) REVERT: A 268 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7460 (mt-10) REVERT: A 296 LYS cc_start: 0.7958 (ttmm) cc_final: 0.7538 (tmtt) REVERT: A 301 MET cc_start: 0.8996 (mmm) cc_final: 0.8449 (mmt) REVERT: A 348 ASP cc_start: 0.7514 (t0) cc_final: 0.7092 (t0) REVERT: A 401 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8480 (tt) REVERT: A 408 ARG cc_start: 0.7877 (tpp-160) cc_final: 0.7634 (tpm170) REVERT: A 438 ASN cc_start: 0.7881 (m-40) cc_final: 0.7452 (m-40) REVERT: A 450 ARG cc_start: 0.7809 (mtt90) cc_final: 0.7572 (mtt90) REVERT: A 464 GLU cc_start: 0.7198 (tt0) cc_final: 0.6924 (tt0) REVERT: A 468 ASN cc_start: 0.8500 (t0) cc_final: 0.8107 (t0) REVERT: A 472 MET cc_start: 0.8356 (ttp) cc_final: 0.8127 (ttp) REVERT: A 513 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7971 (mtm-85) REVERT: B 268 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7570 (mt-10) REVERT: B 296 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7458 (tmtt) REVERT: B 416 GLU cc_start: 0.8585 (tt0) cc_final: 0.8221 (tt0) REVERT: B 457 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9013 (tt) REVERT: C 72 ILE cc_start: 0.8429 (mm) cc_final: 0.8185 (pt) REVERT: C 136 HIS cc_start: 0.7837 (m90) cc_final: 0.7409 (m-70) REVERT: C 268 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7333 (mt-10) REVERT: C 296 LYS cc_start: 0.7771 (ttmm) cc_final: 0.7272 (tmtt) REVERT: C 468 ASN cc_start: 0.8652 (t0) cc_final: 0.8156 (t0) REVERT: D 72 ILE cc_start: 0.8314 (mm) cc_final: 0.8013 (pt) REVERT: D 83 MET cc_start: 0.8162 (mmm) cc_final: 0.7905 (mmm) REVERT: D 87 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7004 (pt0) REVERT: D 268 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7461 (mt-10) REVERT: D 296 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7539 (tmtt) REVERT: D 301 MET cc_start: 0.8994 (mmm) cc_final: 0.8465 (mmt) REVERT: D 348 ASP cc_start: 0.7511 (t0) cc_final: 0.7082 (t0) REVERT: D 401 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8481 (tt) REVERT: D 408 ARG cc_start: 0.7876 (tpp-160) cc_final: 0.7642 (tpm170) REVERT: D 438 ASN cc_start: 0.7876 (m-40) cc_final: 0.7445 (m-40) REVERT: D 450 ARG cc_start: 0.7811 (mtt90) cc_final: 0.7574 (mtt90) REVERT: D 464 GLU cc_start: 0.7192 (tt0) cc_final: 0.6922 (tt0) REVERT: D 468 ASN cc_start: 0.8502 (t0) cc_final: 0.8108 (t0) REVERT: D 472 MET cc_start: 0.8368 (ttp) cc_final: 0.8135 (ttp) REVERT: D 513 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7967 (mtm-85) REVERT: E 268 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7557 (mt-10) REVERT: E 296 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7461 (tmtt) REVERT: E 416 GLU cc_start: 0.8586 (tt0) cc_final: 0.8224 (tt0) REVERT: E 457 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9015 (tt) REVERT: F 72 ILE cc_start: 0.8424 (mm) cc_final: 0.8181 (pt) REVERT: F 136 HIS cc_start: 0.7830 (m90) cc_final: 0.7405 (m-70) REVERT: F 268 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7343 (mt-10) REVERT: F 296 LYS cc_start: 0.7766 (ttmm) cc_final: 0.7270 (tmtt) REVERT: F 468 ASN cc_start: 0.8652 (t0) cc_final: 0.8162 (t0) REVERT: G 72 ILE cc_start: 0.8305 (mm) cc_final: 0.8010 (pt) REVERT: G 83 MET cc_start: 0.8146 (mmm) cc_final: 0.7890 (mmm) REVERT: G 87 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7006 (pt0) REVERT: G 268 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7466 (mt-10) REVERT: G 296 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7536 (tmtt) REVERT: G 301 MET cc_start: 0.9001 (mmm) cc_final: 0.8467 (mmt) REVERT: G 348 ASP cc_start: 0.7507 (t0) cc_final: 0.7076 (t0) REVERT: G 401 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8482 (tt) REVERT: G 408 ARG cc_start: 0.7894 (tpp-160) cc_final: 0.7650 (tpm170) REVERT: G 438 ASN cc_start: 0.7880 (m-40) cc_final: 0.7450 (m-40) REVERT: G 450 ARG cc_start: 0.7808 (mtt90) cc_final: 0.7574 (mtt90) REVERT: G 464 GLU cc_start: 0.7189 (tt0) cc_final: 0.6915 (tt0) REVERT: G 468 ASN cc_start: 0.8498 (t0) cc_final: 0.8101 (t0) REVERT: G 472 MET cc_start: 0.8361 (ttp) cc_final: 0.8126 (ttp) REVERT: G 513 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7972 (mtm-85) REVERT: H 268 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7521 (mt-10) REVERT: H 296 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7469 (tmtt) REVERT: H 416 GLU cc_start: 0.8588 (tt0) cc_final: 0.8222 (tt0) REVERT: H 457 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9015 (tt) REVERT: I 72 ILE cc_start: 0.8433 (mm) cc_final: 0.8190 (pt) REVERT: I 136 HIS cc_start: 0.7823 (m90) cc_final: 0.7401 (m-70) REVERT: I 268 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7330 (mt-10) REVERT: I 296 LYS cc_start: 0.7765 (ttmm) cc_final: 0.7270 (tmtt) REVERT: I 468 ASN cc_start: 0.8647 (t0) cc_final: 0.8160 (t0) REVERT: J 72 ILE cc_start: 0.8307 (mm) cc_final: 0.8012 (pt) REVERT: J 83 MET cc_start: 0.8162 (mmm) cc_final: 0.7905 (mmm) REVERT: J 87 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7000 (pt0) REVERT: J 268 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7467 (mt-10) REVERT: J 296 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7540 (tmtt) REVERT: J 301 MET cc_start: 0.9000 (mmm) cc_final: 0.8464 (mmt) REVERT: J 348 ASP cc_start: 0.7507 (t0) cc_final: 0.7083 (t0) REVERT: J 401 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8484 (tt) REVERT: J 408 ARG cc_start: 0.7882 (tpp-160) cc_final: 0.7634 (tpm170) REVERT: J 438 ASN cc_start: 0.7880 (m-40) cc_final: 0.7452 (m-40) REVERT: J 450 ARG cc_start: 0.7808 (mtt90) cc_final: 0.7572 (mtt90) REVERT: J 464 GLU cc_start: 0.7195 (tt0) cc_final: 0.6917 (tt0) REVERT: J 468 ASN cc_start: 0.8494 (t0) cc_final: 0.8102 (t0) REVERT: J 472 MET cc_start: 0.8358 (ttp) cc_final: 0.8119 (ttp) REVERT: J 513 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7971 (mtm-85) REVERT: K 268 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7528 (mt-10) REVERT: K 296 LYS cc_start: 0.7944 (ttmm) cc_final: 0.7461 (tmtt) REVERT: K 416 GLU cc_start: 0.8586 (tt0) cc_final: 0.8222 (tt0) REVERT: K 457 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9014 (tt) REVERT: L 72 ILE cc_start: 0.8432 (mm) cc_final: 0.8196 (pt) REVERT: L 136 HIS cc_start: 0.7827 (m90) cc_final: 0.7402 (m-70) REVERT: L 268 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7337 (mt-10) REVERT: L 296 LYS cc_start: 0.7770 (ttmm) cc_final: 0.7274 (tmtt) REVERT: L 468 ASN cc_start: 0.8645 (t0) cc_final: 0.8156 (t0) outliers start: 213 outliers final: 100 residues processed: 1024 average time/residue: 0.2709 time to fit residues: 449.4218 Evaluate side-chains 752 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 636 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 513 ARG Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 513 ARG Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 90 ASN Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 457 LEU Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 401 LEU Chi-restraints excluded: chain I residue 457 LEU Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 254 LEU Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain J residue 513 ARG Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 401 LEU Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 494 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 202 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 306 optimal weight: 8.9990 chunk 165 optimal weight: 0.0970 chunk 467 optimal weight: 0.6980 chunk 228 optimal weight: 0.5980 chunk 411 optimal weight: 7.9990 chunk 239 optimal weight: 4.9990 chunk 164 optimal weight: 0.0970 chunk 170 optimal weight: 2.9990 chunk 326 optimal weight: 2.9990 overall best weight: 0.8978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 90 ASN C 85 ASN D 85 ASN E 85 ASN E 90 ASN F 85 ASN G 85 ASN H 85 ASN H 90 ASN I 85 ASN J 85 ASN K 90 ASN L 85 ASN L 255 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.177243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139181 restraints weight = 53857.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.137181 restraints weight = 49317.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.139339 restraints weight = 55434.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.139558 restraints weight = 37649.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.140505 restraints weight = 35518.515| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 42072 Z= 0.144 Angle : 0.700 9.572 56760 Z= 0.371 Chirality : 0.044 0.218 6228 Planarity : 0.004 0.036 7404 Dihedral : 6.938 57.883 5728 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.30 % Favored : 96.23 % Rotamer: Outliers : 4.24 % Allowed : 17.86 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 aren not related in a simple way. whole: -2.72 (0.11), residues: 5088 helix: -1.59 (0.10), residues: 2268 sheet: -1.71 (0.22), residues: 384 loop : -1.96 (0.11), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 450 TYR 0.009 0.001 TYR C 314 PHE 0.012 0.001 PHE K 365 TRP 0.012 0.001 TRP L 285 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00299 (42048) covalent geometry : angle 0.69966 (56760) hydrogen bonds : bond 0.03109 ( 1414) hydrogen bonds : angle 5.36899 ( 4026) Misc. bond : bond 0.00363 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 733 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8404 (mm) cc_final: 0.8071 (pt) REVERT: A 83 MET cc_start: 0.8001 (mmm) cc_final: 0.7567 (tpp) REVERT: A 268 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7458 (mt-10) REVERT: A 296 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7551 (tmtt) REVERT: A 348 ASP cc_start: 0.7618 (t0) cc_final: 0.7248 (t0) REVERT: A 401 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8433 (tt) REVERT: A 468 ASN cc_start: 0.8630 (t0) cc_final: 0.8326 (t0) REVERT: A 472 MET cc_start: 0.8394 (ttp) cc_final: 0.8188 (ttp) REVERT: A 513 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7930 (mtm-85) REVERT: B 268 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7479 (mt-10) REVERT: B 296 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7578 (tmtt) REVERT: B 328 MET cc_start: 0.6056 (ttm) cc_final: 0.5852 (mtp) REVERT: C 72 ILE cc_start: 0.8463 (mm) cc_final: 0.8139 (pt) REVERT: C 87 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6870 (pt0) REVERT: C 126 MET cc_start: 0.7814 (mmt) cc_final: 0.7605 (mmm) REVERT: C 268 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7456 (mt-10) REVERT: C 296 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7349 (tmtt) REVERT: C 361 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7605 (t0) REVERT: C 408 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7353 (tpp-160) REVERT: C 468 ASN cc_start: 0.8635 (t0) cc_final: 0.8277 (t0) REVERT: D 72 ILE cc_start: 0.8437 (mm) cc_final: 0.8103 (pt) REVERT: D 83 MET cc_start: 0.8042 (mmm) cc_final: 0.7585 (tpp) REVERT: D 268 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7489 (mt-10) REVERT: D 296 LYS cc_start: 0.7999 (ttmm) cc_final: 0.7549 (tmtt) REVERT: D 348 ASP cc_start: 0.7556 (t0) cc_final: 0.7203 (t0) REVERT: D 401 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8430 (tt) REVERT: D 468 ASN cc_start: 0.8625 (t0) cc_final: 0.8325 (t0) REVERT: D 472 MET cc_start: 0.8394 (ttp) cc_final: 0.8189 (ttp) REVERT: D 513 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7924 (mtm-85) REVERT: E 268 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7483 (mt-10) REVERT: E 296 LYS cc_start: 0.8114 (ttmm) cc_final: 0.7582 (tmtt) REVERT: E 434 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7175 (tm-30) REVERT: F 72 ILE cc_start: 0.8473 (mm) cc_final: 0.8137 (pt) REVERT: F 87 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6876 (pt0) REVERT: F 126 MET cc_start: 0.7806 (mmt) cc_final: 0.7600 (mmm) REVERT: F 268 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7449 (mt-10) REVERT: F 296 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7351 (tmtt) REVERT: F 361 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7578 (t0) REVERT: F 408 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.7366 (tpp-160) REVERT: F 468 ASN cc_start: 0.8645 (t0) cc_final: 0.8292 (t0) REVERT: G 72 ILE cc_start: 0.8438 (mm) cc_final: 0.8103 (pt) REVERT: G 83 MET cc_start: 0.8033 (mmm) cc_final: 0.7579 (tpp) REVERT: G 268 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7497 (mt-10) REVERT: G 296 LYS cc_start: 0.7995 (ttmm) cc_final: 0.7555 (tmtt) REVERT: G 348 ASP cc_start: 0.7557 (t0) cc_final: 0.7207 (t0) REVERT: G 401 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8434 (tt) REVERT: G 468 ASN cc_start: 0.8630 (t0) cc_final: 0.8325 (t0) REVERT: G 472 MET cc_start: 0.8396 (ttp) cc_final: 0.8184 (ttp) REVERT: G 513 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7924 (mtm-85) REVERT: H 268 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7488 (mt-10) REVERT: H 296 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7583 (tmtt) REVERT: H 328 MET cc_start: 0.6065 (ttm) cc_final: 0.5859 (mtp) REVERT: H 434 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7166 (tm-30) REVERT: I 72 ILE cc_start: 0.8466 (mm) cc_final: 0.8140 (pt) REVERT: I 87 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6852 (pt0) REVERT: I 126 MET cc_start: 0.7808 (mmt) cc_final: 0.7600 (mmm) REVERT: I 268 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7441 (mt-10) REVERT: I 296 LYS cc_start: 0.7840 (ttmm) cc_final: 0.7352 (tmtt) REVERT: I 361 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7577 (t0) REVERT: I 408 ARG cc_start: 0.7770 (ttm-80) cc_final: 0.7353 (tpp-160) REVERT: I 468 ASN cc_start: 0.8644 (t0) cc_final: 0.8285 (t0) REVERT: J 72 ILE cc_start: 0.8439 (mm) cc_final: 0.8107 (pt) REVERT: J 83 MET cc_start: 0.8035 (mmm) cc_final: 0.7577 (tpp) REVERT: J 268 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7503 (mt-10) REVERT: J 296 LYS cc_start: 0.7997 (ttmm) cc_final: 0.7557 (tmtt) REVERT: J 348 ASP cc_start: 0.7555 (t0) cc_final: 0.7206 (t0) REVERT: J 401 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8427 (tt) REVERT: J 468 ASN cc_start: 0.8628 (t0) cc_final: 0.8326 (t0) REVERT: J 472 MET cc_start: 0.8401 (ttp) cc_final: 0.8188 (ttp) REVERT: J 513 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7927 (mtm-85) REVERT: K 268 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7476 (mt-10) REVERT: K 296 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7579 (tmtt) REVERT: K 328 MET cc_start: 0.6058 (ttm) cc_final: 0.5856 (mtp) REVERT: K 434 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7159 (tm-30) REVERT: L 72 ILE cc_start: 0.8464 (mm) cc_final: 0.8142 (pt) REVERT: L 87 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6854 (pt0) REVERT: L 126 MET cc_start: 0.7807 (mmt) cc_final: 0.7601 (mmm) REVERT: L 268 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7450 (mt-10) REVERT: L 296 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7347 (tmtt) REVERT: L 361 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7556 (t0) REVERT: L 408 ARG cc_start: 0.7772 (ttm-80) cc_final: 0.7351 (tpp-160) REVERT: L 468 ASN cc_start: 0.8636 (t0) cc_final: 0.8277 (t0) outliers start: 185 outliers final: 85 residues processed: 882 average time/residue: 0.2552 time to fit residues: 374.3818 Evaluate side-chains 754 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 653 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 513 ARG Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain E residue 472 MET Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 457 LEU Chi-restraints excluded: chain G residue 513 ARG Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 472 MET Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 361 ASP Chi-restraints excluded: chain I residue 457 LEU Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 457 LEU Chi-restraints excluded: chain J residue 513 ARG Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain K residue 472 MET Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 282 ARG Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 361 ASP Chi-restraints excluded: chain L residue 457 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 28 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 288 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 333 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 293 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 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 85 ASN C 85 ASN C 382 GLN D 85 ASN E 85 ASN F 85 ASN F 382 GLN G 85 ASN H 85 ASN I 85 ASN I 382 GLN J 85 ASN L 85 ASN L 382 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.176858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.139496 restraints weight = 54291.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136870 restraints weight = 55574.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.138526 restraints weight = 59325.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.139277 restraints weight = 41956.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.139582 restraints weight = 39151.809| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 42072 Z= 0.141 Angle : 0.677 9.920 56760 Z= 0.356 Chirality : 0.044 0.245 6228 Planarity : 0.004 0.033 7404 Dihedral : 6.341 59.000 5688 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.72 % Favored : 94.81 % Rotamer: Outliers : 4.10 % Allowed : 18.70 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 aren not related in a simple way. whole: -2.22 (0.11), residues: 5088 helix: -1.03 (0.10), residues: 2256 sheet: -1.31 (0.24), residues: 384 loop : -1.87 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 278 TYR 0.008 0.001 TYR A 86 PHE 0.010 0.001 PHE K 365 TRP 0.007 0.001 TRP J 285 HIS 0.004 0.001 HIS L 326 Details of bonding type rmsd covalent geometry : bond 0.00310 (42048) covalent geometry : angle 0.67664 (56760) hydrogen bonds : bond 0.02820 ( 1414) hydrogen bonds : angle 5.10425 ( 4026) Misc. bond : bond 0.00279 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 678 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8455 (mm) cc_final: 0.8082 (pt) REVERT: A 268 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7465 (mt-10) REVERT: A 296 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7528 (tmtt) REVERT: A 401 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8418 (tt) REVERT: A 416 GLU cc_start: 0.8443 (tt0) cc_final: 0.8112 (tt0) REVERT: A 468 ASN cc_start: 0.8568 (t0) cc_final: 0.8287 (t0) REVERT: A 487 MET cc_start: 0.8309 (ttp) cc_final: 0.8081 (ttm) REVERT: A 513 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7900 (mtm-85) REVERT: B 268 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7502 (mt-10) REVERT: B 296 LYS cc_start: 0.8183 (ttmm) cc_final: 0.7574 (tmtt) REVERT: B 401 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8518 (tt) REVERT: C 72 ILE cc_start: 0.8512 (mm) cc_final: 0.8227 (pt) REVERT: C 84 ASN cc_start: 0.7867 (t0) cc_final: 0.7567 (m-40) REVERT: C 268 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7629 (mt-10) REVERT: C 296 LYS cc_start: 0.7878 (ttmm) cc_final: 0.7382 (tmtt) REVERT: C 361 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7457 (t70) REVERT: C 468 ASN cc_start: 0.8567 (t0) cc_final: 0.8270 (t0) REVERT: C 504 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8063 (tm-30) REVERT: D 72 ILE cc_start: 0.8460 (mm) cc_final: 0.8085 (pt) REVERT: D 124 ASN cc_start: 0.7274 (p0) cc_final: 0.6900 (m110) REVERT: D 268 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7498 (mt-10) REVERT: D 296 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7532 (tmtt) REVERT: D 401 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8414 (tt) REVERT: D 416 GLU cc_start: 0.8431 (tt0) cc_final: 0.8098 (tt0) REVERT: D 468 ASN cc_start: 0.8570 (t0) cc_final: 0.8297 (t0) REVERT: D 487 MET cc_start: 0.8307 (ttp) cc_final: 0.8083 (ttm) REVERT: D 513 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7900 (mtm-85) REVERT: E 268 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7513 (mt-10) REVERT: E 296 LYS cc_start: 0.8177 (ttmm) cc_final: 0.7569 (tmtt) REVERT: E 401 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8521 (tt) REVERT: F 72 ILE cc_start: 0.8511 (mm) cc_final: 0.8239 (pt) REVERT: F 84 ASN cc_start: 0.7863 (t0) cc_final: 0.7574 (m-40) REVERT: F 268 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7590 (mt-10) REVERT: F 296 LYS cc_start: 0.7882 (ttmm) cc_final: 0.7383 (tmtt) REVERT: F 361 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7469 (t70) REVERT: F 468 ASN cc_start: 0.8567 (t0) cc_final: 0.8269 (t0) REVERT: F 504 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8058 (tm-30) REVERT: G 72 ILE cc_start: 0.8468 (mm) cc_final: 0.8093 (pt) REVERT: G 124 ASN cc_start: 0.7284 (p0) cc_final: 0.6903 (m110) REVERT: G 268 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7504 (mt-10) REVERT: G 296 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7525 (tmtt) REVERT: G 401 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8425 (tt) REVERT: G 416 GLU cc_start: 0.8424 (tt0) cc_final: 0.8097 (tt0) REVERT: G 468 ASN cc_start: 0.8570 (t0) cc_final: 0.8292 (t0) REVERT: G 487 MET cc_start: 0.8311 (ttp) cc_final: 0.8095 (ttm) REVERT: G 513 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7903 (mtm-85) REVERT: H 268 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7509 (mt-10) REVERT: H 296 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7579 (tmtt) REVERT: H 401 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8522 (tt) REVERT: I 72 ILE cc_start: 0.8504 (mm) cc_final: 0.8230 (pt) REVERT: I 84 ASN cc_start: 0.7862 (t0) cc_final: 0.7568 (m-40) REVERT: I 268 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7591 (mt-10) REVERT: I 296 LYS cc_start: 0.7882 (ttmm) cc_final: 0.7392 (tmtt) REVERT: I 361 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7454 (t70) REVERT: I 468 ASN cc_start: 0.8566 (t0) cc_final: 0.8266 (t0) REVERT: I 504 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8058 (tm-30) REVERT: J 72 ILE cc_start: 0.8463 (mm) cc_final: 0.8097 (pt) REVERT: J 124 ASN cc_start: 0.7267 (p0) cc_final: 0.6893 (m110) REVERT: J 268 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7471 (mt-10) REVERT: J 296 LYS cc_start: 0.7976 (ttmm) cc_final: 0.7531 (tmtt) REVERT: J 401 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8426 (tt) REVERT: J 416 GLU cc_start: 0.8431 (tt0) cc_final: 0.8100 (tt0) REVERT: J 468 ASN cc_start: 0.8571 (t0) cc_final: 0.8290 (t0) REVERT: J 487 MET cc_start: 0.8314 (ttp) cc_final: 0.8087 (ttm) REVERT: J 513 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7902 (mtm-85) REVERT: K 268 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7512 (mt-10) REVERT: K 296 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7577 (tmtt) REVERT: K 401 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8519 (tt) REVERT: L 72 ILE cc_start: 0.8505 (mm) cc_final: 0.8233 (pt) REVERT: L 84 ASN cc_start: 0.7854 (t0) cc_final: 0.7561 (m-40) REVERT: L 268 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7593 (mt-10) REVERT: L 296 LYS cc_start: 0.7889 (ttmm) cc_final: 0.7388 (tmtt) REVERT: L 361 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7452 (t70) REVERT: L 468 ASN cc_start: 0.8562 (t0) cc_final: 0.8264 (t0) REVERT: L 504 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8061 (tm-30) outliers start: 179 outliers final: 99 residues processed: 803 average time/residue: 0.2605 time to fit residues: 345.2507 Evaluate side-chains 742 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 627 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 513 ARG Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain E residue 472 MET Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 513 ARG Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 221 MET Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 312 VAL Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 472 MET Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 361 ASP Chi-restraints excluded: chain I residue 401 LEU Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 469 MET Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain J residue 513 ARG Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 221 MET Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 401 LEU Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain K residue 472 MET Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 282 ARG Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 361 ASP Chi-restraints excluded: chain L residue 401 LEU Chi-restraints excluded: chain L residue 415 GLU Chi-restraints excluded: chain L residue 469 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 95 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 1 optimal weight: 0.0980 chunk 4 optimal weight: 8.9990 chunk 351 optimal weight: 2.9990 chunk 346 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 319 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 453 optimal weight: 7.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 255 HIS A 382 GLN B 255 HIS B 382 GLN D 255 HIS D 382 GLN E 255 HIS E 382 GLN G 255 HIS G 382 GLN H 255 HIS H 382 GLN J 255 HIS J 382 GLN K 255 HIS K 382 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.172341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.135499 restraints weight = 54523.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.134362 restraints weight = 52486.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136043 restraints weight = 51635.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.136021 restraints weight = 39444.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.136710 restraints weight = 37670.503| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 42072 Z= 0.237 Angle : 0.736 8.404 56760 Z= 0.388 Chirality : 0.047 0.183 6228 Planarity : 0.004 0.061 7404 Dihedral : 6.516 59.114 5688 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.58 % Favored : 93.95 % Rotamer: Outliers : 4.37 % Allowed : 18.89 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -2.29 (0.11), residues: 5088 helix: -1.12 (0.10), residues: 2280 sheet: -1.16 (0.26), residues: 384 loop : -1.93 (0.11), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 278 TYR 0.017 0.002 TYR I 208 PHE 0.014 0.002 PHE B 157 TRP 0.008 0.001 TRP B 437 HIS 0.003 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00567 (42048) covalent geometry : angle 0.73556 (56760) hydrogen bonds : bond 0.03268 ( 1414) hydrogen bonds : angle 5.28409 ( 4026) Misc. bond : bond 0.00319 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 657 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8505 (mm) cc_final: 0.8212 (pt) REVERT: A 83 MET cc_start: 0.8137 (tpp) cc_final: 0.7782 (tpp) REVERT: A 268 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7672 (mt-10) REVERT: A 296 LYS cc_start: 0.8103 (ttmm) cc_final: 0.7679 (tmtt) REVERT: A 401 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8623 (tt) REVERT: A 416 GLU cc_start: 0.8474 (tt0) cc_final: 0.8253 (tt0) REVERT: A 426 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8069 (tt) REVERT: A 434 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6633 (tm-30) REVERT: A 438 ASN cc_start: 0.7687 (m-40) cc_final: 0.6586 (m-40) REVERT: A 457 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8907 (tp) REVERT: A 468 ASN cc_start: 0.8587 (t0) cc_final: 0.8276 (t0) REVERT: B 87 GLU cc_start: 0.7634 (pt0) cc_final: 0.6719 (pt0) REVERT: B 124 ASN cc_start: 0.7268 (p0) cc_final: 0.6973 (m110) REVERT: B 268 GLU cc_start: 0.8634 (mm-30) cc_final: 0.7727 (mt-10) REVERT: B 296 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7394 (tmtt) REVERT: B 401 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8654 (tt) REVERT: C 72 ILE cc_start: 0.8533 (mm) cc_final: 0.8199 (pt) REVERT: C 84 ASN cc_start: 0.8083 (t0) cc_final: 0.7751 (m-40) REVERT: C 268 GLU cc_start: 0.8628 (mm-30) cc_final: 0.7680 (mt-10) REVERT: C 296 LYS cc_start: 0.8027 (ttmm) cc_final: 0.7439 (tmtt) REVERT: C 361 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7637 (t0) REVERT: C 426 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7970 (tt) REVERT: C 468 ASN cc_start: 0.8684 (t0) cc_final: 0.8287 (t0) REVERT: D 72 ILE cc_start: 0.8576 (mm) cc_final: 0.8250 (pt) REVERT: D 83 MET cc_start: 0.8141 (tpp) cc_final: 0.7773 (tpp) REVERT: D 268 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7677 (mt-10) REVERT: D 296 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7680 (tmtt) REVERT: D 401 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8624 (tt) REVERT: D 416 GLU cc_start: 0.8465 (tt0) cc_final: 0.8245 (tt0) REVERT: D 426 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8014 (tt) REVERT: D 434 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6646 (tm-30) REVERT: D 438 ASN cc_start: 0.7692 (m-40) cc_final: 0.6588 (m-40) REVERT: D 457 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8901 (tp) REVERT: D 468 ASN cc_start: 0.8598 (t0) cc_final: 0.8288 (t0) REVERT: E 124 ASN cc_start: 0.7260 (p0) cc_final: 0.6969 (m110) REVERT: E 268 GLU cc_start: 0.8629 (mm-30) cc_final: 0.7766 (mt-10) REVERT: E 296 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7388 (tmtt) REVERT: E 401 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8648 (tt) REVERT: F 72 ILE cc_start: 0.8532 (mm) cc_final: 0.8200 (pt) REVERT: F 84 ASN cc_start: 0.8093 (t0) cc_final: 0.7764 (m-40) REVERT: F 268 GLU cc_start: 0.8627 (mm-30) cc_final: 0.7670 (mt-10) REVERT: F 296 LYS cc_start: 0.8027 (ttmm) cc_final: 0.7448 (tmtt) REVERT: F 361 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7658 (t0) REVERT: F 426 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7960 (tt) REVERT: F 468 ASN cc_start: 0.8678 (t0) cc_final: 0.8287 (t0) REVERT: G 72 ILE cc_start: 0.8573 (mm) cc_final: 0.8247 (pt) REVERT: G 83 MET cc_start: 0.8137 (tpp) cc_final: 0.7764 (tpp) REVERT: G 268 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7715 (mt-10) REVERT: G 296 LYS cc_start: 0.8107 (ttmm) cc_final: 0.7671 (tmtt) REVERT: G 401 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8632 (tt) REVERT: G 416 GLU cc_start: 0.8459 (tt0) cc_final: 0.8237 (tt0) REVERT: G 426 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8025 (tt) REVERT: G 434 GLU cc_start: 0.7358 (tm-30) cc_final: 0.6642 (tm-30) REVERT: G 438 ASN cc_start: 0.7678 (m-40) cc_final: 0.6573 (m-40) REVERT: G 457 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8897 (tp) REVERT: G 468 ASN cc_start: 0.8607 (t0) cc_final: 0.8291 (t0) REVERT: H 124 ASN cc_start: 0.7267 (p0) cc_final: 0.6967 (m110) REVERT: H 268 GLU cc_start: 0.8604 (mm-30) cc_final: 0.7758 (mt-10) REVERT: H 296 LYS cc_start: 0.8150 (ttmm) cc_final: 0.7390 (tmtt) REVERT: H 401 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8654 (tt) REVERT: I 72 ILE cc_start: 0.8524 (mm) cc_final: 0.8187 (pt) REVERT: I 84 ASN cc_start: 0.8101 (t0) cc_final: 0.7776 (m-40) REVERT: I 268 GLU cc_start: 0.8632 (mm-30) cc_final: 0.7680 (mt-10) REVERT: I 296 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7442 (tmtt) REVERT: I 361 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7656 (t0) REVERT: I 426 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7975 (tt) REVERT: I 468 ASN cc_start: 0.8673 (t0) cc_final: 0.8282 (t0) REVERT: J 72 ILE cc_start: 0.8573 (mm) cc_final: 0.8250 (pt) REVERT: J 83 MET cc_start: 0.8140 (tpp) cc_final: 0.7780 (tpp) REVERT: J 136 HIS cc_start: 0.8032 (m-70) cc_final: 0.7832 (m-70) REVERT: J 268 GLU cc_start: 0.8564 (mm-30) cc_final: 0.7677 (mt-10) REVERT: J 296 LYS cc_start: 0.8110 (ttmm) cc_final: 0.7674 (tmtt) REVERT: J 401 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8630 (tt) REVERT: J 416 GLU cc_start: 0.8468 (tt0) cc_final: 0.8251 (tt0) REVERT: J 426 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8023 (tt) REVERT: J 434 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6637 (tm-30) REVERT: J 438 ASN cc_start: 0.7694 (m-40) cc_final: 0.6594 (m-40) REVERT: J 457 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8901 (tp) REVERT: J 468 ASN cc_start: 0.8594 (t0) cc_final: 0.8286 (t0) REVERT: K 87 GLU cc_start: 0.7634 (pt0) cc_final: 0.6719 (pt0) REVERT: K 124 ASN cc_start: 0.7274 (p0) cc_final: 0.6975 (m110) REVERT: K 268 GLU cc_start: 0.8632 (mm-30) cc_final: 0.7732 (mt-10) REVERT: K 296 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7390 (tmtt) REVERT: K 401 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8650 (tt) REVERT: L 72 ILE cc_start: 0.8526 (mm) cc_final: 0.8196 (pt) REVERT: L 84 ASN cc_start: 0.8084 (t0) cc_final: 0.7756 (m-40) REVERT: L 268 GLU cc_start: 0.8611 (mm-30) cc_final: 0.7678 (mt-10) REVERT: L 296 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7435 (tmtt) REVERT: L 361 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7634 (t0) REVERT: L 426 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7974 (tt) REVERT: L 468 ASN cc_start: 0.8644 (t0) cc_final: 0.8278 (t0) outliers start: 191 outliers final: 104 residues processed: 805 average time/residue: 0.2551 time to fit residues: 341.0691 Evaluate side-chains 757 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 629 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain E residue 472 MET Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 415 GLU Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 457 LEU Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 312 VAL Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 472 MET Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 361 ASP Chi-restraints excluded: chain I residue 401 LEU Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 415 GLU Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 457 LEU Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 144 SER Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 401 LEU Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain K residue 472 MET Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 361 ASP Chi-restraints excluded: chain L residue 401 LEU Chi-restraints excluded: chain L residue 415 GLU Chi-restraints excluded: chain L residue 426 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 122 optimal weight: 0.0870 chunk 184 optimal weight: 2.9990 chunk 369 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 349 optimal weight: 8.9990 chunk 382 optimal weight: 0.9980 chunk 424 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 302 GLN G 302 GLN J 302 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.175135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.136313 restraints weight = 53525.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133562 restraints weight = 57267.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135467 restraints weight = 55361.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136349 restraints weight = 39076.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.136482 restraints weight = 35266.179| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 42072 Z= 0.131 Angle : 0.643 10.708 56760 Z= 0.341 Chirality : 0.043 0.189 6228 Planarity : 0.004 0.029 7404 Dihedral : 5.893 57.770 5668 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.15 % Favored : 94.38 % Rotamer: Outliers : 3.59 % Allowed : 20.22 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -1.84 (0.11), residues: 5088 helix: -0.56 (0.11), residues: 2280 sheet: -1.09 (0.25), residues: 384 loop : -1.88 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 278 TYR 0.010 0.001 TYR F 208 PHE 0.010 0.001 PHE K 157 TRP 0.008 0.001 TRP J 285 HIS 0.004 0.001 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00289 (42048) covalent geometry : angle 0.64309 (56760) hydrogen bonds : bond 0.02632 ( 1414) hydrogen bonds : angle 4.90598 ( 4026) Misc. bond : bond 0.00247 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 662 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8500 (mm) cc_final: 0.8168 (pt) REVERT: A 83 MET cc_start: 0.8138 (tpp) cc_final: 0.7886 (tpp) REVERT: A 268 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7499 (mt-10) REVERT: A 296 LYS cc_start: 0.8038 (ttmm) cc_final: 0.7544 (tmtt) REVERT: A 401 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8547 (tt) REVERT: A 416 GLU cc_start: 0.8501 (tt0) cc_final: 0.8160 (tt0) REVERT: A 438 ASN cc_start: 0.7769 (m-40) cc_final: 0.7466 (m-40) REVERT: A 457 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8865 (tp) REVERT: A 468 ASN cc_start: 0.8441 (t0) cc_final: 0.8196 (t0) REVERT: B 87 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6463 (pt0) REVERT: B 124 ASN cc_start: 0.7406 (p0) cc_final: 0.7106 (m-40) REVERT: B 236 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8655 (p) REVERT: B 268 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7634 (mt-10) REVERT: B 296 LYS cc_start: 0.8127 (ttmm) cc_final: 0.7360 (tmtt) REVERT: B 330 MET cc_start: 0.8160 (ttp) cc_final: 0.7884 (ttm) REVERT: B 401 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8572 (tt) REVERT: C 72 ILE cc_start: 0.8505 (mm) cc_final: 0.8142 (pt) REVERT: C 84 ASN cc_start: 0.8006 (t0) cc_final: 0.7781 (m-40) REVERT: C 268 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7420 (mt-10) REVERT: C 296 LYS cc_start: 0.8008 (ttmm) cc_final: 0.7554 (tmtt) REVERT: C 361 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7474 (t0) REVERT: C 426 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7701 (tt) REVERT: C 468 ASN cc_start: 0.8583 (t0) cc_final: 0.8265 (t0) REVERT: D 72 ILE cc_start: 0.8575 (mm) cc_final: 0.8209 (pt) REVERT: D 83 MET cc_start: 0.8144 (tpp) cc_final: 0.7873 (tpp) REVERT: D 268 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7516 (mt-10) REVERT: D 296 LYS cc_start: 0.8037 (ttmm) cc_final: 0.7551 (tmtt) REVERT: D 401 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8544 (tt) REVERT: D 416 GLU cc_start: 0.8503 (tt0) cc_final: 0.8160 (tt0) REVERT: D 438 ASN cc_start: 0.7775 (m-40) cc_final: 0.7472 (m-40) REVERT: D 457 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8864 (tp) REVERT: D 468 ASN cc_start: 0.8453 (t0) cc_final: 0.8207 (t0) REVERT: E 124 ASN cc_start: 0.7408 (p0) cc_final: 0.7109 (m-40) REVERT: E 135 ASN cc_start: 0.8827 (t0) cc_final: 0.8500 (t0) REVERT: E 236 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8655 (p) REVERT: E 268 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7619 (mt-10) REVERT: E 296 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7359 (tmtt) REVERT: E 330 MET cc_start: 0.8162 (ttp) cc_final: 0.7887 (ttm) REVERT: E 401 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8570 (tt) REVERT: F 72 ILE cc_start: 0.8497 (mm) cc_final: 0.8129 (pt) REVERT: F 84 ASN cc_start: 0.8019 (t0) cc_final: 0.7790 (m-40) REVERT: F 268 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7515 (mt-10) REVERT: F 296 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7557 (tmtt) REVERT: F 361 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7491 (t0) REVERT: F 426 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7722 (tt) REVERT: F 468 ASN cc_start: 0.8588 (t0) cc_final: 0.8273 (t0) REVERT: G 72 ILE cc_start: 0.8568 (mm) cc_final: 0.8198 (pt) REVERT: G 83 MET cc_start: 0.8144 (tpp) cc_final: 0.7872 (tpp) REVERT: G 268 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7518 (mt-10) REVERT: G 296 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7562 (tmtt) REVERT: G 401 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8549 (tt) REVERT: G 416 GLU cc_start: 0.8492 (tt0) cc_final: 0.8155 (tt0) REVERT: G 438 ASN cc_start: 0.7773 (m-40) cc_final: 0.7464 (m-40) REVERT: G 457 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8861 (tp) REVERT: G 468 ASN cc_start: 0.8453 (t0) cc_final: 0.8207 (t0) REVERT: H 124 ASN cc_start: 0.7426 (p0) cc_final: 0.7117 (m-40) REVERT: H 135 ASN cc_start: 0.8838 (t0) cc_final: 0.8505 (t0) REVERT: H 236 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8652 (p) REVERT: H 268 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7613 (mt-10) REVERT: H 296 LYS cc_start: 0.8123 (ttmm) cc_final: 0.7360 (tmtt) REVERT: H 330 MET cc_start: 0.8165 (ttp) cc_final: 0.7893 (ttm) REVERT: H 401 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8570 (tt) REVERT: I 72 ILE cc_start: 0.8503 (mm) cc_final: 0.8135 (pt) REVERT: I 84 ASN cc_start: 0.8017 (t0) cc_final: 0.7791 (m-40) REVERT: I 268 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7516 (mt-10) REVERT: I 296 LYS cc_start: 0.8008 (ttmm) cc_final: 0.7566 (tmtt) REVERT: I 361 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7494 (t0) REVERT: I 426 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7571 (tt) REVERT: I 468 ASN cc_start: 0.8583 (t0) cc_final: 0.8269 (t0) REVERT: J 72 ILE cc_start: 0.8571 (mm) cc_final: 0.8210 (pt) REVERT: J 83 MET cc_start: 0.8135 (tpp) cc_final: 0.7879 (tpp) REVERT: J 268 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7510 (mt-10) REVERT: J 296 LYS cc_start: 0.8038 (ttmm) cc_final: 0.7556 (tmtt) REVERT: J 401 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8550 (tt) REVERT: J 416 GLU cc_start: 0.8503 (tt0) cc_final: 0.8165 (tt0) REVERT: J 438 ASN cc_start: 0.7776 (m-40) cc_final: 0.7467 (m-40) REVERT: J 457 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8864 (tp) REVERT: J 468 ASN cc_start: 0.8448 (t0) cc_final: 0.8205 (t0) REVERT: K 87 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6449 (pt0) REVERT: K 124 ASN cc_start: 0.7422 (p0) cc_final: 0.7113 (m-40) REVERT: K 236 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8655 (p) REVERT: K 268 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7636 (mt-10) REVERT: K 296 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7350 (tmtt) REVERT: K 330 MET cc_start: 0.8175 (ttp) cc_final: 0.7893 (ttm) REVERT: K 401 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8573 (tt) REVERT: L 72 ILE cc_start: 0.8504 (mm) cc_final: 0.8142 (pt) REVERT: L 84 ASN cc_start: 0.8012 (t0) cc_final: 0.7788 (m-40) REVERT: L 268 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7516 (mt-10) REVERT: L 296 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7550 (tmtt) REVERT: L 361 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7420 (t0) REVERT: L 426 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7697 (tt) REVERT: L 468 ASN cc_start: 0.8569 (t0) cc_final: 0.8258 (t0) outliers start: 157 outliers final: 102 residues processed: 780 average time/residue: 0.2198 time to fit residues: 288.1393 Evaluate side-chains 760 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 632 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain E residue 472 MET Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 237 TYR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 415 GLU Chi-restraints excluded: chain G residue 457 LEU Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 221 MET Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 472 MET Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 237 TYR Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 361 ASP Chi-restraints excluded: chain I residue 401 LEU Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 415 GLU Chi-restraints excluded: chain J residue 457 LEU Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 221 MET Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 401 LEU Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain K residue 472 MET Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 237 TYR Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 361 ASP Chi-restraints excluded: chain L residue 401 LEU Chi-restraints excluded: chain L residue 415 GLU Chi-restraints excluded: chain L residue 426 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 166 optimal weight: 4.9990 chunk 366 optimal weight: 7.9990 chunk 321 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 194 optimal weight: 0.3980 chunk 488 optimal weight: 1.9990 chunk 446 optimal weight: 7.9990 chunk 190 optimal weight: 0.9980 chunk 273 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 295 optimal weight: 0.2980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.176966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.138171 restraints weight = 53377.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137005 restraints weight = 51023.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.138447 restraints weight = 49551.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.138842 restraints weight = 37674.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139219 restraints weight = 33487.851| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 42072 Z= 0.131 Angle : 0.647 8.482 56760 Z= 0.344 Chirality : 0.043 0.182 6228 Planarity : 0.004 0.030 7404 Dihedral : 5.664 54.418 5668 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.54 % Favored : 93.99 % Rotamer: Outliers : 3.59 % Allowed : 20.83 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % 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 aren not related in a simple way. whole: -1.57 (0.11), residues: 5088 helix: -0.21 (0.11), residues: 2280 sheet: -1.00 (0.25), residues: 384 loop : -1.86 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 278 TYR 0.009 0.001 TYR C 208 PHE 0.011 0.001 PHE D 365 TRP 0.008 0.001 TRP J 285 HIS 0.004 0.001 HIS J 136 Details of bonding type rmsd covalent geometry : bond 0.00287 (42048) covalent geometry : angle 0.64718 (56760) hydrogen bonds : bond 0.02561 ( 1414) hydrogen bonds : angle 4.76386 ( 4026) Misc. bond : bond 0.00231 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 638 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8495 (mm) cc_final: 0.8163 (pt) REVERT: A 83 MET cc_start: 0.8223 (tpp) cc_final: 0.7890 (tpp) REVERT: A 268 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7383 (mt-10) REVERT: A 296 LYS cc_start: 0.8059 (ttmm) cc_final: 0.7445 (tmtt) REVERT: A 416 GLU cc_start: 0.8486 (tt0) cc_final: 0.8150 (tt0) REVERT: A 438 ASN cc_start: 0.7780 (m-40) cc_final: 0.7488 (m-40) REVERT: A 457 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8778 (tp) REVERT: A 468 ASN cc_start: 0.8442 (t0) cc_final: 0.8232 (t0) REVERT: B 87 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6342 (pt0) REVERT: B 124 ASN cc_start: 0.7404 (p0) cc_final: 0.7168 (m-40) REVERT: B 236 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8680 (p) REVERT: B 268 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7573 (mt-10) REVERT: B 296 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7328 (tmtt) REVERT: B 330 MET cc_start: 0.8119 (ttp) cc_final: 0.7826 (ttm) REVERT: B 401 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8579 (tt) REVERT: B 408 ARG cc_start: 0.8073 (tpp-160) cc_final: 0.7764 (tpt90) REVERT: C 72 ILE cc_start: 0.8491 (mm) cc_final: 0.8120 (pt) REVERT: C 268 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7484 (mt-10) REVERT: C 296 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7588 (tmtt) REVERT: C 361 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7260 (t0) REVERT: C 426 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7532 (tt) REVERT: C 468 ASN cc_start: 0.8513 (t0) cc_final: 0.8219 (t0) REVERT: D 72 ILE cc_start: 0.8541 (mm) cc_final: 0.8185 (pt) REVERT: D 83 MET cc_start: 0.8220 (tpp) cc_final: 0.7887 (tpp) REVERT: D 268 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7384 (mt-10) REVERT: D 296 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7447 (tmtt) REVERT: D 416 GLU cc_start: 0.8492 (tt0) cc_final: 0.8151 (tt0) REVERT: D 438 ASN cc_start: 0.7780 (m-40) cc_final: 0.7492 (m-40) REVERT: D 457 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8784 (tp) REVERT: D 468 ASN cc_start: 0.8439 (t0) cc_final: 0.8235 (t0) REVERT: E 124 ASN cc_start: 0.7409 (p0) cc_final: 0.7173 (m-40) REVERT: E 135 ASN cc_start: 0.8849 (t0) cc_final: 0.8480 (t0) REVERT: E 236 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8685 (p) REVERT: E 268 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7564 (mt-10) REVERT: E 296 LYS cc_start: 0.8046 (ttmm) cc_final: 0.7325 (tmtt) REVERT: E 330 MET cc_start: 0.8184 (ttp) cc_final: 0.7904 (ttm) REVERT: E 401 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8572 (tt) REVERT: E 408 ARG cc_start: 0.8066 (tpp-160) cc_final: 0.7764 (tpt90) REVERT: F 72 ILE cc_start: 0.8474 (mm) cc_final: 0.8100 (pt) REVERT: F 268 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7486 (mt-10) REVERT: F 296 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7606 (tmtt) REVERT: F 361 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7239 (t0) REVERT: F 426 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7754 (tt) REVERT: F 468 ASN cc_start: 0.8516 (t0) cc_final: 0.8221 (t0) REVERT: G 72 ILE cc_start: 0.8562 (mm) cc_final: 0.8210 (pt) REVERT: G 83 MET cc_start: 0.8201 (tpp) cc_final: 0.7869 (tpp) REVERT: G 268 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7405 (mt-10) REVERT: G 296 LYS cc_start: 0.8050 (ttmm) cc_final: 0.7451 (tmtt) REVERT: G 416 GLU cc_start: 0.8481 (tt0) cc_final: 0.8147 (tt0) REVERT: G 438 ASN cc_start: 0.7775 (m-40) cc_final: 0.7487 (m-40) REVERT: G 457 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8776 (tp) REVERT: G 468 ASN cc_start: 0.8454 (t0) cc_final: 0.8244 (t0) REVERT: H 124 ASN cc_start: 0.7420 (p0) cc_final: 0.7174 (m-40) REVERT: H 135 ASN cc_start: 0.8858 (t0) cc_final: 0.8486 (t0) REVERT: H 236 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8681 (p) REVERT: H 268 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7565 (mt-10) REVERT: H 296 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7341 (tmtt) REVERT: H 330 MET cc_start: 0.8149 (ttp) cc_final: 0.7867 (ttm) REVERT: H 401 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8576 (tt) REVERT: H 408 ARG cc_start: 0.8059 (tpp-160) cc_final: 0.7758 (tpt90) REVERT: I 72 ILE cc_start: 0.8479 (mm) cc_final: 0.8106 (pt) REVERT: I 268 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7490 (mt-10) REVERT: I 296 LYS cc_start: 0.7977 (ttmm) cc_final: 0.7599 (tmtt) REVERT: I 361 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7256 (t0) REVERT: I 426 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7542 (tt) REVERT: I 468 ASN cc_start: 0.8519 (t0) cc_final: 0.8226 (t0) REVERT: J 72 ILE cc_start: 0.8570 (mm) cc_final: 0.8217 (pt) REVERT: J 83 MET cc_start: 0.8203 (tpp) cc_final: 0.7879 (tpp) REVERT: J 268 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7404 (mt-10) REVERT: J 296 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7453 (tmtt) REVERT: J 416 GLU cc_start: 0.8487 (tt0) cc_final: 0.8154 (tt0) REVERT: J 438 ASN cc_start: 0.7778 (m-40) cc_final: 0.7488 (m-40) REVERT: J 457 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8774 (tp) REVERT: J 468 ASN cc_start: 0.8447 (t0) cc_final: 0.8241 (t0) REVERT: K 87 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6338 (pt0) REVERT: K 124 ASN cc_start: 0.7425 (p0) cc_final: 0.7174 (m-40) REVERT: K 236 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8685 (p) REVERT: K 268 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7579 (mt-10) REVERT: K 296 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7337 (tmtt) REVERT: K 330 MET cc_start: 0.8149 (ttp) cc_final: 0.7859 (ttm) REVERT: K 401 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8579 (tt) REVERT: K 408 ARG cc_start: 0.8068 (tpp-160) cc_final: 0.7761 (tpt90) REVERT: L 72 ILE cc_start: 0.8484 (mm) cc_final: 0.8127 (pt) REVERT: L 268 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7473 (mt-10) REVERT: L 296 LYS cc_start: 0.7976 (ttmm) cc_final: 0.7593 (tmtt) REVERT: L 361 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7228 (t70) REVERT: L 426 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7530 (tt) REVERT: L 468 ASN cc_start: 0.8521 (t0) cc_final: 0.8229 (t0) outliers start: 157 outliers final: 94 residues processed: 761 average time/residue: 0.2283 time to fit residues: 288.2050 Evaluate side-chains 736 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 620 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 237 TYR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain E residue 472 MET Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 237 TYR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 237 TYR Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 415 GLU Chi-restraints excluded: chain G residue 457 LEU Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 472 MET Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 237 TYR Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 361 ASP Chi-restraints excluded: chain I residue 401 LEU Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 237 TYR Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 415 GLU Chi-restraints excluded: chain J residue 457 LEU Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 359 MET Chi-restraints excluded: chain K residue 401 LEU Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain K residue 472 MET Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 237 TYR Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 361 ASP Chi-restraints excluded: chain L residue 401 LEU Chi-restraints excluded: chain L residue 415 GLU Chi-restraints excluded: chain L residue 426 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 124 optimal weight: 0.0020 chunk 444 optimal weight: 3.9990 chunk 112 optimal weight: 0.0060 chunk 37 optimal weight: 1.9990 chunk 336 optimal weight: 7.9990 chunk 169 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 301 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.9208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN B 302 GLN E 302 GLN H 302 GLN K 85 ASN K 302 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.178057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139881 restraints weight = 53330.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.137973 restraints weight = 53623.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.139890 restraints weight = 52444.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140022 restraints weight = 39235.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.140341 restraints weight = 35670.559| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 42072 Z= 0.128 Angle : 0.637 9.804 56760 Z= 0.339 Chirality : 0.042 0.181 6228 Planarity : 0.004 0.031 7404 Dihedral : 5.432 48.431 5659 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.17 % Favored : 94.28 % Rotamer: Outliers : 3.11 % Allowed : 21.63 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % 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 aren not related in a simple way. whole: -1.38 (0.11), residues: 5088 helix: -0.01 (0.11), residues: 2280 sheet: -0.87 (0.25), residues: 384 loop : -1.81 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 278 TYR 0.008 0.001 TYR L 208 PHE 0.011 0.001 PHE A 365 TRP 0.007 0.001 TRP D 285 HIS 0.003 0.001 HIS J 136 Details of bonding type rmsd covalent geometry : bond 0.00281 (42048) covalent geometry : angle 0.63674 (56760) hydrogen bonds : bond 0.02450 ( 1414) hydrogen bonds : angle 4.64326 ( 4026) Misc. bond : bond 0.00225 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 646 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8483 (mm) cc_final: 0.8145 (pt) REVERT: A 83 MET cc_start: 0.8264 (tpp) cc_final: 0.7940 (tpp) REVERT: A 268 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7399 (mt-10) REVERT: A 296 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7378 (tmtt) REVERT: A 416 GLU cc_start: 0.8471 (tt0) cc_final: 0.8148 (tt0) REVERT: A 438 ASN cc_start: 0.7771 (m-40) cc_final: 0.7464 (m-40) REVERT: B 87 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6248 (pt0) REVERT: B 124 ASN cc_start: 0.7376 (p0) cc_final: 0.7120 (m-40) REVERT: B 135 ASN cc_start: 0.8795 (t0) cc_final: 0.8417 (t0) REVERT: B 236 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8721 (p) REVERT: B 268 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7698 (mt-10) REVERT: B 296 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7322 (tmtt) REVERT: B 408 ARG cc_start: 0.8054 (tpp-160) cc_final: 0.7741 (tpt90) REVERT: C 72 ILE cc_start: 0.8477 (mm) cc_final: 0.8126 (pt) REVERT: C 268 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7542 (mt-10) REVERT: C 296 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7624 (tmtt) REVERT: C 468 ASN cc_start: 0.8516 (t0) cc_final: 0.8194 (t0) REVERT: D 72 ILE cc_start: 0.8563 (mm) cc_final: 0.8187 (pt) REVERT: D 83 MET cc_start: 0.8284 (tpp) cc_final: 0.7934 (tpp) REVERT: D 268 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7410 (mt-10) REVERT: D 296 LYS cc_start: 0.8011 (ttmm) cc_final: 0.7385 (tmtt) REVERT: D 416 GLU cc_start: 0.8494 (tt0) cc_final: 0.8171 (tt0) REVERT: D 426 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7698 (tt) REVERT: D 438 ASN cc_start: 0.7766 (m-40) cc_final: 0.7466 (m-40) REVERT: E 124 ASN cc_start: 0.7364 (p0) cc_final: 0.7112 (m-40) REVERT: E 135 ASN cc_start: 0.8795 (t0) cc_final: 0.8415 (t0) REVERT: E 236 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8726 (p) REVERT: E 268 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7656 (mt-10) REVERT: E 296 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7328 (tmtt) REVERT: E 408 ARG cc_start: 0.8049 (tpp-160) cc_final: 0.7742 (tpt90) REVERT: F 72 ILE cc_start: 0.8453 (mm) cc_final: 0.8089 (pt) REVERT: F 268 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7553 (mt-10) REVERT: F 296 LYS cc_start: 0.8047 (ttmm) cc_final: 0.7634 (tmtt) REVERT: F 468 ASN cc_start: 0.8520 (t0) cc_final: 0.8200 (t0) REVERT: G 72 ILE cc_start: 0.8586 (mm) cc_final: 0.8216 (pt) REVERT: G 83 MET cc_start: 0.8264 (tpp) cc_final: 0.7917 (tpp) REVERT: G 268 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7425 (mt-10) REVERT: G 296 LYS cc_start: 0.8009 (ttmm) cc_final: 0.7396 (tmtt) REVERT: G 416 GLU cc_start: 0.8490 (tt0) cc_final: 0.8169 (tt0) REVERT: G 426 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7688 (tt) REVERT: G 438 ASN cc_start: 0.7765 (m-40) cc_final: 0.7467 (m-40) REVERT: H 124 ASN cc_start: 0.7401 (p0) cc_final: 0.7134 (m-40) REVERT: H 135 ASN cc_start: 0.8793 (t0) cc_final: 0.8413 (t0) REVERT: H 236 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8725 (p) REVERT: H 268 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7649 (mt-10) REVERT: H 296 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7346 (tmtt) REVERT: H 408 ARG cc_start: 0.8040 (tpp-160) cc_final: 0.7737 (tpt90) REVERT: I 72 ILE cc_start: 0.8456 (mm) cc_final: 0.8097 (pt) REVERT: I 268 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7555 (mt-10) REVERT: I 296 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7631 (tmtt) REVERT: I 468 ASN cc_start: 0.8526 (t0) cc_final: 0.8203 (t0) REVERT: J 72 ILE cc_start: 0.8592 (mm) cc_final: 0.8217 (pt) REVERT: J 83 MET cc_start: 0.8272 (tpp) cc_final: 0.7936 (tpp) REVERT: J 268 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7422 (mt-10) REVERT: J 296 LYS cc_start: 0.8013 (ttmm) cc_final: 0.7389 (tmtt) REVERT: J 416 GLU cc_start: 0.8476 (tt0) cc_final: 0.8150 (tt0) REVERT: J 426 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7692 (tt) REVERT: J 438 ASN cc_start: 0.7777 (m-40) cc_final: 0.7473 (m-40) REVERT: K 87 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6242 (pt0) REVERT: K 124 ASN cc_start: 0.7391 (p0) cc_final: 0.7129 (m-40) REVERT: K 135 ASN cc_start: 0.8794 (t0) cc_final: 0.8416 (t0) REVERT: K 236 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8727 (p) REVERT: K 268 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7684 (mt-10) REVERT: K 296 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7339 (tmtt) REVERT: K 408 ARG cc_start: 0.8063 (tpp-160) cc_final: 0.7750 (tpt90) REVERT: L 72 ILE cc_start: 0.8471 (mm) cc_final: 0.8125 (pt) REVERT: L 268 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7531 (mt-10) REVERT: L 296 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7623 (tmtt) REVERT: L 337 GLN cc_start: 0.7770 (pt0) cc_final: 0.7540 (pt0) REVERT: L 468 ASN cc_start: 0.8525 (t0) cc_final: 0.8207 (t0) outliers start: 136 outliers final: 81 residues processed: 751 average time/residue: 0.2578 time to fit residues: 316.9789 Evaluate side-chains 708 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 618 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 237 TYR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 237 TYR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 237 TYR Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 415 GLU Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 237 TYR Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 330 MET Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 237 TYR Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 415 GLU Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 359 MET Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 237 TYR Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 415 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 66 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 354 optimal weight: 0.8980 chunk 350 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 367 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 445 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.176573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139572 restraints weight = 53999.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.136622 restraints weight = 60346.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138543 restraints weight = 57494.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.139492 restraints weight = 37878.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139937 restraints weight = 35406.153| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 42072 Z= 0.165 Angle : 0.672 9.760 56760 Z= 0.357 Chirality : 0.044 0.179 6228 Planarity : 0.004 0.040 7404 Dihedral : 5.363 46.265 5651 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.60 % Favored : 93.77 % Rotamer: Outliers : 3.00 % Allowed : 22.05 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % 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 aren not related in a simple way. whole: -1.38 (0.11), residues: 5088 helix: -0.03 (0.11), residues: 2280 sheet: -0.83 (0.25), residues: 384 loop : -1.80 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 278 TYR 0.008 0.001 TYR K 86 PHE 0.011 0.001 PHE A 157 TRP 0.006 0.001 TRP B 437 HIS 0.004 0.001 HIS J 136 Details of bonding type rmsd covalent geometry : bond 0.00383 (42048) covalent geometry : angle 0.67237 (56760) hydrogen bonds : bond 0.02670 ( 1414) hydrogen bonds : angle 4.76575 ( 4026) Misc. bond : bond 0.00228 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 625 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8560 (mm) cc_final: 0.8229 (pt) REVERT: A 83 MET cc_start: 0.8332 (tpp) cc_final: 0.7979 (tpp) REVERT: A 268 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7499 (mt-10) REVERT: A 296 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7398 (tmtt) REVERT: A 416 GLU cc_start: 0.8460 (tt0) cc_final: 0.8103 (tt0) REVERT: A 426 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7803 (tt) REVERT: A 438 ASN cc_start: 0.7788 (m-40) cc_final: 0.7454 (m-40) REVERT: B 124 ASN cc_start: 0.7455 (p0) cc_final: 0.7170 (m-40) REVERT: B 268 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7723 (mt-10) REVERT: B 296 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7347 (tmtt) REVERT: B 330 MET cc_start: 0.8140 (ttp) cc_final: 0.7829 (ttm) REVERT: B 346 GLU cc_start: 0.8112 (pm20) cc_final: 0.7797 (pm20) REVERT: B 408 ARG cc_start: 0.8108 (tpp-160) cc_final: 0.7825 (tpt90) REVERT: C 72 ILE cc_start: 0.8466 (mm) cc_final: 0.8104 (pt) REVERT: C 83 MET cc_start: 0.8197 (tpp) cc_final: 0.7839 (tpp) REVERT: C 268 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7654 (mt-10) REVERT: C 296 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7597 (tmtt) REVERT: C 426 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7890 (tt) REVERT: C 468 ASN cc_start: 0.8533 (t0) cc_final: 0.8183 (t0) REVERT: D 72 ILE cc_start: 0.8515 (mm) cc_final: 0.8213 (pt) REVERT: D 77 ASP cc_start: 0.8101 (t0) cc_final: 0.7842 (t0) REVERT: D 83 MET cc_start: 0.8305 (tpp) cc_final: 0.7977 (tpp) REVERT: D 268 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7506 (mt-10) REVERT: D 296 LYS cc_start: 0.8011 (ttmm) cc_final: 0.7394 (tmtt) REVERT: D 416 GLU cc_start: 0.8464 (tt0) cc_final: 0.8117 (tt0) REVERT: D 434 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6615 (tm-30) REVERT: D 438 ASN cc_start: 0.7690 (m-40) cc_final: 0.6306 (m-40) REVERT: E 124 ASN cc_start: 0.7456 (p0) cc_final: 0.7168 (m-40) REVERT: E 268 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7584 (mt-10) REVERT: E 296 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7353 (tmtt) REVERT: E 330 MET cc_start: 0.8177 (ttp) cc_final: 0.7875 (ttm) REVERT: E 408 ARG cc_start: 0.8111 (tpp-160) cc_final: 0.7834 (tpt90) REVERT: F 72 ILE cc_start: 0.8460 (mm) cc_final: 0.8100 (pt) REVERT: F 83 MET cc_start: 0.8195 (tpp) cc_final: 0.7834 (tpp) REVERT: F 268 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7668 (mt-10) REVERT: F 296 LYS cc_start: 0.8033 (ttmm) cc_final: 0.7589 (tmtt) REVERT: F 426 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7902 (tt) REVERT: F 468 ASN cc_start: 0.8535 (t0) cc_final: 0.8194 (t0) REVERT: G 72 ILE cc_start: 0.8505 (mm) cc_final: 0.8205 (pt) REVERT: G 77 ASP cc_start: 0.8112 (t0) cc_final: 0.7865 (t0) REVERT: G 83 MET cc_start: 0.8306 (tpp) cc_final: 0.7977 (tpp) REVERT: G 268 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7507 (mt-10) REVERT: G 296 LYS cc_start: 0.8002 (ttmm) cc_final: 0.7401 (tmtt) REVERT: G 416 GLU cc_start: 0.8469 (tt0) cc_final: 0.8112 (tt0) REVERT: G 434 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6612 (tm-30) REVERT: G 438 ASN cc_start: 0.7692 (m-40) cc_final: 0.6310 (m-40) REVERT: H 124 ASN cc_start: 0.7469 (p0) cc_final: 0.7172 (m-40) REVERT: H 268 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7576 (mt-10) REVERT: H 296 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7361 (tmtt) REVERT: H 408 ARG cc_start: 0.8107 (tpp-160) cc_final: 0.7831 (tpt90) REVERT: I 72 ILE cc_start: 0.8459 (mm) cc_final: 0.8100 (pt) REVERT: I 83 MET cc_start: 0.8199 (tpp) cc_final: 0.7843 (tpp) REVERT: I 268 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7666 (mt-10) REVERT: I 296 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7586 (tmtt) REVERT: I 426 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7900 (tt) REVERT: I 468 ASN cc_start: 0.8535 (t0) cc_final: 0.8183 (t0) REVERT: J 72 ILE cc_start: 0.8505 (mm) cc_final: 0.8204 (pt) REVERT: J 77 ASP cc_start: 0.8112 (t0) cc_final: 0.7859 (t0) REVERT: J 83 MET cc_start: 0.8306 (tpp) cc_final: 0.7974 (tpp) REVERT: J 268 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7512 (mt-10) REVERT: J 296 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7401 (tmtt) REVERT: J 416 GLU cc_start: 0.8469 (tt0) cc_final: 0.8117 (tt0) REVERT: J 434 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6610 (tm-30) REVERT: J 438 ASN cc_start: 0.7689 (m-40) cc_final: 0.6299 (m-40) REVERT: K 124 ASN cc_start: 0.7478 (p0) cc_final: 0.7185 (m-40) REVERT: K 135 ASN cc_start: 0.8892 (t0) cc_final: 0.8481 (t0) REVERT: K 268 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7703 (mt-10) REVERT: K 296 LYS cc_start: 0.7990 (ttmm) cc_final: 0.7359 (tmtt) REVERT: K 408 ARG cc_start: 0.8105 (tpp-160) cc_final: 0.7825 (tpt90) REVERT: L 72 ILE cc_start: 0.8464 (mm) cc_final: 0.8103 (pt) REVERT: L 83 MET cc_start: 0.8198 (tpp) cc_final: 0.7841 (tpp) REVERT: L 268 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7650 (mt-10) REVERT: L 296 LYS cc_start: 0.8042 (ttmm) cc_final: 0.7588 (tmtt) REVERT: L 426 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7889 (tt) REVERT: L 468 ASN cc_start: 0.8540 (t0) cc_final: 0.8190 (t0) outliers start: 131 outliers final: 101 residues processed: 717 average time/residue: 0.2599 time to fit residues: 303.9434 Evaluate side-chains 710 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 604 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 472 MET Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 237 TYR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 TYR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 237 TYR Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 415 GLU Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 472 MET Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 330 MET Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 472 MET Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 237 TYR Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 415 GLU Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 237 TYR Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain K residue 472 MET Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 415 GLU Chi-restraints excluded: chain L residue 426 LEU Chi-restraints excluded: chain L residue 472 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 345 optimal weight: 0.0040 chunk 268 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 477 optimal weight: 9.9990 chunk 305 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 chunk 460 optimal weight: 0.0570 chunk 5 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 497 optimal weight: 3.9990 overall best weight: 0.5914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.179538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140765 restraints weight = 53507.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.139433 restraints weight = 52456.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.140779 restraints weight = 49015.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.141296 restraints weight = 37938.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141571 restraints weight = 34383.884| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 42072 Z= 0.124 Angle : 0.647 9.936 56760 Z= 0.345 Chirality : 0.043 0.183 6228 Planarity : 0.004 0.047 7404 Dihedral : 5.182 46.984 5651 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.71 % Allowed : 4.58 % Favored : 94.71 % Rotamer: Outliers : 2.01 % Allowed : 23.26 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % 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 aren not related in a simple way. whole: -1.19 (0.12), residues: 5088 helix: 0.12 (0.11), residues: 2304 sheet: -0.63 (0.26), residues: 384 loop : -1.74 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 339 TYR 0.009 0.001 TYR F 208 PHE 0.011 0.001 PHE A 365 TRP 0.009 0.001 TRP E 285 HIS 0.004 0.001 HIS J 136 Details of bonding type rmsd covalent geometry : bond 0.00265 (42048) covalent geometry : angle 0.64705 (56760) hydrogen bonds : bond 0.02392 ( 1414) hydrogen bonds : angle 4.53160 ( 4026) Misc. bond : bond 0.00219 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 647 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8504 (mm) cc_final: 0.8169 (pt) REVERT: A 77 ASP cc_start: 0.8056 (t0) cc_final: 0.7833 (t0) REVERT: A 83 MET cc_start: 0.8227 (tpp) cc_final: 0.7908 (tpp) REVERT: A 296 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7285 (tmtt) REVERT: A 416 GLU cc_start: 0.8475 (tt0) cc_final: 0.8163 (tt0) REVERT: A 438 ASN cc_start: 0.7770 (m-40) cc_final: 0.7400 (m-40) REVERT: B 124 ASN cc_start: 0.7444 (p0) cc_final: 0.7149 (m-40) REVERT: B 268 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7684 (mt-10) REVERT: B 296 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7283 (tmtt) REVERT: B 346 GLU cc_start: 0.8060 (pm20) cc_final: 0.7702 (pm20) REVERT: B 408 ARG cc_start: 0.8014 (tpp-160) cc_final: 0.7709 (tpt90) REVERT: C 72 ILE cc_start: 0.8461 (mm) cc_final: 0.8104 (pt) REVERT: C 87 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6352 (pt0) REVERT: C 268 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7569 (mt-10) REVERT: C 296 LYS cc_start: 0.8021 (ttmm) cc_final: 0.7632 (tmtt) REVERT: C 333 ASP cc_start: 0.8117 (t0) cc_final: 0.7861 (t70) REVERT: C 468 ASN cc_start: 0.8479 (t0) cc_final: 0.8131 (t0) REVERT: D 72 ILE cc_start: 0.8516 (mm) cc_final: 0.8193 (pt) REVERT: D 83 MET cc_start: 0.8222 (tpp) cc_final: 0.7892 (tpp) REVERT: D 268 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7384 (mt-10) REVERT: D 296 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7291 (tmtt) REVERT: D 416 GLU cc_start: 0.8496 (tt0) cc_final: 0.8186 (tt0) REVERT: D 438 ASN cc_start: 0.7778 (m-40) cc_final: 0.7399 (m-40) REVERT: E 124 ASN cc_start: 0.7410 (p0) cc_final: 0.7119 (m-40) REVERT: E 268 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7649 (mt-10) REVERT: E 296 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7293 (tmtt) REVERT: E 408 ARG cc_start: 0.8006 (tpp-160) cc_final: 0.7714 (tpt90) REVERT: F 72 ILE cc_start: 0.8441 (mm) cc_final: 0.8066 (pt) REVERT: F 87 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6327 (pt0) REVERT: F 268 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7588 (mt-10) REVERT: F 296 LYS cc_start: 0.8010 (ttmm) cc_final: 0.7628 (tmtt) REVERT: F 333 ASP cc_start: 0.8102 (t0) cc_final: 0.7836 (t70) REVERT: F 468 ASN cc_start: 0.8488 (t0) cc_final: 0.8145 (t0) REVERT: G 72 ILE cc_start: 0.8532 (mm) cc_final: 0.8207 (pt) REVERT: G 83 MET cc_start: 0.8209 (tpp) cc_final: 0.7888 (tpp) REVERT: G 296 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7308 (tmtt) REVERT: G 416 GLU cc_start: 0.8498 (tt0) cc_final: 0.8184 (tt0) REVERT: G 438 ASN cc_start: 0.7786 (m-40) cc_final: 0.7408 (m-40) REVERT: H 124 ASN cc_start: 0.7444 (p0) cc_final: 0.7139 (m-40) REVERT: H 268 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7645 (mt-10) REVERT: H 296 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7310 (tmtt) REVERT: H 408 ARG cc_start: 0.8003 (tpp-160) cc_final: 0.7715 (tpt90) REVERT: I 72 ILE cc_start: 0.8448 (mm) cc_final: 0.8085 (pt) REVERT: I 87 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6330 (pt0) REVERT: I 268 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7581 (mt-10) REVERT: I 296 LYS cc_start: 0.8018 (ttmm) cc_final: 0.7617 (tmtt) REVERT: I 333 ASP cc_start: 0.8111 (t0) cc_final: 0.7848 (t70) REVERT: I 468 ASN cc_start: 0.8482 (t0) cc_final: 0.8132 (t0) REVERT: J 72 ILE cc_start: 0.8523 (mm) cc_final: 0.8199 (pt) REVERT: J 83 MET cc_start: 0.8199 (tpp) cc_final: 0.7880 (tpp) REVERT: J 268 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7367 (mt-10) REVERT: J 296 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7309 (tmtt) REVERT: J 416 GLU cc_start: 0.8501 (tt0) cc_final: 0.8184 (tt0) REVERT: J 438 ASN cc_start: 0.7713 (m-40) cc_final: 0.7329 (m-40) REVERT: K 124 ASN cc_start: 0.7459 (p0) cc_final: 0.7162 (m-40) REVERT: K 268 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7670 (mt-10) REVERT: K 296 LYS cc_start: 0.8002 (ttmm) cc_final: 0.7305 (tmtt) REVERT: K 408 ARG cc_start: 0.8023 (tpp-160) cc_final: 0.7714 (tpt90) REVERT: L 72 ILE cc_start: 0.8460 (mm) cc_final: 0.8104 (pt) REVERT: L 87 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6323 (pt0) REVERT: L 268 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7578 (mt-10) REVERT: L 296 LYS cc_start: 0.8025 (ttmm) cc_final: 0.7618 (tmtt) REVERT: L 333 ASP cc_start: 0.8122 (t0) cc_final: 0.7803 (t70) REVERT: L 468 ASN cc_start: 0.8491 (t0) cc_final: 0.8132 (t0) outliers start: 88 outliers final: 67 residues processed: 708 average time/residue: 0.2810 time to fit residues: 319.5038 Evaluate side-chains 682 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 611 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 237 TYR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 TYR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 237 TYR Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain J residue 86 TYR Chi-restraints excluded: chain J residue 237 TYR Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 237 TYR Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 439 ASP Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 287 VAL Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 415 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 226 optimal weight: 0.8980 chunk 317 optimal weight: 5.9990 chunk 468 optimal weight: 3.9990 chunk 428 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.175144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.136602 restraints weight = 53807.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.135098 restraints weight = 48058.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.136506 restraints weight = 52872.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.137251 restraints weight = 38556.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.137606 restraints weight = 35448.714| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 42072 Z= 0.162 Angle : 0.679 10.077 56760 Z= 0.361 Chirality : 0.044 0.178 6228 Planarity : 0.004 0.057 7404 Dihedral : 5.264 45.549 5651 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.50 % Favored : 93.79 % Rotamer: Outliers : 2.29 % Allowed : 23.28 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 3.63 % 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 aren not related in a simple way. whole: -1.19 (0.11), residues: 5088 helix: 0.18 (0.11), residues: 2280 sheet: -0.72 (0.25), residues: 384 loop : -1.76 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 339 TYR 0.008 0.001 TYR E 86 PHE 0.011 0.001 PHE A 157 TRP 0.005 0.001 TRP I 437 HIS 0.004 0.001 HIS G 136 Details of bonding type rmsd covalent geometry : bond 0.00375 (42048) covalent geometry : angle 0.67868 (56760) hydrogen bonds : bond 0.02596 ( 1414) hydrogen bonds : angle 4.64844 ( 4026) Misc. bond : bond 0.00225 ( 24) =============================================================================== Job complete usr+sys time: 7851.68 seconds wall clock time: 136 minutes 26.48 seconds (8186.48 seconds total)