Starting phenix.real_space_refine on Sat Mar 7 11:14:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zxl_11524/03_2026/6zxl_11524.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zxl_11524/03_2026/6zxl_11524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zxl_11524/03_2026/6zxl_11524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zxl_11524/03_2026/6zxl_11524.map" model { file = "/net/cci-nas-00/data/ceres_data/6zxl_11524/03_2026/6zxl_11524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zxl_11524/03_2026/6zxl_11524.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 40 5.16 5 C 26441 2.51 5 N 7348 2.21 5 O 8343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 176 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42172 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3961 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 8, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 130 Chain: "B" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3977 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "C" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3977 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "D" Number of atoms: 3970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3970 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 505} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "E" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3977 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "F" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3977 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "G" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3977 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "H" Number of atoms: 5378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5378 Classifications: {'peptide': 699} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 680} Chain breaks: 1 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLU:plan': 16, 'GLN:plan1': 9, 'TYR:plan': 2, 'ASP:plan': 9, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 190 Chain: "I" Number of atoms: 4739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 4739 Classifications: {'peptide': 710} Incomplete info: {'truncation_to_alanine': 310} Link IDs: {'PTRANS': 18, 'TRANS': 691} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1133 Unresolved non-hydrogen angles: 1423 Unresolved non-hydrogen dihedrals: 927 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 19, 'GLU:plan': 39, 'ASP:plan': 29, 'TYR:plan': 10, 'ASN:plan1': 20, 'ARG:plan': 14, 'HIS:plan': 9, 'PHE:plan': 12, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 645 Chain: "J" Number of atoms: 4239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 4239 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 327} Link IDs: {'PTRANS': 16, 'TRANS': 644} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1245 Unresolved non-hydrogen angles: 1551 Unresolved non-hydrogen dihedrals: 1039 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'ASP:plan': 27, 'GLU:plan': 41, 'TYR:plan': 13, 'ASN:plan1': 23, 'GLN:plan1': 21, 'ARG:plan': 16, 'HIS:plan': 8, 'PHE:plan': 14, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 711 Time building chain proxies: 9.48, per 1000 atoms: 0.22 Number of scatterers: 42172 At special positions: 0 Unit cell: (182.97, 179.76, 176.55, 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 40 16.00 O 8343 8.00 N 7348 7.00 C 26441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 1.8 seconds 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11038 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 82 sheets defined 35.8% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.522A pdb=" N HIS A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 212' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 234 through 241 removed outlier: 3.669A pdb=" N VAL A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.824A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.862A pdb=" N MET A 350 " --> pdb=" O TRP A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 477 through 487 Proline residue: A 482 - end of helix Processing helix chain 'A' and resid 512 through 517 removed outlier: 4.017A pdb=" N THR A 517 " --> pdb=" O PRO A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 removed outlier: 3.623A pdb=" N PHE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.509A pdb=" N LEU A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 4.561A pdb=" N ASP A 579 " --> pdb=" O THR A 576 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 581 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.578A pdb=" N VAL A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 637 removed outlier: 3.552A pdb=" N LYS A 637 " --> pdb=" O ASP A 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 637' Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.706A pdb=" N ASN A 664 " --> pdb=" O ASP A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 683 removed outlier: 4.097A pdb=" N ASP A 683 " --> pdb=" O LYS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 207 through 213 removed outlier: 3.821A pdb=" N GLU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 removed outlier: 3.707A pdb=" N VAL B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 240 " --> pdb=" O PHE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.823A pdb=" N HIS B 253 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 477 through 487 Proline residue: B 482 - end of helix Processing helix chain 'B' and resid 512 through 517 removed outlier: 3.774A pdb=" N THR B 517 " --> pdb=" O PRO B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 532 removed outlier: 3.614A pdb=" N GLY B 532 " --> pdb=" O LYS B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 550 No H-bonds generated for 'chain 'B' and resid 548 through 550' Processing helix chain 'B' and resid 555 through 568 removed outlier: 3.581A pdb=" N GLU B 568 " --> pdb=" O ASN B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 581 removed outlier: 4.395A pdb=" N ASP B 579 " --> pdb=" O THR B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 removed outlier: 3.590A pdb=" N VAL B 612 " --> pdb=" O ASP B 608 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 614 " --> pdb=" O SER B 610 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 615 " --> pdb=" O VAL B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 637 removed outlier: 3.522A pdb=" N LYS B 637 " --> pdb=" O ASP B 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 637' Processing helix chain 'B' and resid 704 through 706 No H-bonds generated for 'chain 'B' and resid 704 through 706' Processing helix chain 'C' and resid 184 through 191 Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.555A pdb=" N HIS C 211 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS C 213 " --> pdb=" O ASN C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 213' Processing helix chain 'C' and resid 234 through 241 removed outlier: 3.739A pdb=" N VAL C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.955A pdb=" N HIS C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 435 through 446 removed outlier: 3.662A pdb=" N PHE C 439 " --> pdb=" O ASN C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Proline residue: C 482 - end of helix Processing helix chain 'C' and resid 512 through 518 Processing helix chain 'C' and resid 522 through 532 removed outlier: 3.580A pdb=" N PHE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 532 " --> pdb=" O LYS C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 568 Processing helix chain 'C' and resid 576 through 581 removed outlier: 4.394A pdb=" N ASP C 579 " --> pdb=" O THR C 576 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 581 " --> pdb=" O LEU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 615 removed outlier: 3.584A pdb=" N VAL C 612 " --> pdb=" O ASP C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 638 Processing helix chain 'C' and resid 702 through 706 Processing helix chain 'C' and resid 730 through 734 removed outlier: 3.788A pdb=" N ILE C 734 " --> pdb=" O GLY C 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 207 through 213 removed outlier: 3.591A pdb=" N GLU D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS D 213 " --> pdb=" O ASN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 241 removed outlier: 3.773A pdb=" N VAL D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.882A pdb=" N HIS D 253 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 435 through 446 removed outlier: 3.742A pdb=" N PHE D 439 " --> pdb=" O ASN D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Proline residue: D 482 - end of helix Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 522 through 531 removed outlier: 3.512A pdb=" N PHE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 568 removed outlier: 3.531A pdb=" N GLU D 568 " --> pdb=" O ASN D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 581 removed outlier: 4.271A pdb=" N ASP D 579 " --> pdb=" O THR D 576 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 581 " --> pdb=" O LEU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 615 removed outlier: 3.657A pdb=" N VAL D 612 " --> pdb=" O ASP D 608 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU D 614 " --> pdb=" O SER D 610 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA D 615 " --> pdb=" O VAL D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 638 Processing helix chain 'D' and resid 702 through 706 Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 207 through 213 removed outlier: 3.583A pdb=" N HIS E 211 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS E 213 " --> pdb=" O ASN E 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 207 through 213' Processing helix chain 'E' and resid 234 through 241 removed outlier: 3.923A pdb=" N VAL E 239 " --> pdb=" O ASP E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.859A pdb=" N HIS E 253 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 477 through 485 Proline residue: E 482 - end of helix Processing helix chain 'E' and resid 512 through 517 removed outlier: 3.915A pdb=" N THR E 517 " --> pdb=" O PRO E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 531 removed outlier: 3.573A pdb=" N PHE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 568 removed outlier: 3.501A pdb=" N GLU E 568 " --> pdb=" O ASN E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 576 through 581 removed outlier: 4.467A pdb=" N ASP E 579 " --> pdb=" O THR E 576 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE E 581 " --> pdb=" O LEU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 615 removed outlier: 3.524A pdb=" N VAL E 612 " --> pdb=" O ASP E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 637 removed outlier: 3.613A pdb=" N LYS E 637 " --> pdb=" O ASP E 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 634 through 637' Processing helix chain 'E' and resid 704 through 706 No H-bonds generated for 'chain 'E' and resid 704 through 706' Processing helix chain 'E' and resid 732 through 734 No H-bonds generated for 'chain 'E' and resid 732 through 734' Processing helix chain 'F' and resid 184 through 191 Processing helix chain 'F' and resid 207 through 213 removed outlier: 3.996A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS F 213 " --> pdb=" O ASN F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 241 removed outlier: 3.595A pdb=" N VAL F 239 " --> pdb=" O ASP F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 253 removed outlier: 3.851A pdb=" N HIS F 253 " --> pdb=" O GLU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 477 through 487 Proline residue: F 482 - end of helix Processing helix chain 'F' and resid 513 through 518 Processing helix chain 'F' and resid 522 through 531 Processing helix chain 'F' and resid 555 through 568 removed outlier: 3.736A pdb=" N GLN F 560 " --> pdb=" O GLN F 556 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN F 561 " --> pdb=" O GLN F 557 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN F 565 " --> pdb=" O ASN F 561 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU F 566 " --> pdb=" O ILE F 562 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA F 567 " --> pdb=" O LYS F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 576 through 581 removed outlier: 4.444A pdb=" N ASP F 579 " --> pdb=" O THR F 576 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE F 581 " --> pdb=" O LEU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 615 Processing helix chain 'F' and resid 634 through 637 Processing helix chain 'F' and resid 704 through 706 No H-bonds generated for 'chain 'F' and resid 704 through 706' Processing helix chain 'F' and resid 732 through 734 No H-bonds generated for 'chain 'F' and resid 732 through 734' Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 207 through 212 removed outlier: 4.095A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 234 through 241 removed outlier: 3.659A pdb=" N VAL G 239 " --> pdb=" O ASP G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.915A pdb=" N HIS G 253 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 350 Processing helix chain 'G' and resid 435 through 446 removed outlier: 3.748A pdb=" N PHE G 439 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 487 Proline residue: G 482 - end of helix Processing helix chain 'G' and resid 512 through 517 removed outlier: 3.651A pdb=" N THR G 517 " --> pdb=" O PRO G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 532 removed outlier: 3.761A pdb=" N GLY G 532 " --> pdb=" O LYS G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 555 through 568 Processing helix chain 'G' and resid 576 through 581 removed outlier: 4.567A pdb=" N ASP G 579 " --> pdb=" O THR G 576 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE G 581 " --> pdb=" O LEU G 578 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 615 removed outlier: 3.521A pdb=" N VAL G 612 " --> pdb=" O ASP G 608 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU G 614 " --> pdb=" O SER G 610 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA G 615 " --> pdb=" O VAL G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 637 Processing helix chain 'G' and resid 704 through 706 No H-bonds generated for 'chain 'G' and resid 704 through 706' Processing helix chain 'G' and resid 730 through 734 removed outlier: 3.895A pdb=" N ILE G 734 " --> pdb=" O GLY G 731 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 66 removed outlier: 4.090A pdb=" N VAL H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 77 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 99 through 103 Processing helix chain 'H' and resid 140 through 159 removed outlier: 4.496A pdb=" N ASN H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL H 147 " --> pdb=" O LYS H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 164 Processing helix chain 'H' and resid 168 through 179 removed outlier: 4.130A pdb=" N VAL H 173 " --> pdb=" O LYS H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 removed outlier: 4.145A pdb=" N ASP H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU H 188 " --> pdb=" O ASP H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 196 Processing helix chain 'H' and resid 202 through 210 Processing helix chain 'H' and resid 210 through 226 Processing helix chain 'H' and resid 229 through 237 Processing helix chain 'H' and resid 237 through 248 Processing helix chain 'H' and resid 250 through 261 removed outlier: 3.688A pdb=" N LEU H 254 " --> pdb=" O GLN H 250 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU H 257 " --> pdb=" O ASN H 253 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU H 259 " --> pdb=" O SER H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 278 removed outlier: 3.627A pdb=" N GLN H 276 " --> pdb=" O GLU H 272 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N HIS H 277 " --> pdb=" O LYS H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 284 Processing helix chain 'H' and resid 286 through 298 removed outlier: 3.573A pdb=" N ILE H 298 " --> pdb=" O LYS H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 312 removed outlier: 3.573A pdb=" N ILE H 307 " --> pdb=" O LYS H 303 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER H 312 " --> pdb=" O ILE H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 321 removed outlier: 3.873A pdb=" N GLU H 317 " --> pdb=" O GLN H 313 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG H 321 " --> pdb=" O GLU H 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 327 removed outlier: 5.649A pdb=" N ASP H 325 " --> pdb=" O ILE H 322 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER H 327 " --> pdb=" O ILE H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 345 removed outlier: 3.610A pdb=" N PHE H 337 " --> pdb=" O GLU H 333 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP H 344 " --> pdb=" O LYS H 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 381 removed outlier: 3.923A pdb=" N PHE H 375 " --> pdb=" O LYS H 371 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS H 378 " --> pdb=" O GLU H 374 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU H 381 " --> pdb=" O LYS H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 396 removed outlier: 3.568A pdb=" N GLN H 393 " --> pdb=" O ASN H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 423 Processing helix chain 'H' and resid 442 through 446 Processing helix chain 'H' and resid 447 through 452 Processing helix chain 'H' and resid 464 through 474 removed outlier: 3.766A pdb=" N GLU H 470 " --> pdb=" O GLY H 466 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN H 474 " --> pdb=" O GLU H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 552 through 575 removed outlier: 3.846A pdb=" N LYS H 558 " --> pdb=" O LYS H 554 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS H 572 " --> pdb=" O GLN H 568 " (cutoff:3.500A) Processing helix chain 'H' and resid 591 through 608 removed outlier: 4.122A pdb=" N TYR H 600 " --> pdb=" O VAL H 596 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU H 601 " --> pdb=" O GLU H 597 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASN H 604 " --> pdb=" O TYR H 600 " (cutoff:3.500A) Processing helix chain 'H' and resid 611 through 624 removed outlier: 3.558A pdb=" N ILE H 615 " --> pdb=" O GLN H 611 " (cutoff:3.500A) Processing helix chain 'H' and resid 635 through 639 Processing helix chain 'H' and resid 640 through 647 removed outlier: 3.703A pdb=" N THR H 644 " --> pdb=" O ALA H 640 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS H 645 " --> pdb=" O GLU H 641 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN H 646 " --> pdb=" O GLN H 642 " (cutoff:3.500A) Processing helix chain 'H' and resid 679 through 701 removed outlier: 3.796A pdb=" N GLY H 683 " --> pdb=" O ASN H 679 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY H 697 " --> pdb=" O ASP H 693 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU H 700 " --> pdb=" O ALA H 696 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP H 701 " --> pdb=" O GLY H 697 " (cutoff:3.500A) Processing helix chain 'H' and resid 711 through 721 removed outlier: 4.219A pdb=" N ASP H 716 " --> pdb=" O LYS H 712 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE H 717 " --> pdb=" O LYS H 713 " (cutoff:3.500A) Processing helix chain 'H' and resid 728 through 731 Processing helix chain 'H' and resid 732 through 745 removed outlier: 3.746A pdb=" N ALA H 738 " --> pdb=" O ALA H 734 " (cutoff:3.500A) Processing helix chain 'H' and resid 748 through 759 Processing helix chain 'H' and resid 759 through 772 removed outlier: 3.728A pdb=" N GLN H 764 " --> pdb=" O PRO H 760 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN H 767 " --> pdb=" O PHE H 763 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP H 768 " --> pdb=" O GLN H 764 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN H 769 " --> pdb=" O PHE H 765 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE H 770 " --> pdb=" O ILE H 766 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE H 772 " --> pdb=" O ASP H 768 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 44 removed outlier: 4.324A pdb=" N LYS I 37 " --> pdb=" O GLU I 33 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU I 38 " --> pdb=" O GLU I 34 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE I 39 " --> pdb=" O HIS I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 65 removed outlier: 3.589A pdb=" N LYS I 56 " --> pdb=" O GLU I 52 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS I 65 " --> pdb=" O LYS I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 77 removed outlier: 3.956A pdb=" N LEU I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 4.157A pdb=" N ALA I 96 " --> pdb=" O ILE I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 158 removed outlier: 3.765A pdb=" N ASN I 146 " --> pdb=" O GLU I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 163 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.510A pdb=" N LYS I 178 " --> pdb=" O LEU I 174 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN I 179 " --> pdb=" O ASN I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 193 through 197 removed outlier: 3.562A pdb=" N GLU I 196 " --> pdb=" O GLN I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 209 removed outlier: 3.710A pdb=" N LEU I 206 " --> pdb=" O SER I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 226 removed outlier: 3.681A pdb=" N GLN I 214 " --> pdb=" O SER I 210 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU I 215 " --> pdb=" O ASN I 211 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL I 216 " --> pdb=" O GLU I 212 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU I 226 " --> pdb=" O ALA I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 237 removed outlier: 4.287A pdb=" N ASP I 231 " --> pdb=" O PRO I 227 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL I 232 " --> pdb=" O GLN I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 251 Processing helix chain 'I' and resid 252 through 261 Processing helix chain 'I' and resid 263 through 285 removed outlier: 4.046A pdb=" N TYR I 278 " --> pdb=" O ILE I 274 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN I 279 " --> pdb=" O LYS I 275 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N HIS I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TRP I 281 " --> pdb=" O HIS I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 298 removed outlier: 3.711A pdb=" N LEU I 292 " --> pdb=" O GLU I 288 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU I 293 " --> pdb=" O GLY I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 312 removed outlier: 4.037A pdb=" N SER I 312 " --> pdb=" O ILE I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 321 removed outlier: 4.084A pdb=" N GLU I 317 " --> pdb=" O GLN I 313 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG I 321 " --> pdb=" O GLU I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 323 through 327 removed outlier: 3.830A pdb=" N SER I 327 " --> pdb=" O ILE I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 338 Processing helix chain 'I' and resid 372 through 383 removed outlier: 3.903A pdb=" N LEU I 376 " --> pdb=" O GLU I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 396 Processing helix chain 'I' and resid 405 through 421 Processing helix chain 'I' and resid 444 through 446 No H-bonds generated for 'chain 'I' and resid 444 through 446' Processing helix chain 'I' and resid 447 through 452 removed outlier: 3.563A pdb=" N ALA I 452 " --> pdb=" O ALA I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 464 through 473 Processing helix chain 'I' and resid 551 through 574 removed outlier: 3.618A pdb=" N LYS I 558 " --> pdb=" O LYS I 554 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU I 561 " --> pdb=" O THR I 557 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA I 562 " --> pdb=" O LYS I 558 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS I 572 " --> pdb=" O GLN I 568 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU I 574 " --> pdb=" O TRP I 570 " (cutoff:3.500A) Processing helix chain 'I' and resid 591 through 608 removed outlier: 3.802A pdb=" N TYR I 600 " --> pdb=" O VAL I 596 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 624 Processing helix chain 'I' and resid 635 through 639 Processing helix chain 'I' and resid 641 through 646 Processing helix chain 'I' and resid 648 through 652 Processing helix chain 'I' and resid 679 through 699 removed outlier: 3.686A pdb=" N HIS I 690 " --> pdb=" O HIS I 686 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA I 691 " --> pdb=" O GLU I 687 " (cutoff:3.500A) Processing helix chain 'I' and resid 707 through 722 removed outlier: 4.093A pdb=" N LYS I 712 " --> pdb=" O VAL I 708 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS I 713 " --> pdb=" O THR I 709 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP I 716 " --> pdb=" O LYS I 712 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE I 717 " --> pdb=" O LYS I 713 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU I 720 " --> pdb=" O ASP I 716 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU I 721 " --> pdb=" O ILE I 717 " (cutoff:3.500A) Processing helix chain 'I' and resid 723 through 725 No H-bonds generated for 'chain 'I' and resid 723 through 725' Processing helix chain 'I' and resid 732 through 745 Processing helix chain 'I' and resid 748 through 759 Processing helix chain 'I' and resid 759 through 770 removed outlier: 4.065A pdb=" N GLN I 764 " --> pdb=" O PRO I 760 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE I 765 " --> pdb=" O LYS I 761 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 65 removed outlier: 3.525A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 77 removed outlier: 4.184A pdb=" N LEU J 71 " --> pdb=" O PRO J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 96 removed outlier: 4.092A pdb=" N ALA J 96 " --> pdb=" O ILE J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 158 removed outlier: 3.622A pdb=" N ASN J 146 " --> pdb=" O GLU J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 163 Processing helix chain 'J' and resid 167 through 179 removed outlier: 3.525A pdb=" N LYS J 178 " --> pdb=" O LEU J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 193 through 197 Processing helix chain 'J' and resid 202 through 209 removed outlier: 3.630A pdb=" N LEU J 206 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU J 207 " --> pdb=" O VAL J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 226 removed outlier: 3.581A pdb=" N GLU J 226 " --> pdb=" O ALA J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 237 removed outlier: 4.029A pdb=" N ASP J 231 " --> pdb=" O PRO J 227 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL J 232 " --> pdb=" O GLN J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 251 Processing helix chain 'J' and resid 252 through 261 removed outlier: 3.501A pdb=" N LEU J 256 " --> pdb=" O ILE J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 285 removed outlier: 3.685A pdb=" N HIS J 277 " --> pdb=" O LYS J 273 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR J 278 " --> pdb=" O ILE J 274 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N HIS J 280 " --> pdb=" O GLN J 276 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP J 281 " --> pdb=" O HIS J 277 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 298 Processing helix chain 'J' and resid 313 through 320 removed outlier: 3.996A pdb=" N GLU J 317 " --> pdb=" O GLN J 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 333 through 338 Processing helix chain 'J' and resid 372 through 383 removed outlier: 3.950A pdb=" N LEU J 376 " --> pdb=" O GLU J 372 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS J 377 " --> pdb=" O LYS J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 388 through 396 Processing helix chain 'J' and resid 406 through 421 removed outlier: 3.665A pdb=" N GLN J 411 " --> pdb=" O ASP J 407 " (cutoff:3.500A) Processing helix chain 'J' and resid 442 through 446 Processing helix chain 'J' and resid 447 through 452 removed outlier: 3.759A pdb=" N ALA J 452 " --> pdb=" O ALA J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 464 through 474 removed outlier: 3.742A pdb=" N GLU J 470 " --> pdb=" O GLY J 466 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASN J 474 " --> pdb=" O GLU J 470 " (cutoff:3.500A) Processing helix chain 'J' and resid 551 through 572 removed outlier: 3.595A pdb=" N LYS J 558 " --> pdb=" O LYS J 554 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU J 561 " --> pdb=" O THR J 557 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS J 572 " --> pdb=" O GLN J 568 " (cutoff:3.500A) Processing helix chain 'J' and resid 591 through 610 removed outlier: 3.732A pdb=" N ILE J 595 " --> pdb=" O TYR J 591 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR J 600 " --> pdb=" O VAL J 596 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU J 601 " --> pdb=" O GLU J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 624 Processing helix chain 'J' and resid 635 through 640 removed outlier: 4.637A pdb=" N ALA J 640 " --> pdb=" O LEU J 636 " (cutoff:3.500A) Processing helix chain 'J' and resid 641 through 646 Processing helix chain 'J' and resid 648 through 652 Processing helix chain 'J' and resid 679 through 700 removed outlier: 4.256A pdb=" N HIS J 690 " --> pdb=" O HIS J 686 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA J 691 " --> pdb=" O GLU J 687 " (cutoff:3.500A) Processing helix chain 'J' and resid 707 through 721 removed outlier: 4.215A pdb=" N LYS J 712 " --> pdb=" O VAL J 708 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS J 713 " --> pdb=" O THR J 709 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP J 716 " --> pdb=" O LYS J 712 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE J 717 " --> pdb=" O LYS J 713 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU J 720 " --> pdb=" O ASP J 716 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU J 721 " --> pdb=" O ILE J 717 " (cutoff:3.500A) Processing helix chain 'J' and resid 722 through 725 removed outlier: 3.687A pdb=" N LEU J 725 " --> pdb=" O GLY J 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 722 through 725' Processing helix chain 'J' and resid 728 through 731 Processing helix chain 'J' and resid 732 through 745 Processing helix chain 'J' and resid 748 through 759 removed outlier: 3.607A pdb=" N VAL J 755 " --> pdb=" O GLU J 751 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN J 756 " --> pdb=" O ARG J 752 " (cutoff:3.500A) Processing helix chain 'J' and resid 759 through 772 removed outlier: 4.100A pdb=" N GLN J 764 " --> pdb=" O PRO J 760 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE J 765 " --> pdb=" O LYS J 761 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE J 770 " --> pdb=" O ILE J 766 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS J 771 " --> pdb=" O ASN J 767 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE J 772 " --> pdb=" O ASP J 768 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 197 removed outlier: 3.597A pdb=" N ASP A 195 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 202 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 394 removed outlier: 7.076A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A 451 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLU A 267 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR A 295 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASP A 265 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N ARG A 297 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N HIS A 263 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE A 269 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN A 361 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU A 271 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG A 359 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 389 through 394 removed outlier: 7.076A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A 451 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLU A 267 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR A 295 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASP A 265 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N ARG A 297 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N HIS A 263 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE A 269 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN A 361 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU A 271 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG A 359 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 364 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 419 " --> pdb=" O ILE A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 458 through 462 removed outlier: 4.245A pdb=" N ILE A 459 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.402A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA7, first strand: chain 'A' and resid 596 through 598 removed outlier: 6.519A pdb=" N HIS A 597 " --> pdb=" O VAL A 605 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 628 through 629 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 7.027A pdb=" N VAL A 701 " --> pdb=" O SER A 640 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR A 642 " --> pdb=" O TYR A 699 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR A 699 " --> pdb=" O TYR A 642 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL A 644 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASN A 697 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE A 646 " --> pdb=" O LYS A 695 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LYS A 695 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ALA A 700 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU A 725 " --> pdb=" O ALA A 700 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 192 through 197 removed outlier: 3.766A pdb=" N ASP B 195 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE B 202 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 389 through 394 removed outlier: 4.943A pdb=" N THR B 390 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 385 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR B 381 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER B 294 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLU B 267 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR B 295 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ASP B 265 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ARG B 297 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N HIS B 263 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS B 263 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE B 269 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN B 361 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU B 271 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG B 359 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 389 through 394 removed outlier: 4.943A pdb=" N THR B 390 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 385 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR B 381 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER B 294 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLU B 267 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR B 295 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ASP B 265 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ARG B 297 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N HIS B 263 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS B 263 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE B 269 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN B 361 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU B 271 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG B 359 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 458 through 462 removed outlier: 4.397A pdb=" N ILE B 459 " --> pdb=" O ASP B 472 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 501 through 506 Processing sheet with id=AB6, first strand: chain 'B' and resid 541 through 542 Processing sheet with id=AB7, first strand: chain 'B' and resid 596 through 598 Processing sheet with id=AB8, first strand: chain 'B' and resid 628 through 629 Processing sheet with id=AB9, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.860A pdb=" N GLU B 645 " --> pdb=" O ASN B 697 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN B 697 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA B 700 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 725 " --> pdb=" O ALA B 700 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 192 through 197 Processing sheet with id=AC2, first strand: chain 'C' and resid 358 through 360 removed outlier: 7.183A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN C 409 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 389 through 394 removed outlier: 6.777A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU C 448 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLU C 267 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR C 295 " --> pdb=" O ASP C 265 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ASP C 265 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N ARG C 297 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N HIS C 263 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 458 through 462 removed outlier: 5.981A pdb=" N SER C 475 " --> pdb=" O ILE C 459 " (cutoff:3.500A) removed outlier: 10.868A pdb=" N THR C 461 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 9.404A pdb=" N THR C 473 " --> pdb=" O THR C 461 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 501 through 506 removed outlier: 8.587A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG C 592 " --> pdb=" O ASP C 551 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AC7, first strand: chain 'C' and resid 596 through 598 Processing sheet with id=AC8, first strand: chain 'C' and resid 628 through 629 Processing sheet with id=AC9, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.687A pdb=" N VAL C 696 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 728 " --> pdb=" O VAL C 696 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL C 698 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA C 700 " --> pdb=" O ILE C 724 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE C 724 " --> pdb=" O ALA C 700 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 192 through 197 removed outlier: 3.632A pdb=" N ASP D 195 " --> pdb=" O PHE D 202 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE D 202 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 262 through 273 removed outlier: 3.956A pdb=" N GLU D 267 " --> pdb=" O ASN D 363 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARG D 359 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 262 through 273 removed outlier: 3.956A pdb=" N GLU D 267 " --> pdb=" O ASN D 363 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARG D 359 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 293 through 298 removed outlier: 4.269A pdb=" N SER D 329 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR D 381 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU D 385 " --> pdb=" O THR D 390 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR D 390 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 458 through 462 removed outlier: 4.639A pdb=" N ILE D 459 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP D 472 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR D 461 " --> pdb=" O ARG D 470 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG D 470 " --> pdb=" O THR D 461 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 501 through 506 removed outlier: 3.549A pdb=" N PHE D 493 " --> pdb=" O VAL D 501 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG D 503 " --> pdb=" O ILE D 491 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE D 491 " --> pdb=" O ARG D 503 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 590 " --> pdb=" O ASN D 553 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AD8, first strand: chain 'D' and resid 596 through 598 Processing sheet with id=AD9, first strand: chain 'D' and resid 628 through 629 Processing sheet with id=AE1, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.217A pdb=" N VAL D 696 " --> pdb=" O SER D 728 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER D 728 " --> pdb=" O VAL D 696 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL D 698 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 724 " --> pdb=" O ALA D 700 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 192 through 197 Processing sheet with id=AE3, first strand: chain 'E' and resid 358 through 360 removed outlier: 3.829A pdb=" N SER E 272 " --> pdb=" O ARG E 359 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN E 409 " --> pdb=" O ASN E 368 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 389 through 394 removed outlier: 5.251A pdb=" N THR E 390 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU E 385 " --> pdb=" O THR E 390 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA E 392 " --> pdb=" O LEU E 383 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR E 381 " --> pdb=" O ILE E 394 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 384 " --> pdb=" O ARG E 449 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG E 449 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLU E 267 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR E 295 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP E 265 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N ARG E 297 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N HIS E 263 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE E 364 " --> pdb=" O ILE E 419 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 458 through 462 removed outlier: 5.873A pdb=" N SER E 475 " --> pdb=" O ILE E 459 " (cutoff:3.500A) removed outlier: 10.935A pdb=" N THR E 461 " --> pdb=" O THR E 473 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N THR E 473 " --> pdb=" O THR E 461 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 501 through 506 removed outlier: 3.667A pdb=" N ARG E 592 " --> pdb=" O ASP E 551 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 541 through 542 Processing sheet with id=AE8, first strand: chain 'E' and resid 596 through 598 removed outlier: 6.229A pdb=" N HIS E 597 " --> pdb=" O VAL E 605 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 628 through 629 Processing sheet with id=AF1, first strand: chain 'E' and resid 654 through 655 removed outlier: 3.531A pdb=" N GLY E 641 " --> pdb=" O VAL E 701 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA E 700 " --> pdb=" O LEU E 725 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU E 725 " --> pdb=" O ALA E 700 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 192 through 197 removed outlier: 3.513A pdb=" N ASP F 195 " --> pdb=" O PHE F 202 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE F 202 " --> pdb=" O ASP F 195 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 290 through 292 removed outlier: 6.701A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN F 368 " --> pdb=" O ASN F 409 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN F 409 " --> pdb=" O ASN F 368 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 358 through 360 removed outlier: 6.701A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE F 364 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE F 419 " --> pdb=" O ILE F 364 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 294 through 297 removed outlier: 3.641A pdb=" N SER F 294 " --> pdb=" O ALA F 333 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG F 449 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL F 384 " --> pdb=" O ARG F 449 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N THR F 393 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU F 383 " --> pdb=" O LEU F 391 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 458 through 462 removed outlier: 4.482A pdb=" N ILE F 459 " --> pdb=" O ASP F 472 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR F 461 " --> pdb=" O ARG F 470 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG F 470 " --> pdb=" O THR F 461 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 501 through 506 removed outlier: 3.746A pdb=" N ARG F 592 " --> pdb=" O ASP F 551 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=AF9, first strand: chain 'F' and resid 596 through 598 removed outlier: 6.456A pdb=" N HIS F 597 " --> pdb=" O VAL F 605 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 628 through 629 Processing sheet with id=AG2, first strand: chain 'F' and resid 654 through 655 removed outlier: 4.269A pdb=" N GLY F 641 " --> pdb=" O VAL F 701 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL F 696 " --> pdb=" O SER F 728 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER F 728 " --> pdb=" O VAL F 696 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL F 698 " --> pdb=" O ILE F 726 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE F 724 " --> pdb=" O ALA F 700 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 192 through 196 Processing sheet with id=AG4, first strand: chain 'G' and resid 389 through 394 removed outlier: 4.773A pdb=" N THR G 390 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU G 385 " --> pdb=" O THR G 390 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR G 381 " --> pdb=" O ILE G 394 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER G 382 " --> pdb=" O ASP G 451 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP G 451 " --> pdb=" O SER G 382 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU G 448 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL G 332 " --> pdb=" O LEU G 448 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 450 " --> pdb=" O SER G 330 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN G 328 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU G 267 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR G 295 " --> pdb=" O ASP G 265 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASP G 265 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ARG G 297 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N HIS G 263 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE G 269 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ASN G 361 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU G 271 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG G 359 " --> pdb=" O LEU G 271 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN G 368 " --> pdb=" O ASN G 409 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 389 through 394 removed outlier: 4.773A pdb=" N THR G 390 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU G 385 " --> pdb=" O THR G 390 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR G 381 " --> pdb=" O ILE G 394 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER G 382 " --> pdb=" O ASP G 451 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP G 451 " --> pdb=" O SER G 382 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU G 448 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL G 332 " --> pdb=" O LEU G 448 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 450 " --> pdb=" O SER G 330 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN G 328 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU G 267 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR G 295 " --> pdb=" O ASP G 265 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASP G 265 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ARG G 297 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N HIS G 263 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE G 269 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ASN G 361 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU G 271 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG G 359 " --> pdb=" O LEU G 271 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 458 through 462 removed outlier: 4.642A pdb=" N ILE G 459 " --> pdb=" O ASP G 472 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP G 472 " --> pdb=" O ILE G 459 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR G 461 " --> pdb=" O ARG G 470 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG G 470 " --> pdb=" O THR G 461 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.586A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 541 through 542 Processing sheet with id=AG9, first strand: chain 'G' and resid 596 through 598 Processing sheet with id=AH1, first strand: chain 'G' and resid 628 through 629 Processing sheet with id=AH2, first strand: chain 'G' and resid 654 through 655 removed outlier: 3.703A pdb=" N LYS G 695 " --> pdb=" O GLU G 647 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL G 696 " --> pdb=" O SER G 728 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER G 728 " --> pdb=" O VAL G 696 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL G 698 " --> pdb=" O ILE G 726 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 81 through 82 removed outlier: 3.923A pdb=" N TYR H 82 " --> pdb=" O LEU H 129 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 436 through 437 Processing sheet with id=AH5, first strand: chain 'H' and resid 436 through 437 removed outlier: 6.722A pdb=" N LYS H 540 " --> pdb=" O LYS H 536 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LYS H 536 " --> pdb=" O LYS H 540 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TYR H 542 " --> pdb=" O ILE H 534 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE H 534 " --> pdb=" O TYR H 542 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ARG H 544 " --> pdb=" O VAL H 532 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL H 532 " --> pdb=" O ARG H 544 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP H 546 " --> pdb=" O LYS H 530 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS H 530 " --> pdb=" O ASP H 546 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS H 548 " --> pdb=" O GLU H 528 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU H 528 " --> pdb=" O LYS H 548 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 485 through 487 Processing sheet with id=AH7, first strand: chain 'H' and resid 630 through 632 Processing sheet with id=AH8, first strand: chain 'I' and resid 82 through 84 removed outlier: 3.504A pdb=" N TYR I 82 " --> pdb=" O LEU I 129 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE I 131 " --> pdb=" O TYR I 82 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 103 through 105 removed outlier: 3.604A pdb=" N ILE I 104 " --> pdb=" O ALA I 112 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 436 through 442 removed outlier: 3.829A pdb=" N LEU I 437 " --> pdb=" O ILE I 503 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU I 499 " --> pdb=" O MET I 441 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG I 498 " --> pdb=" O ILE I 543 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE I 545 " --> pdb=" O ARG I 498 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LYS I 500 " --> pdb=" O ILE I 545 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ALA I 547 " --> pdb=" O LYS I 500 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ARG I 502 " --> pdb=" O ALA I 547 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL I 549 " --> pdb=" O ARG I 502 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN I 504 " --> pdb=" O VAL I 549 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP I 546 " --> pdb=" O ASP I 531 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP I 531 " --> pdb=" O ASP I 546 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS I 548 " --> pdb=" O ILE I 529 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE I 529 " --> pdb=" O LYS I 548 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL I 550 " --> pdb=" O LEU I 527 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU I 527 " --> pdb=" O VAL I 550 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 455 through 456 removed outlier: 5.818A pdb=" N LYS I 462 " --> pdb=" O ASP I 456 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'I' and resid 485 through 487 Processing sheet with id=AI4, first strand: chain 'I' and resid 583 through 586 removed outlier: 3.535A pdb=" N THR I 584 " --> pdb=" O PHE I 629 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE I 631 " --> pdb=" O THR I 584 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 83 through 84 removed outlier: 4.154A pdb=" N VAL J 128 " --> pdb=" O LYS J 122 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS J 122 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL J 130 " --> pdb=" O TYR J 120 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR J 120 " --> pdb=" O VAL J 130 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 103 through 105 Processing sheet with id=AI7, first strand: chain 'J' and resid 436 through 441 removed outlier: 4.454A pdb=" N LEU J 437 " --> pdb=" O ILE J 503 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE J 503 " --> pdb=" O LEU J 437 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU J 499 " --> pdb=" O MET J 441 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS J 500 " --> pdb=" O ILE J 545 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA J 547 " --> pdb=" O LYS J 500 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ARG J 502 " --> pdb=" O ALA J 547 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL J 549 " --> pdb=" O ARG J 502 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN J 504 " --> pdb=" O VAL J 549 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS J 540 " --> pdb=" O LYS J 536 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS J 536 " --> pdb=" O LYS J 540 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR J 542 " --> pdb=" O ILE J 534 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE J 534 " --> pdb=" O TYR J 542 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ARG J 544 " --> pdb=" O VAL J 532 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL J 532 " --> pdb=" O ARG J 544 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ASP J 546 " --> pdb=" O LYS J 530 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'J' and resid 455 through 456 removed outlier: 5.923A pdb=" N LYS J 462 " --> pdb=" O ASP J 456 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'J' and resid 485 through 487 Processing sheet with id=AJ1, first strand: chain 'J' and resid 583 through 586 removed outlier: 3.813A pdb=" N THR J 584 " --> pdb=" O PHE J 629 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE J 631 " --> pdb=" O THR J 584 " (cutoff:3.500A) 1590 hydrogen bonds defined for protein. 4329 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: 10.00 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.47: 24694 1.47 - 1.85: 18171 1.85 - 2.23: 0 2.23 - 2.61: 0 2.61 - 2.98: 2 Bond restraints: 42867 Sorted by residual: bond pdb=" C SER D 301 " pdb=" N GLY D 323 " ideal model delta sigma weight residual 1.331 2.985 -1.654 1.46e-02 4.69e+03 1.28e+04 bond pdb=" C SER G 301 " pdb=" N GLY G 323 " ideal model delta sigma weight residual 1.331 2.984 -1.654 1.46e-02 4.69e+03 1.28e+04 bond pdb=" C THR C 517 " pdb=" N LYS C 518 " ideal model delta sigma weight residual 1.340 1.091 0.249 5.87e-02 2.90e+02 1.80e+01 bond pdb=" C THR G 517 " pdb=" N LYS G 518 " ideal model delta sigma weight residual 1.340 1.096 0.244 5.87e-02 2.90e+02 1.73e+01 bond pdb=" C THR B 517 " pdb=" N LYS B 518 " ideal model delta sigma weight residual 1.340 1.106 0.234 5.87e-02 2.90e+02 1.59e+01 ... (remaining 42862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.80: 58368 9.80 - 19.61: 80 19.61 - 29.41: 4 29.41 - 39.22: 0 39.22 - 49.02: 2 Bond angle restraints: 58454 Sorted by residual: angle pdb=" O SER D 301 " pdb=" C SER D 301 " pdb=" N GLY D 323 " ideal model delta sigma weight residual 121.74 72.72 49.02 1.31e+00 5.83e-01 1.40e+03 angle pdb=" O SER G 301 " pdb=" C SER G 301 " pdb=" N GLY G 323 " ideal model delta sigma weight residual 121.74 81.39 40.35 1.31e+00 5.83e-01 9.49e+02 angle pdb=" C SER D 301 " pdb=" N GLY D 323 " pdb=" CA GLY D 323 " ideal model delta sigma weight residual 121.41 101.61 19.80 1.96e+00 2.60e-01 1.02e+02 angle pdb=" C SER G 301 " pdb=" N GLY G 323 " pdb=" CA GLY G 323 " ideal model delta sigma weight residual 121.41 105.49 15.92 1.96e+00 2.60e-01 6.60e+01 angle pdb=" CA LEU H 582 " pdb=" CB LEU H 582 " pdb=" CG LEU H 582 " ideal model delta sigma weight residual 116.30 139.48 -23.18 3.50e+00 8.16e-02 4.39e+01 ... (remaining 58449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 24201 17.98 - 35.97: 1473 35.97 - 53.95: 175 53.95 - 71.93: 43 71.93 - 89.92: 19 Dihedral angle restraints: 25911 sinusoidal: 8929 harmonic: 16982 Sorted by residual: dihedral pdb=" CA GLN H 165 " pdb=" C GLN H 165 " pdb=" N PRO H 166 " pdb=" CA PRO H 166 " ideal model delta harmonic sigma weight residual 0.00 34.96 -34.96 0 5.00e+00 4.00e-02 4.89e+01 dihedral pdb=" CA LYS D 197 " pdb=" C LYS D 197 " pdb=" N ASN D 198 " pdb=" CA ASN D 198 " ideal model delta harmonic sigma weight residual -180.00 -151.76 -28.24 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA LYS E 197 " pdb=" C LYS E 197 " pdb=" N ASN E 198 " pdb=" CA ASN E 198 " ideal model delta harmonic sigma weight residual 180.00 -152.36 -27.64 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 25908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 6058 0.099 - 0.199: 767 0.199 - 0.298: 68 0.298 - 0.397: 5 0.397 - 0.497: 1 Chirality restraints: 6899 Sorted by residual: chirality pdb=" CB VAL D 175 " pdb=" CA VAL D 175 " pdb=" CG1 VAL D 175 " pdb=" CG2 VAL D 175 " both_signs ideal model delta sigma weight residual False -2.63 -2.13 -0.50 2.00e-01 2.50e+01 6.16e+00 chirality pdb=" CA ARG F 252 " pdb=" N ARG F 252 " pdb=" C ARG F 252 " pdb=" CB ARG F 252 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CB ILE B 432 " pdb=" CA ILE B 432 " pdb=" CG1 ILE B 432 " pdb=" CG2 ILE B 432 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 6896 not shown) Planarity restraints: 7709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 301 " 0.191 2.00e-02 2.50e+03 2.55e-01 6.52e+02 pdb=" C SER D 301 " -0.428 2.00e-02 2.50e+03 pdb=" O SER D 301 " 0.198 2.00e-02 2.50e+03 pdb=" N GLY D 323 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 301 " -0.174 2.00e-02 2.50e+03 2.36e-01 5.59e+02 pdb=" C SER G 301 " 0.399 2.00e-02 2.50e+03 pdb=" O SER G 301 " -0.180 2.00e-02 2.50e+03 pdb=" N GLY G 323 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN I 384 " -0.093 5.00e-02 4.00e+02 1.39e-01 3.09e+01 pdb=" N PRO I 385 " 0.240 5.00e-02 4.00e+02 pdb=" CA PRO I 385 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO I 385 " -0.072 5.00e-02 4.00e+02 ... (remaining 7706 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 482 2.50 - 3.10: 37707 3.10 - 3.70: 64892 3.70 - 4.30: 89173 4.30 - 4.90: 137378 Nonbonded interactions: 329632 Sorted by model distance: nonbonded pdb=" OD1 ASP A 265 " pdb=" OG1 THR A 295 " model vdw 1.897 3.040 nonbonded pdb=" O ILE A 210 " pdb=" NZ LYS A 214 " model vdw 1.946 3.120 nonbonded pdb=" OG SER C 234 " pdb=" OE1 GLU C 237 " model vdw 1.959 3.040 nonbonded pdb=" OG1 THR B 522 " pdb=" OE1 GLU B 525 " model vdw 1.983 3.040 nonbonded pdb=" OG SER C 248 " pdb=" OE1 GLU C 250 " model vdw 2.020 3.040 ... (remaining 329627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 174 through 734) selection = (chain 'B' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) selection = (chain 'C' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) selection = (chain 'D' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) selection = (chain 'E' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) selection = (chain 'F' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) selection = (chain 'G' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) } ncs_group { reference = (chain 'H' and ((resid 55 through 56 and (name N or name CA or name C or name O \ or name CB )) or resid 57 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 72 or (resid 73 and (name N or na \ me CA or name C or name O or name CB )) or resid 74 through 79 or (resid 80 and \ (name N or name CA or name C or name O or name CB )) or resid 81 through 86 or ( \ resid 87 through 90 and (name N or name CA or name C or name O or name CB )) or \ resid 91 through 94 or (resid 95 through 96 and (name N or name CA or name C or \ name O or name CB )) or resid 97 or (resid 98 through 103 and (name N or name CA \ or name C or name O or name CB )) or resid 104 or (resid 105 through 106 and (n \ ame N or name CA or name C or name O or name CB )) or resid 107 through 110 or ( \ resid 111 through 113 and (name N or name CA or name C or name O or name CB )) o \ r resid 114 through 119 or (resid 120 through 121 and (name N or name CA or name \ C or name O or name CB )) or resid 122 or (resid 123 and (name N or name CA or \ name C or name O or name CB )) or resid 124 or (resid 125 through 126 and (name \ N or name CA or name C or name O or name CB )) or resid 127 through 161 or (resi \ d 162 and (name N or name CA or name C or name O or name CB )) or resid 163 or ( \ resid 164 through 165 and (name N or name CA or name C or name O or name CB )) o \ r resid 166 through 167 or (resid 168 through 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 192 or (resid 193 and (name N or \ name CA or name C or name O or name CB )) or resid 194 or (resid 195 and (name \ N or name CA or name C or name O or name CB )) or resid 196 through 249 or (resi \ d 250 through 251 and (name N or name CA or name C or name O or name CB )) or re \ sid 252 through 262 or (resid 263 through 270 and (name N or name CA or name C o \ r name O or name CB )) or resid 271 through 272 or (resid 273 through 276 and (n \ ame N or name CA or name C or name O or name CB )) or resid 277 through 279 or ( \ resid 280 and (name N or name CA or name C or name O or name CB )) or resid 281 \ through 283 or (resid 284 through 288 and (name N or name CA or name C or name O \ or name CB )) or resid 289 or (resid 290 and (name N or name CA or name C or na \ me O or name CB )) or (resid 291 through 301 and (name N or name CA or name C or \ name O or name CB )) or (resid 309 through 320 and (name N or name CA or name C \ or name O or name CB )) or (resid 332 through 338 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 369 through 384 and (name N or name CA or \ name C or name O or name CB )) or resid 385 through 387 or (resid 388 through 39 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 392 or (resi \ d 393 through 395 and (name N or name CA or name C or name O or name CB )) or re \ sid 396 through 397 or (resid 405 through 407 and (name N or name CA or name C o \ r name O or name CB )) or resid 408 or (resid 409 through 414 and (name N or nam \ e CA or name C or name O or name CB )) or resid 415 or (resid 416 through 417 an \ d (name N or name CA or name C or name O or name CB )) or resid 418 through 419 \ or (resid 420 through 427 and (name N or name CA or name C or name O or name CB \ )) or resid 428 or (resid 433 through 436 and (name N or name CA or name C or na \ me O or name CB )) or resid 437 through 445 or (resid 446 through 450 and (name \ N or name CA or name C or name O or name CB )) or (resid 451 through 453 and (na \ me N or name CA or name C or name O or name CB )) or resid 454 through 456 or (r \ esid 457 through 459 and (name N or name CA or name C or name O or name CB )) or \ resid 460 through 461 or (resid 462 and (name N or name CA or name C or name O \ or name CB )) or resid 463 or (resid 464 through 465 and (name N or name CA or n \ ame C or name O or name CB )) or resid 466 through 471 or (resid 472 through 473 \ and (name N or name CA or name C or name O or name CB )) or resid 474 or (resid \ 475 through 476 and (name N or name CA or name C or name O or name CB )) or res \ id 477 through 478 or (resid 479 through 480 and (name N or name CA or name C or \ name O or name CB )) or resid 481 through 482 or (resid 483 through 487 and (na \ me N or name CA or name C or name O or name CB )) or resid 488 or (resid 489 thr \ ough 491 and (name N or name CA or name C or name O or name CB )) or resid 492 t \ hrough 494 or (resid 495 through 498 and (name N or name CA or name C or name O \ or name CB )) or resid 499 through 500 or (resid 501 through 502 and (name N or \ name CA or name C or name O or name CB )) or resid 503 through 508 or (resid 509 \ through 511 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 12 through 513 or (resid 514 through 516 and (name N or name CA or name C or nam \ e O or name CB )) or resid 517 or (resid 518 through 525 and (name N or name CA \ or name C or name O or name CB )) or resid 526 or (resid 527 through 533 and (na \ me N or name CA or name C or name O or name CB )) or resid 534 through 536 or (r \ esid 537 and (name N or name CA or name C or name O or name CB )) or resid 538 o \ r (resid 539 through 543 and (name N or name CA or name C or name O or name CB ) \ ) or resid 544 through 547 or (resid 548 and (name N or name CA or name C or nam \ e O or name CB )) or resid 549 or (resid 550 and (name N or name CA or name C or \ name O or name CB )) or resid 551 through 557 or (resid 558 and (name N or name \ CA or name C or name O or name CB )) or resid 559 through 560 or (resid 561 thr \ ough 563 and (name N or name CA or name C or name O or name CB )) or resid 564 o \ r (resid 565 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 66 or (resid 567 through 569 and (name N or name CA or name C or name O or name \ CB )) or resid 570 or (resid 571 through 574 and (name N or name CA or name C or \ name O or name CB )) or resid 575 through 577 or (resid 578 through 579 and (na \ me N or name CA or name C or name O or name CB )) or resid 580 or (resid 581 thr \ ough 582 and (name N or name CA or name C or name O or name CB )) or resid 583 t \ hrough 584 or (resid 585 and (name N or name CA or name C or name O or name CB ) \ ) or resid 586 through 590 or (resid 591 through 592 and (name N or name CA or n \ ame C or name O or name CB )) or resid 593 through 596 or (resid 597 and (name N \ or name CA or name C or name O or name CB )) or resid 598 through 601 or (resid \ 602 through 604 and (name N or name CA or name C or name O or name CB )) or res \ id 605 or (resid 606 through 614 and (name N or name CA or name C or name O or n \ ame CB )) or resid 615 or (resid 616 through 617 and (name N or name CA or name \ C or name O or name CB )) or resid 618 or (resid 619 through 624 and (name N or \ name CA or name C or name O or name CB )) or resid 625 or (resid 626 and (name N \ or name CA or name C or name O or name CB )) or resid 627 or (resid 628 and (na \ me N or name CA or name C or name O or name CB )) or resid 629 through 630 or (r \ esid 631 through 636 and (name N or name CA or name C or name O or name CB )) or \ resid 637 or (resid 638 through 656 and (name N or name CA or name C or name O \ or name CB )) or resid 657 or (resid 658 through 669 and (name N or name CA or n \ ame C or name O or name CB )) or resid 670 or (resid 671 through 673 and (name N \ or name CA or name C or name O or name CB )) or resid 674 or (resid 675 through \ 682 and (name N or name CA or name C or name O or name CB )) or resid 683 or (r \ esid 684 through 688 and (name N or name CA or name C or name O or name CB )) or \ resid 689 or (resid 690 through 696 and (name N or name CA or name C or name O \ or name CB )) or resid 697 or (resid 698 through 710 and (name N or name CA or n \ ame C or name O or name CB )) or resid 711 through 714 or (resid 715 through 721 \ and (name N or name CA or name C or name O or name CB )) or resid 722 or (resid \ 723 through 728 and (name N or name CA or name C or name O or name CB )) or res \ id 729 or (resid 730 through 759 and (name N or name CA or name C or name O or n \ ame CB )) or resid 760 or (resid 761 through 763 and (name N or name CA or name \ C or name O or name CB )) or resid 764 through 765 or (resid 766 through 767 and \ (name N or name CA or name C or name O or name CB )) or resid 768 or (resid 769 \ through 770 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 71 or (resid 772 and (name N or name CA or name C or name O or name CB )) or res \ id 773)) selection = (chain 'I' and ((resid 55 through 56 and (name N or name CA or name C or name O \ or name CB )) or resid 57 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 87 or (resid 88 through 90 and (n \ ame N or name CA or name C or name O or name CB )) or resid 91 through 110 or (r \ esid 111 through 113 and (name N or name CA or name C or name O or name CB )) or \ resid 114 through 115 or (resid 116 and (name N or name CA or name C or name O \ or name CB )) or resid 117 through 119 or (resid 120 through 121 and (name N or \ name CA or name C or name O or name CB )) or resid 122 through 161 or (resid 162 \ and (name N or name CA or name C or name O or name CB )) or resid 163 through 1 \ 67 or (resid 168 through 169 and (name N or name CA or name C or name O or name \ CB )) or resid 170 through 262 or (resid 263 through 270 and (name N or name CA \ or name C or name O or name CB )) or resid 271 or (resid 272 through 276 and (na \ me N or name CA or name C or name O or name CB )) or resid 277 or (resid 278 thr \ ough 280 and (name N or name CA or name C or name O or name CB )) or resid 281 t \ hrough 282 or (resid 283 through 288 and (name N or name CA or name C or name O \ or name CB )) or (resid 289 through 301 and (name N or name CA or name C or name \ O or name CB )) or resid 309 through 320 or resid 332 through 338 or resid 369 \ through 397 or resid 405 through 412 or (resid 413 through 414 and (name N or na \ me CA or name C or name O or name CB )) or resid 415 through 422 or (resid 423 t \ hrough 427 and (name N or name CA or name C or name O or name CB )) or resid 428 \ or resid 433 through 461 or (resid 462 and (name N or name CA or name C or name \ O or name CB )) or resid 463 or (resid 464 through 465 and (name N or name CA o \ r name C or name O or name CB )) or resid 466 through 471 or (resid 472 through \ 473 and (name N or name CA or name C or name O or name CB )) or resid 474 or (re \ sid 475 through 476 and (name N or name CA or name C or name O or name CB )) or \ resid 477 through 490 or (resid 491 and (name N or name CA or name C or name O o \ r name CB )) or resid 492 through 494 or (resid 495 through 498 and (name N or n \ ame CA or name C or name O or name CB )) or resid 499 or (resid 500 through 502 \ and (name N or name CA or name C or name O or name CB )) or resid 503 through 51 \ 5 or (resid 516 and (name N or name CA or name C or name O or name CB )) or resi \ d 517 or (resid 518 through 525 and (name N or name CA or name C or name O or na \ me CB )) or (resid 526 through 533 and (name N or name CA or name C or name O or \ name CB )) or resid 534 through 536 or (resid 537 and (name N or name CA or nam \ e C or name O or name CB )) or resid 538 or (resid 539 through 543 and (name N o \ r name CA or name C or name O or name CB )) or resid 544 through 547 or (resid 5 \ 48 and (name N or name CA or name C or name O or name CB )) or resid 549 through \ 562 or (resid 563 and (name N or name CA or name C or name O or name CB )) or r \ esid 564 through 578 or (resid 579 and (name N or name CA or name C or name O or \ name CB )) or resid 580 through 590 or (resid 591 through 592 and (name N or na \ me CA or name C or name O or name CB )) or resid 593 through 596 or (resid 597 a \ nd (name N or name CA or name C or name O or name CB )) or resid 598 through 606 \ or (resid 607 through 614 and (name N or name CA or name C or name O or name CB \ )) or resid 615 through 618 or (resid 619 through 624 and (name N or name CA or \ name C or name O or name CB )) or resid 625 or (resid 626 and (name N or name C \ A or name C or name O or name CB )) or resid 627 through 683 or (resid 684 throu \ gh 688 and (name N or name CA or name C or name O or name CB )) or resid 689 thr \ ough 753 or (resid 754 through 759 and (name N or name CA or name C or name O or \ name CB )) or resid 760 through 768 or (resid 769 through 770 and (name N or na \ me CA or name C or name O or name CB )) or resid 771 or (resid 772 and (name N o \ r name CA or name C or name O or name CB )) or resid 773)) selection = (chain 'J' and (resid 55 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 87 or (resid 88 through 90 and (na \ me N or name CA or name C or name O or name CB )) or resid 91 through 115 or (re \ sid 116 and (name N or name CA or name C or name O or name CB )) or resid 117 th \ rough 124 or (resid 125 through 126 and (name N or name CA or name C or name O o \ r name CB )) or resid 127 through 192 or (resid 193 and (name N or name CA or na \ me C or name O or name CB )) or resid 194 through 249 or (resid 250 through 251 \ and (name N or name CA or name C or name O or name CB )) or resid 252 through 27 \ 3 or (resid 274 through 276 and (name N or name CA or name C or name O or name C \ B )) or resid 277 or (resid 278 through 280 and (name N or name CA or name C or \ name O or name CB )) or resid 281 through 337 or (resid 338 and (name N or name \ CA or name C or name O or name CB )) or resid 369 through 389 or (resid 390 thro \ ugh 391 and (name N or name CA or name C or name O or name CB )) or resid 392 th \ rough 393 or (resid 394 through 395 and (name N or name CA or name C or name O o \ r name CB )) or resid 396 through 397 or (resid 405 through 407 and (name N or n \ ame CA or name C or name O or name CB )) or resid 408 through 410 or (resid 411 \ through 414 and (name N or name CA or name C or name O or name CB )) or resid 41 \ 5 through 423 or (resid 424 through 427 and (name N or name CA or name C or name \ O or name CB )) or resid 428 or (resid 433 through 436 and (name N or name CA o \ r name C or name O or name CB )) or resid 437 through 501 or (resid 502 and (nam \ e N or name CA or name C or name O or name CB )) or resid 503 through 518 or (re \ sid 519 through 525 and (name N or name CA or name C or name O or name CB )) or \ resid 526 through 581 or (resid 582 and (name N or name CA or name C or name O o \ r name CB )) or resid 583 through 663 or (resid 664 through 669 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 670 through 696 and (name N o \ r name CA or name C or name O or name CB )) or resid 697 through 746 or (resid 7 \ 47 through 759 and (name N or name CA or name C or name O or name CB )) or resid \ 760 through 769 or (resid 770 and (name N or name CA or name C or name O or nam \ e CB )) or resid 771 through 773)) } 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: 3.250 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: 0.050 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 38.950 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 : 0.017 1.654 42867 Z= 0.964 Angle : 1.383 49.025 58454 Z= 0.762 Chirality : 0.066 0.497 6899 Planarity : 0.009 0.255 7709 Dihedral : 11.909 89.916 14873 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 32.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.03 % Favored : 91.62 % Rotamer: Outliers : 0.10 % Allowed : 0.52 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.10), residues: 5704 helix: -1.84 (0.12), residues: 1499 sheet: -0.98 (0.16), residues: 901 loop : -2.19 (0.09), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 297 TYR 0.069 0.004 TYR I 167 PHE 0.070 0.005 PHE B 531 TRP 0.089 0.005 TRP I 501 HIS 0.032 0.004 HIS D 299 Details of bonding type rmsd covalent geometry : bond 0.01685 (42867) covalent geometry : angle 1.38266 (58454) hydrogen bonds : bond 0.28626 ( 1503) hydrogen bonds : angle 9.99719 ( 4329) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 954 time to evaluate : 1.506 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.9031 (p0) cc_final: 0.8784 (p0) REVERT: A 225 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8466 (ttpt) REVERT: A 247 VAL cc_start: 0.9558 (t) cc_final: 0.9193 (p) REVERT: A 368 ASN cc_start: 0.8560 (t0) cc_final: 0.8359 (t0) REVERT: A 383 LEU cc_start: 0.8667 (tp) cc_final: 0.8231 (tt) REVERT: A 391 LEU cc_start: 0.9383 (mm) cc_final: 0.9130 (mm) REVERT: A 415 ASN cc_start: 0.8766 (m110) cc_final: 0.8436 (m110) REVERT: A 450 LEU cc_start: 0.8791 (mt) cc_final: 0.8046 (mp) REVERT: A 462 TYR cc_start: 0.8031 (t80) cc_final: 0.7721 (t80) REVERT: A 465 GLU cc_start: 0.8582 (mp0) cc_final: 0.8129 (pp20) REVERT: A 512 ASP cc_start: 0.8314 (t0) cc_final: 0.8069 (t0) REVERT: A 583 LEU cc_start: 0.9524 (mt) cc_final: 0.9104 (mt) REVERT: A 584 ASN cc_start: 0.9055 (m110) cc_final: 0.8656 (t0) REVERT: A 727 PHE cc_start: 0.8783 (t80) cc_final: 0.8393 (t80) REVERT: B 192 TYR cc_start: 0.9165 (p90) cc_final: 0.8093 (p90) REVERT: B 262 VAL cc_start: 0.9462 (t) cc_final: 0.9115 (p) REVERT: B 293 THR cc_start: 0.8054 (p) cc_final: 0.7454 (p) REVERT: B 328 ASN cc_start: 0.8161 (t0) cc_final: 0.7673 (t0) REVERT: B 368 ASN cc_start: 0.9049 (t0) cc_final: 0.8844 (t0) REVERT: B 404 ILE cc_start: 0.9313 (mm) cc_final: 0.8811 (mp) REVERT: B 437 ASN cc_start: 0.9265 (m110) cc_final: 0.8799 (t0) REVERT: B 439 PHE cc_start: 0.9431 (t80) cc_final: 0.9139 (t80) REVERT: B 486 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8474 (tm-30) REVERT: B 524 LYS cc_start: 0.9282 (tmtt) cc_final: 0.8938 (tptp) REVERT: B 561 ASN cc_start: 0.8964 (m110) cc_final: 0.8600 (m110) REVERT: B 581 ILE cc_start: 0.9211 (mt) cc_final: 0.8976 (mm) REVERT: B 590 LEU cc_start: 0.9128 (tp) cc_final: 0.8909 (tp) REVERT: B 616 HIS cc_start: 0.9177 (m90) cc_final: 0.8889 (m90) REVERT: B 705 ASN cc_start: 0.9170 (m-40) cc_final: 0.8639 (p0) REVERT: B 726 ILE cc_start: 0.8739 (mm) cc_final: 0.8526 (mm) REVERT: B 727 PHE cc_start: 0.8112 (t80) cc_final: 0.7525 (t80) REVERT: C 326 ASN cc_start: 0.8025 (p0) cc_final: 0.7622 (p0) REVERT: C 343 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7538 (mp0) REVERT: C 408 ASN cc_start: 0.9277 (t0) cc_final: 0.9026 (t0) REVERT: C 434 MET cc_start: 0.8812 (ppp) cc_final: 0.8516 (ppp) REVERT: C 437 ASN cc_start: 0.9324 (m110) cc_final: 0.8790 (t0) REVERT: C 439 PHE cc_start: 0.9426 (t80) cc_final: 0.9189 (t80) REVERT: C 528 LYS cc_start: 0.9227 (ttmm) cc_final: 0.8772 (mmtt) REVERT: C 552 PHE cc_start: 0.9129 (m-80) cc_final: 0.8852 (m-10) REVERT: C 583 LEU cc_start: 0.9471 (mm) cc_final: 0.9151 (mm) REVERT: C 727 PHE cc_start: 0.7601 (t80) cc_final: 0.7265 (t80) REVERT: D 292 ASN cc_start: 0.8976 (m110) cc_final: 0.8466 (t0) REVERT: D 365 ARG cc_start: 0.7221 (ttm-80) cc_final: 0.6866 (tpp-160) REVERT: D 394 ILE cc_start: 0.9309 (mm) cc_final: 0.9080 (mp) REVERT: D 439 PHE cc_start: 0.9458 (t80) cc_final: 0.9256 (t80) REVERT: D 454 GLN cc_start: 0.8743 (mp10) cc_final: 0.8514 (mp10) REVERT: D 462 TYR cc_start: 0.8457 (t80) cc_final: 0.8043 (t80) REVERT: D 486 GLU cc_start: 0.8026 (tt0) cc_final: 0.7796 (tt0) REVERT: D 501 VAL cc_start: 0.9468 (t) cc_final: 0.9221 (p) REVERT: D 525 GLU cc_start: 0.8838 (tp30) cc_final: 0.8186 (tp30) REVERT: D 565 GLN cc_start: 0.9460 (mm-40) cc_final: 0.9250 (mm110) REVERT: E 192 TYR cc_start: 0.9192 (p90) cc_final: 0.8848 (p90) REVERT: E 195 ASP cc_start: 0.7898 (p0) cc_final: 0.7515 (p0) REVERT: E 203 LEU cc_start: 0.8314 (tp) cc_final: 0.8020 (tp) REVERT: E 242 ARG cc_start: 0.8946 (mpp-170) cc_final: 0.8574 (mtm-85) REVERT: E 247 VAL cc_start: 0.9445 (t) cc_final: 0.9200 (p) REVERT: E 436 TYR cc_start: 0.8957 (t80) cc_final: 0.8602 (t80) REVERT: E 472 ASP cc_start: 0.8954 (t0) cc_final: 0.8586 (t0) REVERT: E 486 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8294 (tp30) REVERT: E 509 ASN cc_start: 0.8904 (t0) cc_final: 0.8676 (t0) REVERT: E 512 ASP cc_start: 0.8544 (t0) cc_final: 0.8338 (t0) REVERT: E 553 ASN cc_start: 0.8985 (m110) cc_final: 0.8664 (m-40) REVERT: E 583 LEU cc_start: 0.9109 (mt) cc_final: 0.8803 (mt) REVERT: E 616 HIS cc_start: 0.9126 (m90) cc_final: 0.8744 (p-80) REVERT: E 704 GLU cc_start: 0.9056 (pt0) cc_final: 0.8762 (pt0) REVERT: F 190 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8359 (tm-30) REVERT: F 195 ASP cc_start: 0.8715 (t0) cc_final: 0.8449 (t0) REVERT: F 226 TRP cc_start: 0.8967 (t60) cc_final: 0.8524 (t-100) REVERT: F 326 ASN cc_start: 0.7827 (m-40) cc_final: 0.7338 (m-40) REVERT: F 366 TYR cc_start: 0.8847 (m-10) cc_final: 0.8561 (m-10) REVERT: F 454 GLN cc_start: 0.8481 (mp10) cc_final: 0.8268 (mp10) REVERT: F 472 ASP cc_start: 0.9404 (t0) cc_final: 0.9154 (t0) REVERT: F 501 VAL cc_start: 0.9134 (t) cc_final: 0.8777 (p) REVERT: F 512 ASP cc_start: 0.7670 (m-30) cc_final: 0.7454 (m-30) REVERT: F 520 ASP cc_start: 0.7674 (t0) cc_final: 0.7380 (t0) REVERT: F 529 ILE cc_start: 0.9217 (mm) cc_final: 0.8914 (tp) REVERT: F 551 ASP cc_start: 0.7325 (t0) cc_final: 0.7039 (t0) REVERT: F 590 LEU cc_start: 0.8484 (mp) cc_final: 0.8063 (pp) REVERT: F 708 ILE cc_start: 0.9060 (pt) cc_final: 0.8774 (tp) REVERT: F 732 TYR cc_start: 0.8680 (p90) cc_final: 0.8208 (p90) REVERT: G 192 TYR cc_start: 0.8541 (p90) cc_final: 0.7796 (p90) REVERT: G 211 HIS cc_start: 0.9185 (m90) cc_final: 0.8847 (m90) REVERT: G 224 GLU cc_start: 0.8649 (tp30) cc_final: 0.7957 (tp30) REVERT: G 515 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8344 (tm-30) REVERT: G 516 THR cc_start: 0.8910 (m) cc_final: 0.8342 (p) REVERT: G 518 LYS cc_start: 0.9452 (pttt) cc_final: 0.9102 (pttp) REVERT: G 551 ASP cc_start: 0.8721 (t0) cc_final: 0.7246 (p0) REVERT: G 561 ASN cc_start: 0.9460 (t0) cc_final: 0.9116 (t0) REVERT: G 565 GLN cc_start: 0.8966 (mt0) cc_final: 0.8607 (mm-40) REVERT: G 629 LEU cc_start: 0.8968 (mm) cc_final: 0.8763 (mm) REVERT: H 74 TYR cc_start: 0.8294 (t80) cc_final: 0.8035 (t80) REVERT: H 120 TYR cc_start: 0.8399 (t80) cc_final: 0.8150 (t80) REVERT: H 201 PHE cc_start: 0.8716 (m-80) cc_final: 0.8177 (m-80) REVERT: H 232 VAL cc_start: 0.9296 (t) cc_final: 0.9046 (t) REVERT: H 236 TYR cc_start: 0.8249 (m-80) cc_final: 0.7919 (m-10) REVERT: H 244 MET cc_start: 0.9214 (tpt) cc_final: 0.8596 (tpp) REVERT: H 391 ARG cc_start: 0.9095 (ppt170) cc_final: 0.8607 (tmm-80) REVERT: H 441 MET cc_start: 0.8615 (tmm) cc_final: 0.8186 (tmm) REVERT: H 484 MET cc_start: 0.8102 (mpp) cc_final: 0.7627 (mpp) REVERT: H 486 VAL cc_start: 0.9100 (m) cc_final: 0.8830 (p) REVERT: H 499 LEU cc_start: 0.8857 (mp) cc_final: 0.8142 (mp) REVERT: H 521 LEU cc_start: 0.9631 (mm) cc_final: 0.9287 (mm) REVERT: H 584 THR cc_start: 0.8132 (t) cc_final: 0.7396 (p) REVERT: H 611 GLN cc_start: 0.7989 (tp-100) cc_final: 0.7785 (tp40) REVERT: H 628 ARG cc_start: 0.8323 (mtm-85) cc_final: 0.7690 (mtm-85) REVERT: H 631 PHE cc_start: 0.9399 (m-80) cc_final: 0.9006 (m-80) REVERT: H 693 ASP cc_start: 0.9025 (t70) cc_final: 0.8772 (t0) REVERT: H 736 PHE cc_start: 0.8544 (t80) cc_final: 0.8074 (t80) REVERT: H 737 PHE cc_start: 0.8984 (m-80) cc_final: 0.8387 (m-80) REVERT: H 741 PHE cc_start: 0.9653 (t80) cc_final: 0.9292 (t80) REVERT: H 745 HIS cc_start: 0.9053 (m90) cc_final: 0.8575 (m90) REVERT: I 35 HIS cc_start: 0.7970 (m90) cc_final: 0.7726 (m90) REVERT: I 150 GLU cc_start: 0.9574 (mm-30) cc_final: 0.9371 (mm-30) REVERT: I 158 ASP cc_start: 0.8897 (m-30) cc_final: 0.8548 (m-30) REVERT: I 182 ASP cc_start: 0.8871 (t0) cc_final: 0.8524 (p0) REVERT: I 205 PHE cc_start: 0.8439 (m-80) cc_final: 0.8167 (m-80) REVERT: I 215 GLU cc_start: 0.8683 (mp0) cc_final: 0.8377 (pm20) REVERT: I 247 PHE cc_start: 0.9637 (t80) cc_final: 0.9345 (t80) REVERT: J 217 PHE cc_start: 0.9203 (t80) cc_final: 0.8741 (t80) REVERT: J 221 PHE cc_start: 0.8963 (t80) cc_final: 0.8220 (t80) REVERT: J 277 HIS cc_start: 0.9149 (t-90) cc_final: 0.8923 (t-90) REVERT: J 436 TYR cc_start: 0.6982 (m-10) cc_final: 0.6509 (m-80) REVERT: J 544 ARG cc_start: 0.4630 (mmp80) cc_final: 0.4344 (mmp80) outliers start: 4 outliers final: 2 residues processed: 956 average time/residue: 0.2382 time to fit residues: 369.3666 Evaluate side-chains 784 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 782 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 394 optimal weight: 0.3980 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 30.0000 chunk 414 optimal weight: 0.0010 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 0.5980 chunk 223 optimal weight: 2.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 602 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 GLN B 588 ASN B 602 ASN C 573 ASN C 602 ASN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN E 483 GLN E 602 ASN F 458 ASN G 263 HIS ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 602 ASN G 616 HIS ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 516 ASN ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 690 HIS ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 469 ASN J 117 HIS J 228 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.160493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.100880 restraints weight = 98540.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.106534 restraints weight = 54750.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108145 restraints weight = 31591.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.109826 restraints weight = 23806.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.110124 restraints weight = 20873.465| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 42867 Z= 0.159 Angle : 0.709 13.022 58454 Z= 0.374 Chirality : 0.047 0.238 6899 Planarity : 0.005 0.075 7709 Dihedral : 4.983 31.886 6111 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.92 % Favored : 96.01 % Rotamer: Outliers : 0.27 % Allowed : 4.44 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.11), residues: 5708 helix: -0.59 (0.12), residues: 1648 sheet: -0.76 (0.15), residues: 1015 loop : -1.21 (0.11), residues: 3045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 449 TYR 0.027 0.002 TYR D 542 PHE 0.026 0.002 PHE I 765 TRP 0.031 0.002 TRP I 501 HIS 0.007 0.001 HIS C 616 Details of bonding type rmsd covalent geometry : bond 0.00344 (42867) covalent geometry : angle 0.70852 (58454) hydrogen bonds : bond 0.05134 ( 1503) hydrogen bonds : angle 6.26728 ( 4329) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 1071 time to evaluate : 1.551 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8700 (p0) cc_final: 0.8398 (p0) REVERT: A 192 TYR cc_start: 0.9002 (p90) cc_final: 0.8329 (p90) REVERT: A 222 SER cc_start: 0.9486 (t) cc_final: 0.9159 (p) REVERT: A 225 LYS cc_start: 0.8847 (ttmt) cc_final: 0.8386 (ttpt) REVERT: A 247 VAL cc_start: 0.9583 (t) cc_final: 0.9215 (p) REVERT: A 250 GLU cc_start: 0.8894 (mp0) cc_final: 0.8530 (tp30) REVERT: A 324 PHE cc_start: 0.8385 (p90) cc_final: 0.7901 (p90) REVERT: A 391 LEU cc_start: 0.9182 (mm) cc_final: 0.8875 (mm) REVERT: A 415 ASN cc_start: 0.8780 (m110) cc_final: 0.8553 (m110) REVERT: A 436 TYR cc_start: 0.9166 (t80) cc_final: 0.8840 (t80) REVERT: A 447 GLN cc_start: 0.8914 (tt0) cc_final: 0.8686 (mm110) REVERT: A 462 TYR cc_start: 0.8119 (t80) cc_final: 0.7835 (t80) REVERT: A 465 GLU cc_start: 0.8662 (mp0) cc_final: 0.8382 (mp0) REVERT: A 485 GLN cc_start: 0.8983 (pm20) cc_final: 0.8726 (pm20) REVERT: A 492 ILE cc_start: 0.9528 (mm) cc_final: 0.9286 (tp) REVERT: A 496 LYS cc_start: 0.9474 (mmtt) cc_final: 0.9171 (mmtt) REVERT: A 512 ASP cc_start: 0.7805 (t0) cc_final: 0.7572 (t0) REVERT: A 525 GLU cc_start: 0.9345 (mp0) cc_final: 0.9066 (pp20) REVERT: A 551 ASP cc_start: 0.8458 (t0) cc_final: 0.7213 (p0) REVERT: A 568 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8711 (pm20) REVERT: A 569 LEU cc_start: 0.9424 (mm) cc_final: 0.9015 (mm) REVERT: A 584 ASN cc_start: 0.9045 (m110) cc_final: 0.8665 (t0) REVERT: A 602 ASN cc_start: 0.8974 (m-40) cc_final: 0.8638 (m110) REVERT: A 727 PHE cc_start: 0.8856 (t80) cc_final: 0.8519 (t80) REVERT: B 192 TYR cc_start: 0.9370 (p90) cc_final: 0.7930 (p90) REVERT: B 219 TYR cc_start: 0.8809 (m-10) cc_final: 0.8494 (m-10) REVERT: B 220 LYS cc_start: 0.9039 (mmmt) cc_final: 0.8611 (mmmm) REVERT: B 225 LYS cc_start: 0.8856 (tttm) cc_final: 0.8656 (tttp) REVERT: B 244 ASP cc_start: 0.8704 (t70) cc_final: 0.7949 (t0) REVERT: B 246 ASN cc_start: 0.9093 (m110) cc_final: 0.8496 (m110) REVERT: B 256 VAL cc_start: 0.9332 (t) cc_final: 0.9073 (p) REVERT: B 328 ASN cc_start: 0.8001 (t0) cc_final: 0.7542 (t0) REVERT: B 368 ASN cc_start: 0.9338 (t0) cc_final: 0.8997 (t0) REVERT: B 378 LEU cc_start: 0.9181 (tp) cc_final: 0.8517 (tt) REVERT: B 439 PHE cc_start: 0.9287 (t80) cc_final: 0.9011 (t80) REVERT: B 486 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8525 (tm-30) REVERT: B 502 GLU cc_start: 0.7460 (tm-30) cc_final: 0.6074 (tm-30) REVERT: B 509 ASN cc_start: 0.8532 (t0) cc_final: 0.8208 (t0) REVERT: B 515 GLU cc_start: 0.8654 (tp30) cc_final: 0.8306 (tp30) REVERT: B 550 PHE cc_start: 0.8916 (m-80) cc_final: 0.8132 (m-80) REVERT: B 561 ASN cc_start: 0.8947 (m110) cc_final: 0.8653 (m110) REVERT: B 581 ILE cc_start: 0.9013 (mt) cc_final: 0.8709 (mm) REVERT: B 583 LEU cc_start: 0.9129 (mp) cc_final: 0.8822 (mp) REVERT: B 705 ASN cc_start: 0.9050 (m-40) cc_final: 0.8663 (p0) REVERT: B 721 ILE cc_start: 0.8596 (mm) cc_final: 0.8372 (mm) REVERT: B 727 PHE cc_start: 0.8319 (t80) cc_final: 0.7896 (t80) REVERT: C 224 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8096 (mp0) REVERT: C 225 LYS cc_start: 0.9004 (tptm) cc_final: 0.8742 (tptm) REVERT: C 231 ASP cc_start: 0.8722 (p0) cc_final: 0.8508 (p0) REVERT: C 243 ILE cc_start: 0.9345 (tp) cc_final: 0.9138 (pt) REVERT: C 244 ASP cc_start: 0.8992 (t0) cc_final: 0.8112 (t70) REVERT: C 297 ARG cc_start: 0.8652 (tpt170) cc_final: 0.8258 (tpt170) REVERT: C 326 ASN cc_start: 0.8222 (p0) cc_final: 0.7610 (p0) REVERT: C 368 ASN cc_start: 0.8720 (t0) cc_final: 0.8510 (t0) REVERT: C 408 ASN cc_start: 0.9164 (t0) cc_final: 0.8962 (t0) REVERT: C 434 MET cc_start: 0.8998 (ppp) cc_final: 0.8714 (ppp) REVERT: C 439 PHE cc_start: 0.9373 (t80) cc_final: 0.8989 (t80) REVERT: C 462 TYR cc_start: 0.9098 (t80) cc_final: 0.8780 (t80) REVERT: C 486 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8596 (tm-30) REVERT: C 487 THR cc_start: 0.9012 (p) cc_final: 0.8736 (p) REVERT: C 550 PHE cc_start: 0.9522 (m-80) cc_final: 0.9314 (m-80) REVERT: C 552 PHE cc_start: 0.8865 (m-80) cc_final: 0.8516 (m-10) REVERT: C 553 ASN cc_start: 0.8730 (t0) cc_final: 0.8366 (t0) REVERT: C 578 LEU cc_start: 0.9534 (pp) cc_final: 0.9333 (pp) REVERT: C 590 LEU cc_start: 0.9407 (tt) cc_final: 0.9057 (tt) REVERT: C 596 PHE cc_start: 0.8916 (m-80) cc_final: 0.8648 (m-10) REVERT: C 636 ARG cc_start: 0.8830 (ptt-90) cc_final: 0.8427 (ptt-90) REVERT: C 727 PHE cc_start: 0.7846 (t80) cc_final: 0.7385 (t80) REVERT: D 195 ASP cc_start: 0.8417 (t0) cc_final: 0.8011 (t0) REVERT: D 252 ARG cc_start: 0.8356 (mtt90) cc_final: 0.8062 (mtt90) REVERT: D 360 LEU cc_start: 0.9226 (tp) cc_final: 0.8681 (tp) REVERT: D 365 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.6970 (tpp-160) REVERT: D 408 ASN cc_start: 0.9156 (t0) cc_final: 0.8915 (t0) REVERT: D 411 TYR cc_start: 0.8024 (t80) cc_final: 0.7811 (t80) REVERT: D 415 ASN cc_start: 0.8773 (m110) cc_final: 0.8333 (p0) REVERT: D 432 ILE cc_start: 0.8348 (mp) cc_final: 0.7234 (mp) REVERT: D 439 PHE cc_start: 0.9447 (t80) cc_final: 0.9120 (t80) REVERT: D 447 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7590 (tm-30) REVERT: D 462 TYR cc_start: 0.8399 (t80) cc_final: 0.7944 (t80) REVERT: D 490 ARG cc_start: 0.6994 (ttm170) cc_final: 0.6645 (ttp-170) REVERT: D 501 VAL cc_start: 0.9304 (t) cc_final: 0.8994 (p) REVERT: D 533 PHE cc_start: 0.8521 (m-10) cc_final: 0.7888 (m-10) REVERT: D 542 TYR cc_start: 0.9133 (t80) cc_final: 0.8849 (t80) REVERT: E 216 LEU cc_start: 0.9047 (mt) cc_final: 0.8750 (mt) REVERT: E 225 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8674 (mtpp) REVERT: E 247 VAL cc_start: 0.9411 (t) cc_final: 0.9176 (p) REVERT: E 436 TYR cc_start: 0.8891 (t80) cc_final: 0.8286 (t80) REVERT: E 472 ASP cc_start: 0.8850 (t0) cc_final: 0.8489 (t0) REVERT: E 475 SER cc_start: 0.8793 (m) cc_final: 0.8354 (p) REVERT: E 494 ASN cc_start: 0.8094 (p0) cc_final: 0.7837 (m-40) REVERT: E 509 ASN cc_start: 0.9016 (t0) cc_final: 0.8763 (t0) REVERT: E 512 ASP cc_start: 0.8054 (t0) cc_final: 0.6754 (t0) REVERT: E 525 GLU cc_start: 0.8770 (pt0) cc_final: 0.8196 (pt0) REVERT: E 553 ASN cc_start: 0.8397 (m110) cc_final: 0.8009 (m-40) REVERT: E 575 TYR cc_start: 0.8343 (m-80) cc_final: 0.7245 (m-80) REVERT: E 616 HIS cc_start: 0.8962 (m90) cc_final: 0.8621 (p-80) REVERT: F 190 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8265 (tm-30) REVERT: F 223 PRO cc_start: 0.9414 (Cg_endo) cc_final: 0.9155 (Cg_exo) REVERT: F 226 TRP cc_start: 0.8930 (t60) cc_final: 0.8624 (t60) REVERT: F 245 LYS cc_start: 0.9113 (mmmm) cc_final: 0.8895 (mmmm) REVERT: F 261 ILE cc_start: 0.9667 (mm) cc_final: 0.9458 (tp) REVERT: F 265 ASP cc_start: 0.8922 (t0) cc_final: 0.8346 (p0) REVERT: F 326 ASN cc_start: 0.7878 (m-40) cc_final: 0.7230 (m-40) REVERT: F 332 VAL cc_start: 0.8041 (p) cc_final: 0.7759 (p) REVERT: F 439 PHE cc_start: 0.9540 (t80) cc_final: 0.9305 (t80) REVERT: F 442 LEU cc_start: 0.9759 (tt) cc_final: 0.9529 (pp) REVERT: F 459 ILE cc_start: 0.8975 (mt) cc_final: 0.8774 (tp) REVERT: F 462 TYR cc_start: 0.7517 (t80) cc_final: 0.7152 (t80) REVERT: F 471 VAL cc_start: 0.8177 (m) cc_final: 0.7357 (t) REVERT: F 501 VAL cc_start: 0.8945 (t) cc_final: 0.8620 (p) REVERT: F 525 GLU cc_start: 0.9458 (mm-30) cc_final: 0.9230 (pt0) REVERT: F 551 ASP cc_start: 0.7081 (t0) cc_final: 0.6728 (t0) REVERT: F 708 ILE cc_start: 0.9035 (pt) cc_final: 0.8730 (tp) REVERT: F 732 TYR cc_start: 0.8673 (p90) cc_final: 0.8239 (p90) REVERT: G 224 GLU cc_start: 0.8249 (tp30) cc_final: 0.7875 (tp30) REVERT: G 325 SER cc_start: 0.8976 (t) cc_final: 0.8714 (p) REVERT: G 440 LEU cc_start: 0.9233 (mt) cc_final: 0.8915 (mt) REVERT: G 453 ASP cc_start: 0.9165 (p0) cc_final: 0.8800 (p0) REVERT: G 472 ASP cc_start: 0.8742 (t0) cc_final: 0.8307 (t0) REVERT: G 479 GLU cc_start: 0.9000 (mp0) cc_final: 0.8572 (mp0) REVERT: G 492 ILE cc_start: 0.9665 (mm) cc_final: 0.9458 (tp) REVERT: G 512 ASP cc_start: 0.8254 (t0) cc_final: 0.6696 (t0) REVERT: G 514 LEU cc_start: 0.9572 (tt) cc_final: 0.9066 (tt) REVERT: G 515 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8491 (mm-30) REVERT: G 551 ASP cc_start: 0.8701 (t0) cc_final: 0.7307 (p0) REVERT: G 560 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8406 (mp10) REVERT: G 561 ASN cc_start: 0.9459 (t0) cc_final: 0.9234 (t0) REVERT: G 602 ASN cc_start: 0.8506 (m-40) cc_final: 0.8166 (m110) REVERT: G 629 LEU cc_start: 0.8705 (mm) cc_final: 0.8369 (mm) REVERT: G 638 ILE cc_start: 0.8990 (pt) cc_final: 0.8133 (mm) REVERT: H 62 LEU cc_start: 0.9475 (mp) cc_final: 0.9189 (mt) REVERT: H 117 HIS cc_start: 0.6138 (m90) cc_final: 0.5833 (m90) REVERT: H 120 TYR cc_start: 0.8444 (t80) cc_final: 0.8000 (t80) REVERT: H 170 PHE cc_start: 0.9302 (t80) cc_final: 0.8787 (t80) REVERT: H 174 LEU cc_start: 0.9599 (mt) cc_final: 0.9339 (mt) REVERT: H 200 ASP cc_start: 0.9318 (p0) cc_final: 0.9070 (p0) REVERT: H 201 PHE cc_start: 0.8664 (m-80) cc_final: 0.8368 (m-80) REVERT: H 217 PHE cc_start: 0.8790 (t80) cc_final: 0.8262 (t80) REVERT: H 281 TRP cc_start: 0.8413 (t60) cc_final: 0.8011 (t60) REVERT: H 391 ARG cc_start: 0.9202 (ppt170) cc_final: 0.8911 (ptm-80) REVERT: H 438 TYR cc_start: 0.8386 (m-80) cc_final: 0.7879 (m-80) REVERT: H 441 MET cc_start: 0.8162 (tmm) cc_final: 0.7919 (tmm) REVERT: H 484 MET cc_start: 0.8375 (mpp) cc_final: 0.7809 (mpp) REVERT: H 486 VAL cc_start: 0.8814 (m) cc_final: 0.8554 (p) REVERT: H 499 LEU cc_start: 0.8647 (mp) cc_final: 0.7792 (mp) REVERT: H 521 LEU cc_start: 0.9535 (mm) cc_final: 0.9114 (mm) REVERT: H 527 LEU cc_start: 0.8419 (mt) cc_final: 0.7898 (mm) REVERT: H 582 LEU cc_start: 0.8943 (pp) cc_final: 0.8545 (mm) REVERT: H 591 TYR cc_start: 0.8920 (t80) cc_final: 0.8219 (t80) REVERT: H 611 GLN cc_start: 0.8139 (tp-100) cc_final: 0.7936 (tp40) REVERT: H 628 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.7959 (mtm-85) REVERT: H 736 PHE cc_start: 0.8674 (t80) cc_final: 0.8230 (t80) REVERT: H 737 PHE cc_start: 0.9037 (m-80) cc_final: 0.8582 (m-80) REVERT: H 772 PHE cc_start: 0.8830 (m-10) cc_final: 0.8481 (m-10) REVERT: I 35 HIS cc_start: 0.7861 (m90) cc_final: 0.7625 (m90) REVERT: I 72 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8408 (mp0) REVERT: I 108 TYR cc_start: 0.8348 (m-10) cc_final: 0.7971 (m-10) REVERT: I 149 TYR cc_start: 0.8944 (t80) cc_final: 0.8639 (t80) REVERT: I 172 ASP cc_start: 0.9234 (m-30) cc_final: 0.9032 (m-30) REVERT: I 182 ASP cc_start: 0.8655 (t0) cc_final: 0.8359 (p0) REVERT: I 205 PHE cc_start: 0.8316 (m-80) cc_final: 0.8028 (m-80) REVERT: I 215 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8541 (pp20) REVERT: I 230 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.7750 (tpp80) REVERT: I 267 ARG cc_start: 0.9385 (ptp90) cc_final: 0.8972 (ptt-90) REVERT: I 268 TYR cc_start: 0.8907 (t80) cc_final: 0.8509 (t80) REVERT: I 441 MET cc_start: 0.4682 (tmm) cc_final: 0.3584 (tmm) REVERT: I 597 GLU cc_start: 0.6947 (mp0) cc_final: 0.6515 (mp0) REVERT: J 170 PHE cc_start: 0.8648 (t80) cc_final: 0.8409 (t80) REVERT: J 217 PHE cc_start: 0.9173 (t80) cc_final: 0.8665 (t80) REVERT: J 221 PHE cc_start: 0.8985 (t80) cc_final: 0.8270 (t80) REVERT: J 223 TYR cc_start: 0.8490 (m-80) cc_final: 0.8161 (m-80) REVERT: J 244 MET cc_start: 0.9277 (tpt) cc_final: 0.9031 (tpp) REVERT: J 277 HIS cc_start: 0.9073 (t-90) cc_final: 0.8847 (t-90) REVERT: J 436 TYR cc_start: 0.6785 (m-10) cc_final: 0.6374 (m-80) REVERT: J 590 ARG cc_start: 0.7400 (tpm170) cc_final: 0.7098 (ttp-110) outliers start: 11 outliers final: 1 residues processed: 1081 average time/residue: 0.2333 time to fit residues: 414.3236 Evaluate side-chains 858 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 853 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 515 optimal weight: 7.9990 chunk 520 optimal weight: 3.9990 chunk 527 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 477 optimal weight: 5.9990 chunk 319 optimal weight: 0.0030 chunk 508 optimal weight: 40.0000 chunk 457 optimal weight: 5.9990 chunk 507 optimal weight: 0.9990 chunk 208 optimal weight: 0.0270 overall best weight: 2.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 GLN B 553 ASN C 246 ASN C 447 GLN C 602 ASN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 GLN D 476 ASN ** D 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN F 328 ASN F 458 ASN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 GLN H 277 HIS ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 745 HIS I 168 GLN J 117 HIS ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.157032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097707 restraints weight = 100646.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.103100 restraints weight = 56007.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.104704 restraints weight = 32422.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.106033 restraints weight = 24985.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.106354 restraints weight = 22157.557| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 42867 Z= 0.190 Angle : 0.655 10.991 58454 Z= 0.343 Chirality : 0.046 0.253 6899 Planarity : 0.005 0.081 7709 Dihedral : 4.784 28.057 6111 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.94 % Favored : 95.01 % Rotamer: Outliers : 0.10 % Allowed : 4.24 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.11), residues: 5708 helix: -0.28 (0.13), residues: 1659 sheet: -0.48 (0.15), residues: 1048 loop : -0.83 (0.11), residues: 3001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 391 TYR 0.024 0.002 TYR I 591 PHE 0.024 0.002 PHE B 531 TRP 0.023 0.002 TRP H 570 HIS 0.006 0.001 HIS H 645 Details of bonding type rmsd covalent geometry : bond 0.00414 (42867) covalent geometry : angle 0.65527 (58454) hydrogen bonds : bond 0.04227 ( 1503) hydrogen bonds : angle 5.63680 ( 4329) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1008 time to evaluate : 1.498 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8625 (p0) cc_final: 0.8279 (p0) REVERT: A 192 TYR cc_start: 0.9032 (p90) cc_final: 0.8419 (p90) REVERT: A 222 SER cc_start: 0.9477 (t) cc_final: 0.9029 (p) REVERT: A 225 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8642 (ttpt) REVERT: A 250 GLU cc_start: 0.8867 (mp0) cc_final: 0.8517 (tp30) REVERT: A 391 LEU cc_start: 0.9165 (mm) cc_final: 0.8822 (mm) REVERT: A 415 ASN cc_start: 0.8834 (m110) cc_final: 0.8603 (m110) REVERT: A 436 TYR cc_start: 0.9174 (t80) cc_final: 0.8907 (t80) REVERT: A 453 ASP cc_start: 0.8594 (p0) cc_final: 0.7954 (p0) REVERT: A 462 TYR cc_start: 0.8085 (t80) cc_final: 0.7866 (t80) REVERT: A 465 GLU cc_start: 0.8691 (mp0) cc_final: 0.8396 (mp0) REVERT: A 512 ASP cc_start: 0.7947 (t0) cc_final: 0.7568 (t0) REVERT: A 525 GLU cc_start: 0.9354 (mp0) cc_final: 0.9131 (mp0) REVERT: A 531 PHE cc_start: 0.8402 (m-10) cc_final: 0.8192 (m-10) REVERT: A 551 ASP cc_start: 0.8468 (t0) cc_final: 0.7564 (p0) REVERT: A 552 PHE cc_start: 0.9246 (m-80) cc_final: 0.8739 (m-80) REVERT: A 584 ASN cc_start: 0.9005 (m110) cc_final: 0.8534 (t0) REVERT: A 592 ARG cc_start: 0.8372 (mtp180) cc_final: 0.8089 (mtp180) REVERT: A 602 ASN cc_start: 0.9065 (m-40) cc_final: 0.8683 (m110) REVERT: A 631 ILE cc_start: 0.9017 (mp) cc_final: 0.8430 (tp) REVERT: A 727 PHE cc_start: 0.8932 (t80) cc_final: 0.8511 (t80) REVERT: B 185 ASP cc_start: 0.8673 (p0) cc_final: 0.8470 (p0) REVERT: B 192 TYR cc_start: 0.9410 (p90) cc_final: 0.8089 (p90) REVERT: B 220 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8508 (mmmm) REVERT: B 225 LYS cc_start: 0.9069 (tttm) cc_final: 0.8683 (ttpt) REVERT: B 236 PHE cc_start: 0.9111 (t80) cc_final: 0.8801 (t80) REVERT: B 243 ILE cc_start: 0.9147 (tt) cc_final: 0.8454 (pt) REVERT: B 244 ASP cc_start: 0.8647 (t70) cc_final: 0.7567 (t0) REVERT: B 246 ASN cc_start: 0.9131 (m110) cc_final: 0.8611 (m110) REVERT: B 256 VAL cc_start: 0.9411 (t) cc_final: 0.9181 (p) REVERT: B 328 ASN cc_start: 0.8067 (t0) cc_final: 0.7637 (t0) REVERT: B 378 LEU cc_start: 0.9161 (tp) cc_final: 0.8266 (tt) REVERT: B 438 GLN cc_start: 0.9434 (mt0) cc_final: 0.9158 (mt0) REVERT: B 439 PHE cc_start: 0.9334 (t80) cc_final: 0.9133 (t80) REVERT: B 470 ARG cc_start: 0.7925 (ptp90) cc_final: 0.7555 (ttp80) REVERT: B 479 GLU cc_start: 0.8123 (pt0) cc_final: 0.7866 (pt0) REVERT: B 486 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8672 (tm-30) REVERT: B 487 THR cc_start: 0.9669 (t) cc_final: 0.9446 (t) REVERT: B 502 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6624 (tm-30) REVERT: B 504 ARG cc_start: 0.7119 (mmm160) cc_final: 0.6782 (mmm-85) REVERT: B 512 ASP cc_start: 0.8252 (t0) cc_final: 0.7908 (t0) REVERT: B 515 GLU cc_start: 0.8577 (tp30) cc_final: 0.8122 (tp30) REVERT: B 524 LYS cc_start: 0.9167 (ptmm) cc_final: 0.8714 (pttm) REVERT: B 541 GLN cc_start: 0.9187 (pt0) cc_final: 0.8888 (pp30) REVERT: B 550 PHE cc_start: 0.8881 (m-80) cc_final: 0.8086 (m-80) REVERT: B 553 ASN cc_start: 0.6871 (m-40) cc_final: 0.5874 (m110) REVERT: B 557 GLN cc_start: 0.8256 (tp40) cc_final: 0.7652 (tp40) REVERT: B 561 ASN cc_start: 0.9023 (m110) cc_final: 0.8415 (m-40) REVERT: B 584 ASN cc_start: 0.8534 (t0) cc_final: 0.8131 (t0) REVERT: B 590 LEU cc_start: 0.8902 (tp) cc_final: 0.8448 (tp) REVERT: B 705 ASN cc_start: 0.9110 (m-40) cc_final: 0.8629 (p0) REVERT: B 727 PHE cc_start: 0.8336 (t80) cc_final: 0.7862 (t80) REVERT: C 195 ASP cc_start: 0.8364 (t0) cc_final: 0.8051 (t0) REVERT: C 224 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8066 (mp0) REVERT: C 225 LYS cc_start: 0.9223 (tptm) cc_final: 0.8964 (tttp) REVERT: C 231 ASP cc_start: 0.8741 (p0) cc_final: 0.8530 (p0) REVERT: C 243 ILE cc_start: 0.9402 (tp) cc_final: 0.9133 (tp) REVERT: C 246 ASN cc_start: 0.9267 (m110) cc_final: 0.9047 (m110) REVERT: C 266 MET cc_start: 0.8338 (tpt) cc_final: 0.8130 (tpt) REVERT: C 326 ASN cc_start: 0.8161 (p0) cc_final: 0.7620 (p0) REVERT: C 336 HIS cc_start: 0.9077 (p-80) cc_final: 0.8744 (p-80) REVERT: C 368 ASN cc_start: 0.8575 (t0) cc_final: 0.8369 (t0) REVERT: C 408 ASN cc_start: 0.9238 (t0) cc_final: 0.9032 (t0) REVERT: C 434 MET cc_start: 0.9047 (ppp) cc_final: 0.8729 (ppp) REVERT: C 439 PHE cc_start: 0.9398 (t80) cc_final: 0.8940 (t80) REVERT: C 453 ASP cc_start: 0.8569 (p0) cc_final: 0.8295 (p0) REVERT: C 486 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8493 (tm-30) REVERT: C 487 THR cc_start: 0.9234 (p) cc_final: 0.8858 (p) REVERT: C 497 ASP cc_start: 0.8059 (p0) cc_final: 0.7794 (p0) REVERT: C 550 PHE cc_start: 0.9546 (m-80) cc_final: 0.8897 (m-80) REVERT: C 551 ASP cc_start: 0.8635 (t0) cc_final: 0.8291 (t0) REVERT: C 552 PHE cc_start: 0.8847 (m-80) cc_final: 0.8481 (m-80) REVERT: C 553 ASN cc_start: 0.8728 (t0) cc_final: 0.8463 (t0) REVERT: C 575 TYR cc_start: 0.7746 (m-80) cc_final: 0.7441 (m-80) REVERT: C 590 LEU cc_start: 0.9384 (tt) cc_final: 0.9042 (tt) REVERT: C 596 PHE cc_start: 0.8980 (m-80) cc_final: 0.8661 (m-80) REVERT: C 636 ARG cc_start: 0.8852 (ptt-90) cc_final: 0.8403 (ptp90) REVERT: C 727 PHE cc_start: 0.7829 (t80) cc_final: 0.7322 (t80) REVERT: D 192 TYR cc_start: 0.9379 (p90) cc_final: 0.8913 (p90) REVERT: D 195 ASP cc_start: 0.8503 (t0) cc_final: 0.8131 (t0) REVERT: D 244 ASP cc_start: 0.8745 (t0) cc_final: 0.8496 (t70) REVERT: D 246 ASN cc_start: 0.9237 (m110) cc_final: 0.8995 (m110) REVERT: D 365 ARG cc_start: 0.7944 (ttm-80) cc_final: 0.7134 (tpp-160) REVERT: D 408 ASN cc_start: 0.9204 (t0) cc_final: 0.8939 (t0) REVERT: D 411 TYR cc_start: 0.8202 (t80) cc_final: 0.7988 (t80) REVERT: D 415 ASN cc_start: 0.8864 (m110) cc_final: 0.8420 (p0) REVERT: D 501 VAL cc_start: 0.9268 (t) cc_final: 0.9005 (p) REVERT: D 525 GLU cc_start: 0.9043 (mp0) cc_final: 0.8727 (mp0) REVERT: D 565 GLN cc_start: 0.9494 (mm-40) cc_final: 0.9073 (mt0) REVERT: E 216 LEU cc_start: 0.9159 (mt) cc_final: 0.8868 (mt) REVERT: E 237 GLU cc_start: 0.8532 (pt0) cc_final: 0.8295 (pt0) REVERT: E 240 THR cc_start: 0.9297 (m) cc_final: 0.8838 (t) REVERT: E 247 VAL cc_start: 0.9325 (t) cc_final: 0.9114 (p) REVERT: E 436 TYR cc_start: 0.8831 (t80) cc_final: 0.8267 (t80) REVERT: E 509 ASN cc_start: 0.9153 (t0) cc_final: 0.8857 (t0) REVERT: E 512 ASP cc_start: 0.8198 (t0) cc_final: 0.7966 (t0) REVERT: E 553 ASN cc_start: 0.8534 (m110) cc_final: 0.7976 (m-40) REVERT: E 575 TYR cc_start: 0.8447 (m-80) cc_final: 0.7383 (m-80) REVERT: E 616 HIS cc_start: 0.9011 (m90) cc_final: 0.8605 (p-80) REVERT: F 176 PRO cc_start: 0.8230 (Cg_exo) cc_final: 0.7920 (Cg_endo) REVERT: F 190 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8335 (tm-30) REVERT: F 195 ASP cc_start: 0.8798 (t0) cc_final: 0.8337 (t0) REVERT: F 223 PRO cc_start: 0.9393 (Cg_endo) cc_final: 0.9097 (Cg_exo) REVERT: F 226 TRP cc_start: 0.9166 (t60) cc_final: 0.8691 (t60) REVERT: F 242 ARG cc_start: 0.8648 (mtm-85) cc_final: 0.7953 (mtm110) REVERT: F 245 LYS cc_start: 0.9245 (mmmm) cc_final: 0.8931 (mmmm) REVERT: F 261 ILE cc_start: 0.9679 (mm) cc_final: 0.9450 (mm) REVERT: F 265 ASP cc_start: 0.8934 (t0) cc_final: 0.8444 (p0) REVERT: F 326 ASN cc_start: 0.8019 (m-40) cc_final: 0.7383 (m-40) REVERT: F 332 VAL cc_start: 0.8112 (p) cc_final: 0.7825 (p) REVERT: F 439 PHE cc_start: 0.9562 (t80) cc_final: 0.9355 (t80) REVERT: F 442 LEU cc_start: 0.9758 (tt) cc_final: 0.9510 (pp) REVERT: F 456 TYR cc_start: 0.8735 (m-80) cc_final: 0.8489 (m-80) REVERT: F 480 VAL cc_start: 0.8521 (t) cc_final: 0.8086 (m) REVERT: F 497 ASP cc_start: 0.8635 (p0) cc_final: 0.8329 (p0) REVERT: F 501 VAL cc_start: 0.9048 (t) cc_final: 0.8734 (p) REVERT: F 551 ASP cc_start: 0.7318 (t0) cc_final: 0.6517 (p0) REVERT: F 599 ASP cc_start: 0.7383 (t70) cc_final: 0.7171 (t70) REVERT: F 636 ARG cc_start: 0.8660 (ptp90) cc_final: 0.8403 (ptp90) REVERT: F 708 ILE cc_start: 0.9089 (pt) cc_final: 0.8798 (tp) REVERT: F 732 TYR cc_start: 0.8689 (p90) cc_final: 0.8287 (p90) REVERT: G 183 ILE cc_start: 0.9689 (mm) cc_final: 0.9318 (tt) REVERT: G 263 HIS cc_start: 0.8953 (p90) cc_final: 0.8677 (p90) REVERT: G 325 SER cc_start: 0.8919 (t) cc_final: 0.8663 (p) REVERT: G 367 VAL cc_start: 0.9293 (t) cc_final: 0.9088 (t) REVERT: G 512 ASP cc_start: 0.8159 (t0) cc_final: 0.6527 (t0) REVERT: G 515 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8441 (mm-30) REVERT: G 551 ASP cc_start: 0.8775 (t0) cc_final: 0.7590 (p0) REVERT: G 602 ASN cc_start: 0.8489 (m-40) cc_final: 0.8192 (m110) REVERT: G 727 PHE cc_start: 0.8219 (t80) cc_final: 0.7683 (t80) REVERT: H 74 TYR cc_start: 0.7961 (t80) cc_final: 0.7613 (t80) REVERT: H 117 HIS cc_start: 0.6220 (m90) cc_final: 0.5867 (m170) REVERT: H 120 TYR cc_start: 0.8444 (t80) cc_final: 0.8012 (t80) REVERT: H 170 PHE cc_start: 0.9276 (t80) cc_final: 0.8610 (t80) REVERT: H 174 LEU cc_start: 0.9624 (mt) cc_final: 0.9341 (mt) REVERT: H 200 ASP cc_start: 0.9254 (p0) cc_final: 0.9034 (p0) REVERT: H 201 PHE cc_start: 0.8639 (m-80) cc_final: 0.8327 (m-80) REVERT: H 217 PHE cc_start: 0.8769 (t80) cc_final: 0.8344 (t80) REVERT: H 234 GLN cc_start: 0.8923 (mt0) cc_final: 0.8312 (mp10) REVERT: H 261 ASP cc_start: 0.9220 (t0) cc_final: 0.9001 (t0) REVERT: H 281 TRP cc_start: 0.8547 (t60) cc_final: 0.8179 (t60) REVERT: H 391 ARG cc_start: 0.9181 (ppt170) cc_final: 0.8838 (ttp80) REVERT: H 438 TYR cc_start: 0.8344 (m-80) cc_final: 0.8091 (m-80) REVERT: H 441 MET cc_start: 0.8213 (tmm) cc_final: 0.7688 (tmm) REVERT: H 484 MET cc_start: 0.8463 (mpp) cc_final: 0.7826 (mpp) REVERT: H 486 VAL cc_start: 0.8789 (m) cc_final: 0.8510 (p) REVERT: H 499 LEU cc_start: 0.8629 (mp) cc_final: 0.7232 (mp) REVERT: H 521 LEU cc_start: 0.9560 (mm) cc_final: 0.9016 (mm) REVERT: H 533 GLN cc_start: 0.8169 (pm20) cc_final: 0.7717 (pm20) REVERT: H 586 ASN cc_start: 0.9424 (t0) cc_final: 0.9211 (t0) REVERT: H 591 TYR cc_start: 0.8617 (t80) cc_final: 0.7983 (t80) REVERT: H 595 ILE cc_start: 0.9487 (mm) cc_final: 0.9218 (mm) REVERT: H 611 GLN cc_start: 0.8166 (tp-100) cc_final: 0.7946 (tp40) REVERT: H 736 PHE cc_start: 0.8747 (t80) cc_final: 0.8302 (t80) REVERT: H 737 PHE cc_start: 0.9063 (m-80) cc_final: 0.8505 (m-80) REVERT: H 741 PHE cc_start: 0.9619 (t80) cc_final: 0.9380 (t80) REVERT: I 72 GLU cc_start: 0.8604 (mp0) cc_final: 0.8302 (mp0) REVERT: I 108 TYR cc_start: 0.8315 (m-10) cc_final: 0.7988 (m-10) REVERT: I 158 ASP cc_start: 0.8756 (m-30) cc_final: 0.8232 (m-30) REVERT: I 172 ASP cc_start: 0.9276 (m-30) cc_final: 0.9037 (m-30) REVERT: I 182 ASP cc_start: 0.8606 (t0) cc_final: 0.8323 (p0) REVERT: I 205 PHE cc_start: 0.8302 (m-80) cc_final: 0.7937 (m-80) REVERT: I 230 ARG cc_start: 0.8421 (ttm-80) cc_final: 0.7920 (ttm170) REVERT: I 259 LEU cc_start: 0.9003 (pp) cc_final: 0.8643 (mt) REVERT: I 267 ARG cc_start: 0.9304 (ptp90) cc_final: 0.8957 (ptt-90) REVERT: I 268 TYR cc_start: 0.8899 (t80) cc_final: 0.8396 (t80) REVERT: I 441 MET cc_start: 0.5841 (tmm) cc_final: 0.5217 (tmm) REVERT: J 217 PHE cc_start: 0.9170 (t80) cc_final: 0.8671 (t80) REVERT: J 221 PHE cc_start: 0.8984 (t80) cc_final: 0.8390 (t80) REVERT: J 223 TYR cc_start: 0.8557 (m-80) cc_final: 0.8206 (m-80) REVERT: J 243 TYR cc_start: 0.8648 (t80) cc_final: 0.7904 (t80) REVERT: J 247 PHE cc_start: 0.9130 (m-80) cc_final: 0.8679 (m-80) REVERT: J 277 HIS cc_start: 0.9063 (t-90) cc_final: 0.8817 (t-90) REVERT: J 411 GLN cc_start: 0.8984 (tp-100) cc_final: 0.8596 (pt0) REVERT: J 436 TYR cc_start: 0.6860 (m-10) cc_final: 0.6505 (m-80) outliers start: 4 outliers final: 1 residues processed: 1011 average time/residue: 0.2286 time to fit residues: 380.5976 Evaluate side-chains 854 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 853 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 251 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 178 optimal weight: 0.6980 chunk 446 optimal weight: 4.9990 chunk 469 optimal weight: 1.9990 chunk 393 optimal weight: 20.0000 chunk 90 optimal weight: 0.8980 chunk 347 optimal weight: 1.9990 chunk 376 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS B 463 ASN B 485 GLN B 541 GLN C 422 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN C 705 ASN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN E 483 GLN E 499 ASN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 594 ASN H 745 HIS J 117 HIS ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.160057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.100817 restraints weight = 98637.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105867 restraints weight = 56826.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.109197 restraints weight = 30435.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.109076 restraints weight = 23788.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.109333 restraints weight = 22145.153| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 42867 Z= 0.142 Angle : 0.600 10.368 58454 Z= 0.314 Chirality : 0.045 0.189 6899 Planarity : 0.004 0.076 7709 Dihedral : 4.615 24.340 6111 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.26 % Favored : 95.71 % Rotamer: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.11), residues: 5708 helix: -0.08 (0.13), residues: 1656 sheet: -0.44 (0.15), residues: 1064 loop : -0.64 (0.12), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 391 TYR 0.029 0.002 TYR A 598 PHE 0.023 0.001 PHE I 471 TRP 0.018 0.001 TRP A 346 HIS 0.004 0.001 HIS H 645 Details of bonding type rmsd covalent geometry : bond 0.00311 (42867) covalent geometry : angle 0.60033 (58454) hydrogen bonds : bond 0.03655 ( 1503) hydrogen bonds : angle 5.33038 ( 4329) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1049 time to evaluate : 1.577 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: 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: 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 192 TYR cc_start: 0.8926 (p90) cc_final: 0.8646 (p90) REVERT: A 200 ARG cc_start: 0.7446 (mpt-90) cc_final: 0.6644 (mpt180) REVERT: A 222 SER cc_start: 0.9446 (t) cc_final: 0.9200 (p) REVERT: A 225 LYS cc_start: 0.9135 (ttmt) cc_final: 0.8630 (ttpt) REVERT: A 250 GLU cc_start: 0.8834 (mp0) cc_final: 0.8609 (tp30) REVERT: A 391 LEU cc_start: 0.9124 (mm) cc_final: 0.8757 (mm) REVERT: A 415 ASN cc_start: 0.8760 (m110) cc_final: 0.8557 (m110) REVERT: A 436 TYR cc_start: 0.9174 (t80) cc_final: 0.8968 (t80) REVERT: A 453 ASP cc_start: 0.8591 (p0) cc_final: 0.8180 (p0) REVERT: A 462 TYR cc_start: 0.8117 (t80) cc_final: 0.7856 (t80) REVERT: A 465 GLU cc_start: 0.8663 (mp0) cc_final: 0.8372 (mp0) REVERT: A 479 GLU cc_start: 0.9282 (mp0) cc_final: 0.8846 (mp0) REVERT: A 485 GLN cc_start: 0.8827 (pm20) cc_final: 0.8380 (pp30) REVERT: A 490 ARG cc_start: 0.8782 (ptm160) cc_final: 0.8439 (ptm-80) REVERT: A 492 ILE cc_start: 0.9623 (mm) cc_final: 0.9305 (mm) REVERT: A 496 LYS cc_start: 0.9393 (mmtt) cc_final: 0.9012 (mmtt) REVERT: A 512 ASP cc_start: 0.7843 (t0) cc_final: 0.7499 (t0) REVERT: A 552 PHE cc_start: 0.9248 (m-80) cc_final: 0.8929 (m-80) REVERT: A 600 ARG cc_start: 0.6882 (tpt170) cc_final: 0.6672 (tpt170) REVERT: A 602 ASN cc_start: 0.8979 (m-40) cc_final: 0.8683 (m110) REVERT: A 631 ILE cc_start: 0.8984 (mp) cc_final: 0.8349 (tp) REVERT: A 727 PHE cc_start: 0.8993 (t80) cc_final: 0.8535 (t80) REVERT: B 185 ASP cc_start: 0.8638 (p0) cc_final: 0.8101 (p0) REVERT: B 190 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8158 (tm-30) REVERT: B 192 TYR cc_start: 0.9297 (p90) cc_final: 0.8099 (p90) REVERT: B 225 LYS cc_start: 0.9110 (tttm) cc_final: 0.8787 (ttpt) REVERT: B 236 PHE cc_start: 0.9091 (t80) cc_final: 0.8822 (t80) REVERT: B 244 ASP cc_start: 0.8578 (t70) cc_final: 0.7894 (t0) REVERT: B 246 ASN cc_start: 0.9084 (m110) cc_final: 0.8597 (m110) REVERT: B 256 VAL cc_start: 0.9428 (t) cc_final: 0.9136 (p) REVERT: B 328 ASN cc_start: 0.8045 (t0) cc_final: 0.7577 (t0) REVERT: B 411 TYR cc_start: 0.8647 (t80) cc_final: 0.8221 (t80) REVERT: B 438 GLN cc_start: 0.9415 (mt0) cc_final: 0.9147 (mt0) REVERT: B 470 ARG cc_start: 0.8035 (ptp90) cc_final: 0.7712 (ttp80) REVERT: B 486 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8649 (tm-30) REVERT: B 502 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6607 (tm-30) REVERT: B 512 ASP cc_start: 0.8251 (t0) cc_final: 0.7922 (t0) REVERT: B 515 GLU cc_start: 0.8567 (tp30) cc_final: 0.8168 (tp30) REVERT: B 524 LYS cc_start: 0.9127 (ptmm) cc_final: 0.8668 (pttt) REVERT: B 550 PHE cc_start: 0.8837 (m-80) cc_final: 0.8012 (m-80) REVERT: B 553 ASN cc_start: 0.6734 (m-40) cc_final: 0.5980 (m-40) REVERT: B 560 GLN cc_start: 0.9313 (tm-30) cc_final: 0.9065 (tm-30) REVERT: B 561 ASN cc_start: 0.9062 (m110) cc_final: 0.8316 (m110) REVERT: B 584 ASN cc_start: 0.8542 (t0) cc_final: 0.8284 (t0) REVERT: B 590 LEU cc_start: 0.8944 (tp) cc_final: 0.8500 (tp) REVERT: B 727 PHE cc_start: 0.8501 (t80) cc_final: 0.8047 (t80) REVERT: C 185 ASP cc_start: 0.8799 (p0) cc_final: 0.8540 (p0) REVERT: C 195 ASP cc_start: 0.8374 (t0) cc_final: 0.7974 (t0) REVERT: C 224 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8023 (mp0) REVERT: C 231 ASP cc_start: 0.8748 (p0) cc_final: 0.8487 (p0) REVERT: C 243 ILE cc_start: 0.9287 (tp) cc_final: 0.9017 (tp) REVERT: C 245 LYS cc_start: 0.9261 (mmpt) cc_final: 0.9020 (mmpt) REVERT: C 246 ASN cc_start: 0.9065 (m110) cc_final: 0.8749 (m110) REVERT: C 252 ARG cc_start: 0.9147 (mpt180) cc_final: 0.8889 (mmt-90) REVERT: C 297 ARG cc_start: 0.8644 (tpt170) cc_final: 0.8293 (tpp-160) REVERT: C 326 ASN cc_start: 0.8212 (p0) cc_final: 0.7648 (p0) REVERT: C 336 HIS cc_start: 0.9094 (p-80) cc_final: 0.8736 (p-80) REVERT: C 361 ASN cc_start: 0.8742 (t0) cc_final: 0.8455 (t0) REVERT: C 434 MET cc_start: 0.9085 (ppp) cc_final: 0.8818 (ppp) REVERT: C 439 PHE cc_start: 0.9409 (t80) cc_final: 0.8918 (t80) REVERT: C 453 ASP cc_start: 0.8646 (p0) cc_final: 0.8313 (p0) REVERT: C 462 TYR cc_start: 0.8945 (t80) cc_final: 0.8646 (t80) REVERT: C 486 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8575 (tm-30) REVERT: C 487 THR cc_start: 0.9179 (p) cc_final: 0.8867 (p) REVERT: C 550 PHE cc_start: 0.9536 (m-80) cc_final: 0.9214 (m-80) REVERT: C 551 ASP cc_start: 0.8630 (t0) cc_final: 0.8343 (t70) REVERT: C 552 PHE cc_start: 0.8797 (m-80) cc_final: 0.8388 (m-80) REVERT: C 553 ASN cc_start: 0.8696 (t0) cc_final: 0.8334 (t0) REVERT: C 575 TYR cc_start: 0.7735 (m-80) cc_final: 0.7408 (m-80) REVERT: C 590 LEU cc_start: 0.9374 (tt) cc_final: 0.9060 (tt) REVERT: C 636 ARG cc_start: 0.8911 (ptt-90) cc_final: 0.8499 (ptp90) REVERT: C 705 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7976 (t0) REVERT: C 727 PHE cc_start: 0.7847 (t80) cc_final: 0.7499 (t80) REVERT: D 192 TYR cc_start: 0.9275 (p90) cc_final: 0.8907 (p90) REVERT: D 195 ASP cc_start: 0.8493 (t0) cc_final: 0.8160 (t0) REVERT: D 265 ASP cc_start: 0.8728 (t70) cc_final: 0.8511 (t70) REVERT: D 365 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7229 (tpp-160) REVERT: D 408 ASN cc_start: 0.9212 (t0) cc_final: 0.8898 (t0) REVERT: D 415 ASN cc_start: 0.8877 (m110) cc_final: 0.8479 (p0) REVERT: D 449 ARG cc_start: 0.8518 (ptp-170) cc_final: 0.8036 (ptp90) REVERT: D 456 TYR cc_start: 0.9021 (m-80) cc_final: 0.8774 (m-80) REVERT: D 462 TYR cc_start: 0.8337 (t80) cc_final: 0.8080 (t80) REVERT: D 486 GLU cc_start: 0.8896 (tt0) cc_final: 0.8635 (tt0) REVERT: D 501 VAL cc_start: 0.9308 (t) cc_final: 0.9028 (p) REVERT: D 525 GLU cc_start: 0.9029 (mp0) cc_final: 0.8677 (mp0) REVERT: D 565 GLN cc_start: 0.9472 (mm-40) cc_final: 0.9045 (mt0) REVERT: D 703 LYS cc_start: 0.9549 (mppt) cc_final: 0.9315 (mmtm) REVERT: E 216 LEU cc_start: 0.9161 (mt) cc_final: 0.8894 (mt) REVERT: E 240 THR cc_start: 0.9159 (m) cc_final: 0.8735 (t) REVERT: E 436 TYR cc_start: 0.8820 (t80) cc_final: 0.8339 (t80) REVERT: E 509 ASN cc_start: 0.9182 (t0) cc_final: 0.8856 (t0) REVERT: E 512 ASP cc_start: 0.8212 (t0) cc_final: 0.7943 (t0) REVERT: E 553 ASN cc_start: 0.8553 (m110) cc_final: 0.7985 (m-40) REVERT: E 560 GLN cc_start: 0.8999 (tm-30) cc_final: 0.8781 (tm-30) REVERT: E 575 TYR cc_start: 0.8418 (m-80) cc_final: 0.7270 (m-80) REVERT: E 616 HIS cc_start: 0.8988 (m90) cc_final: 0.8698 (p-80) REVERT: F 176 PRO cc_start: 0.8635 (Cg_exo) cc_final: 0.7987 (Cg_endo) REVERT: F 190 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8307 (tm-30) REVERT: F 195 ASP cc_start: 0.8712 (t0) cc_final: 0.8317 (t0) REVERT: F 223 PRO cc_start: 0.9412 (Cg_endo) cc_final: 0.9116 (Cg_exo) REVERT: F 226 TRP cc_start: 0.9201 (t60) cc_final: 0.8808 (t60) REVERT: F 242 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8126 (mtm110) REVERT: F 261 ILE cc_start: 0.9690 (mm) cc_final: 0.9451 (mm) REVERT: F 265 ASP cc_start: 0.8923 (t0) cc_final: 0.8383 (p0) REVERT: F 326 ASN cc_start: 0.7963 (m-40) cc_final: 0.7420 (m-40) REVERT: F 332 VAL cc_start: 0.7974 (p) cc_final: 0.7742 (p) REVERT: F 439 PHE cc_start: 0.9608 (t80) cc_final: 0.9347 (t80) REVERT: F 442 LEU cc_start: 0.9748 (tt) cc_final: 0.9526 (pp) REVERT: F 456 TYR cc_start: 0.8676 (m-80) cc_final: 0.8424 (m-80) REVERT: F 501 VAL cc_start: 0.9063 (t) cc_final: 0.8769 (p) REVERT: F 512 ASP cc_start: 0.7756 (m-30) cc_final: 0.7531 (m-30) REVERT: F 523 LEU cc_start: 0.9441 (tp) cc_final: 0.9209 (tp) REVERT: F 551 ASP cc_start: 0.7448 (t0) cc_final: 0.6670 (p0) REVERT: F 599 ASP cc_start: 0.7508 (t70) cc_final: 0.7306 (t70) REVERT: F 602 ASN cc_start: 0.9293 (m-40) cc_final: 0.8913 (m-40) REVERT: F 635 ILE cc_start: 0.9397 (mm) cc_final: 0.9084 (mm) REVERT: F 636 ARG cc_start: 0.8647 (ptp90) cc_final: 0.8080 (ptp90) REVERT: F 708 ILE cc_start: 0.9060 (pt) cc_final: 0.8744 (tp) REVERT: G 183 ILE cc_start: 0.9686 (mm) cc_final: 0.9316 (tt) REVERT: G 231 ASP cc_start: 0.9162 (p0) cc_final: 0.8907 (p0) REVERT: G 238 LYS cc_start: 0.9298 (mmmm) cc_final: 0.8935 (mmmm) REVERT: G 242 ARG cc_start: 0.8597 (mtt90) cc_final: 0.8014 (mmm-85) REVERT: G 263 HIS cc_start: 0.8943 (p90) cc_final: 0.8655 (p90) REVERT: G 325 SER cc_start: 0.8918 (t) cc_final: 0.8589 (p) REVERT: G 440 LEU cc_start: 0.9222 (mt) cc_final: 0.8910 (mt) REVERT: G 462 TYR cc_start: 0.8516 (t80) cc_final: 0.7750 (t80) REVERT: G 479 GLU cc_start: 0.9016 (mp0) cc_final: 0.8665 (mp0) REVERT: G 514 LEU cc_start: 0.9566 (tt) cc_final: 0.9148 (tt) REVERT: G 521 MET cc_start: 0.7077 (pmm) cc_final: 0.6809 (pmm) REVERT: G 551 ASP cc_start: 0.8779 (t0) cc_final: 0.7562 (p0) REVERT: G 569 LEU cc_start: 0.9222 (mm) cc_final: 0.8915 (mt) REVERT: G 602 ASN cc_start: 0.8406 (m-40) cc_final: 0.8114 (m110) REVERT: G 727 PHE cc_start: 0.8286 (t80) cc_final: 0.7774 (t80) REVERT: H 120 TYR cc_start: 0.8379 (t80) cc_final: 0.8131 (t80) REVERT: H 168 GLN cc_start: 0.9292 (tm-30) cc_final: 0.9054 (tm-30) REVERT: H 170 PHE cc_start: 0.9303 (t80) cc_final: 0.8771 (t80) REVERT: H 174 LEU cc_start: 0.9622 (mt) cc_final: 0.9369 (mt) REVERT: H 200 ASP cc_start: 0.9352 (p0) cc_final: 0.9132 (p0) REVERT: H 201 PHE cc_start: 0.8804 (m-80) cc_final: 0.8487 (m-80) REVERT: H 217 PHE cc_start: 0.8744 (t80) cc_final: 0.8162 (t80) REVERT: H 234 GLN cc_start: 0.8932 (mt0) cc_final: 0.8396 (mp10) REVERT: H 259 LEU cc_start: 0.9463 (mm) cc_final: 0.9260 (mm) REVERT: H 261 ASP cc_start: 0.9203 (t0) cc_final: 0.9001 (t0) REVERT: H 281 TRP cc_start: 0.8561 (t60) cc_final: 0.8052 (t60) REVERT: H 390 GLN cc_start: 0.8921 (mp10) cc_final: 0.8721 (mp10) REVERT: H 438 TYR cc_start: 0.8345 (m-80) cc_final: 0.8066 (m-80) REVERT: H 486 VAL cc_start: 0.8793 (m) cc_final: 0.8533 (p) REVERT: H 499 LEU cc_start: 0.8676 (mp) cc_final: 0.8031 (mp) REVERT: H 521 LEU cc_start: 0.9585 (mm) cc_final: 0.9352 (mm) REVERT: H 582 LEU cc_start: 0.8959 (pp) cc_final: 0.8505 (mm) REVERT: H 586 ASN cc_start: 0.9411 (t0) cc_final: 0.9152 (t0) REVERT: H 611 GLN cc_start: 0.8142 (tp-100) cc_final: 0.7924 (tp40) REVERT: H 736 PHE cc_start: 0.8770 (t80) cc_final: 0.8545 (t80) REVERT: H 737 PHE cc_start: 0.9088 (m-80) cc_final: 0.8707 (m-80) REVERT: H 739 GLU cc_start: 0.8681 (mp0) cc_final: 0.8454 (mp0) REVERT: I 108 TYR cc_start: 0.8192 (m-10) cc_final: 0.7822 (m-10) REVERT: I 182 ASP cc_start: 0.8581 (t0) cc_final: 0.8356 (p0) REVERT: I 205 PHE cc_start: 0.8285 (m-80) cc_final: 0.7901 (m-80) REVERT: I 230 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.7864 (ttm170) REVERT: I 260 LYS cc_start: 0.9261 (mtmm) cc_final: 0.9003 (mttt) REVERT: I 267 ARG cc_start: 0.9276 (ptp90) cc_final: 0.8939 (ptt-90) REVERT: I 268 TYR cc_start: 0.8870 (t80) cc_final: 0.8484 (t80) REVERT: I 441 MET cc_start: 0.5958 (tmm) cc_final: 0.5161 (tmm) REVERT: I 546 ASP cc_start: 0.8182 (p0) cc_final: 0.6908 (p0) REVERT: I 597 GLU cc_start: 0.6970 (mp0) cc_final: 0.6558 (mp0) REVERT: J 64 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8656 (mm-30) REVERT: J 217 PHE cc_start: 0.9174 (t80) cc_final: 0.8368 (t80) REVERT: J 221 PHE cc_start: 0.8941 (t80) cc_final: 0.8413 (t80) REVERT: J 223 TYR cc_start: 0.8563 (m-80) cc_final: 0.8160 (m-80) REVERT: J 243 TYR cc_start: 0.8565 (t80) cc_final: 0.8064 (t80) REVERT: J 244 MET cc_start: 0.9250 (tpt) cc_final: 0.9046 (tpp) REVERT: J 247 PHE cc_start: 0.9139 (m-80) cc_final: 0.8867 (m-80) REVERT: J 277 HIS cc_start: 0.9047 (t-90) cc_final: 0.8797 (t-90) REVERT: J 411 GLN cc_start: 0.8973 (tp-100) cc_final: 0.8586 (pt0) REVERT: J 436 TYR cc_start: 0.6765 (m-10) cc_final: 0.6454 (m-80) REVERT: J 502 ARG cc_start: 0.6995 (mtm-85) cc_final: 0.6293 (mtm-85) REVERT: J 544 ARG cc_start: 0.4606 (mmp80) cc_final: 0.4249 (mmt180) REVERT: J 590 ARG cc_start: 0.7581 (mmm160) cc_final: 0.6631 (mtm110) outliers start: 1 outliers final: 0 residues processed: 1050 average time/residue: 0.2208 time to fit residues: 383.7189 Evaluate side-chains 865 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 864 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 395 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 356 optimal weight: 50.0000 chunk 28 optimal weight: 5.9990 chunk 410 optimal weight: 3.9990 chunk 461 optimal weight: 50.0000 chunk 194 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 354 optimal weight: 20.0000 chunk 326 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN B 485 GLN C 246 ASN C 602 ASN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 ASN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN E 483 GLN E 499 ASN E 556 GLN F 388 ASN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 594 ASN H 745 HIS J 117 HIS J 248 ASN J 560 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.153719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.095313 restraints weight = 99095.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.098935 restraints weight = 53995.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.101306 restraints weight = 36688.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.102786 restraints weight = 28430.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103814 restraints weight = 24116.157| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.170 42867 Z= 0.320 Angle : 0.738 12.691 58454 Z= 0.388 Chirality : 0.047 0.240 6899 Planarity : 0.005 0.118 7709 Dihedral : 5.104 23.201 6111 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.94 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.11), residues: 5708 helix: 0.00 (0.13), residues: 1594 sheet: -0.45 (0.15), residues: 1076 loop : -0.75 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 391 TYR 0.044 0.002 TYR I 167 PHE 0.028 0.002 PHE B 550 TRP 0.021 0.002 TRP H 570 HIS 0.010 0.002 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00690 (42867) covalent geometry : angle 0.73827 (58454) hydrogen bonds : bond 0.04176 ( 1503) hydrogen bonds : angle 5.47820 ( 4329) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 901 time to evaluate : 1.442 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8238 (tm-30) REVERT: A 192 TYR cc_start: 0.9091 (p90) cc_final: 0.8458 (p90) REVERT: A 200 ARG cc_start: 0.7457 (mpt-90) cc_final: 0.6355 (mpt180) REVERT: A 225 LYS cc_start: 0.9005 (ttmt) cc_final: 0.8544 (ttpt) REVERT: A 250 GLU cc_start: 0.8905 (mp0) cc_final: 0.8638 (tp30) REVERT: A 391 LEU cc_start: 0.9273 (mm) cc_final: 0.9048 (mm) REVERT: A 415 ASN cc_start: 0.8815 (m110) cc_final: 0.8534 (m110) REVERT: A 439 PHE cc_start: 0.9320 (t80) cc_final: 0.9116 (t80) REVERT: A 453 ASP cc_start: 0.8796 (p0) cc_final: 0.8333 (p0) REVERT: A 465 GLU cc_start: 0.8622 (mp0) cc_final: 0.8341 (mp0) REVERT: A 525 GLU cc_start: 0.9354 (mp0) cc_final: 0.9017 (pm20) REVERT: A 531 PHE cc_start: 0.8529 (m-10) cc_final: 0.8240 (m-10) REVERT: A 583 LEU cc_start: 0.9245 (mt) cc_final: 0.8886 (mt) REVERT: A 584 ASN cc_start: 0.8421 (p0) cc_final: 0.8017 (p0) REVERT: A 602 ASN cc_start: 0.9083 (m-40) cc_final: 0.8716 (m-40) REVERT: A 727 PHE cc_start: 0.9002 (t80) cc_final: 0.8569 (t80) REVERT: B 185 ASP cc_start: 0.8702 (p0) cc_final: 0.8080 (p0) REVERT: B 190 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8393 (tm-30) REVERT: B 192 TYR cc_start: 0.9189 (p90) cc_final: 0.8266 (p90) REVERT: B 244 ASP cc_start: 0.8660 (t70) cc_final: 0.8008 (t70) REVERT: B 246 ASN cc_start: 0.9151 (m110) cc_final: 0.8679 (m110) REVERT: B 265 ASP cc_start: 0.8436 (t0) cc_final: 0.8079 (t0) REVERT: B 328 ASN cc_start: 0.7957 (t0) cc_final: 0.7492 (t0) REVERT: B 439 PHE cc_start: 0.9359 (t80) cc_final: 0.9141 (t80) REVERT: B 456 TYR cc_start: 0.7659 (m-10) cc_final: 0.7395 (m-10) REVERT: B 470 ARG cc_start: 0.8153 (ptp90) cc_final: 0.7547 (ttp80) REVERT: B 478 SER cc_start: 0.9464 (m) cc_final: 0.9161 (p) REVERT: B 479 GLU cc_start: 0.8414 (pt0) cc_final: 0.8187 (tt0) REVERT: B 486 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8789 (tm-30) REVERT: B 512 ASP cc_start: 0.8349 (t0) cc_final: 0.7984 (t0) REVERT: B 515 GLU cc_start: 0.8630 (tp30) cc_final: 0.8092 (tp30) REVERT: B 524 LYS cc_start: 0.9154 (ptmm) cc_final: 0.8730 (pttm) REVERT: B 553 ASN cc_start: 0.7233 (m-40) cc_final: 0.6105 (m-40) REVERT: B 561 ASN cc_start: 0.8980 (m110) cc_final: 0.8646 (m110) REVERT: B 584 ASN cc_start: 0.8780 (t0) cc_final: 0.8402 (t0) REVERT: B 590 LEU cc_start: 0.8889 (tp) cc_final: 0.8343 (tp) REVERT: B 727 PHE cc_start: 0.8489 (t80) cc_final: 0.8076 (t80) REVERT: C 190 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7079 (tm-30) REVERT: C 195 ASP cc_start: 0.8313 (t0) cc_final: 0.7869 (t0) REVERT: C 225 LYS cc_start: 0.9361 (tptm) cc_final: 0.8881 (ttmm) REVERT: C 243 ILE cc_start: 0.9428 (tp) cc_final: 0.9054 (tp) REVERT: C 246 ASN cc_start: 0.9025 (m-40) cc_final: 0.8611 (m-40) REVERT: C 297 ARG cc_start: 0.8725 (tpt170) cc_final: 0.8276 (tpp-160) REVERT: C 326 ASN cc_start: 0.8104 (p0) cc_final: 0.7722 (p0) REVERT: C 336 HIS cc_start: 0.9072 (p-80) cc_final: 0.8688 (p-80) REVERT: C 361 ASN cc_start: 0.8838 (t0) cc_final: 0.8574 (t0) REVERT: C 368 ASN cc_start: 0.8873 (t0) cc_final: 0.8561 (t0) REVERT: C 408 ASN cc_start: 0.9290 (t0) cc_final: 0.9043 (t0) REVERT: C 434 MET cc_start: 0.8951 (ppp) cc_final: 0.8661 (ppp) REVERT: C 439 PHE cc_start: 0.9341 (t80) cc_final: 0.8878 (t80) REVERT: C 528 LYS cc_start: 0.9143 (ttmm) cc_final: 0.8672 (mmtt) REVERT: C 552 PHE cc_start: 0.8731 (m-80) cc_final: 0.8422 (m-80) REVERT: C 575 TYR cc_start: 0.7828 (m-80) cc_final: 0.7467 (m-80) REVERT: C 590 LEU cc_start: 0.9414 (tt) cc_final: 0.9093 (tt) REVERT: C 636 ARG cc_start: 0.8813 (ptt-90) cc_final: 0.8574 (ptp90) REVERT: C 727 PHE cc_start: 0.7810 (t80) cc_final: 0.7473 (t80) REVERT: D 195 ASP cc_start: 0.8625 (t0) cc_final: 0.8248 (t70) REVERT: D 197 LYS cc_start: 0.9039 (tptt) cc_final: 0.8500 (tptt) REVERT: D 265 ASP cc_start: 0.8583 (t70) cc_final: 0.8311 (t0) REVERT: D 297 ARG cc_start: 0.8437 (ttp80) cc_final: 0.8088 (ttp80) REVERT: D 365 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7283 (tpp-160) REVERT: D 367 VAL cc_start: 0.9441 (t) cc_final: 0.9236 (t) REVERT: D 402 SER cc_start: 0.8667 (m) cc_final: 0.7993 (t) REVERT: D 408 ASN cc_start: 0.9207 (t0) cc_final: 0.8847 (t0) REVERT: D 444 LYS cc_start: 0.9594 (mptt) cc_final: 0.9258 (mmtt) REVERT: D 447 GLN cc_start: 0.8580 (pp30) cc_final: 0.8151 (pp30) REVERT: D 525 GLU cc_start: 0.9019 (mp0) cc_final: 0.8799 (mp0) REVERT: D 565 GLN cc_start: 0.9470 (mm-40) cc_final: 0.9075 (mt0) REVERT: D 703 LYS cc_start: 0.9538 (mppt) cc_final: 0.9254 (mmtm) REVERT: E 240 THR cc_start: 0.9453 (m) cc_final: 0.9174 (p) REVERT: E 243 ILE cc_start: 0.9532 (tp) cc_final: 0.9238 (tp) REVERT: E 434 MET cc_start: 0.8287 (tmm) cc_final: 0.8077 (tmm) REVERT: E 436 TYR cc_start: 0.8834 (t80) cc_final: 0.8507 (t80) REVERT: E 512 ASP cc_start: 0.8418 (t0) cc_final: 0.8018 (t0) REVERT: E 518 LYS cc_start: 0.9428 (ptmt) cc_final: 0.9149 (ptmm) REVERT: E 553 ASN cc_start: 0.8835 (m110) cc_final: 0.8448 (m-40) REVERT: E 616 HIS cc_start: 0.8940 (m90) cc_final: 0.8533 (p-80) REVERT: E 635 ILE cc_start: 0.9684 (mm) cc_final: 0.9459 (pt) REVERT: F 176 PRO cc_start: 0.8609 (Cg_exo) cc_final: 0.8311 (Cg_endo) REVERT: F 190 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8178 (tm-30) REVERT: F 195 ASP cc_start: 0.8901 (t0) cc_final: 0.8434 (t0) REVERT: F 223 PRO cc_start: 0.9340 (Cg_endo) cc_final: 0.9031 (Cg_exo) REVERT: F 226 TRP cc_start: 0.9391 (t60) cc_final: 0.9102 (t-100) REVERT: F 242 ARG cc_start: 0.8707 (mtm-85) cc_final: 0.8159 (mtm180) REVERT: F 261 ILE cc_start: 0.9682 (mm) cc_final: 0.9444 (mm) REVERT: F 265 ASP cc_start: 0.8931 (t0) cc_final: 0.8422 (p0) REVERT: F 326 ASN cc_start: 0.8105 (m-40) cc_final: 0.7573 (m-40) REVERT: F 366 TYR cc_start: 0.8999 (m-10) cc_final: 0.8674 (m-10) REVERT: F 439 PHE cc_start: 0.9451 (t80) cc_final: 0.9151 (t80) REVERT: F 454 GLN cc_start: 0.8219 (mp10) cc_final: 0.7720 (mp10) REVERT: F 497 ASP cc_start: 0.8739 (p0) cc_final: 0.8509 (p0) REVERT: F 501 VAL cc_start: 0.9219 (t) cc_final: 0.8907 (p) REVERT: F 512 ASP cc_start: 0.7800 (m-30) cc_final: 0.7557 (m-30) REVERT: F 523 LEU cc_start: 0.9535 (tp) cc_final: 0.9290 (tp) REVERT: F 551 ASP cc_start: 0.7627 (t0) cc_final: 0.6988 (p0) REVERT: G 192 TYR cc_start: 0.7967 (p90) cc_final: 0.7143 (p90) REVERT: G 238 LYS cc_start: 0.9392 (mmmm) cc_final: 0.8966 (mmmm) REVERT: G 242 ARG cc_start: 0.8852 (mtt90) cc_final: 0.8253 (mmm-85) REVERT: G 325 SER cc_start: 0.8925 (t) cc_final: 0.8701 (p) REVERT: G 448 LEU cc_start: 0.9446 (mm) cc_final: 0.9240 (mm) REVERT: G 479 GLU cc_start: 0.8995 (mp0) cc_final: 0.8505 (mp0) REVERT: G 512 ASP cc_start: 0.8360 (t0) cc_final: 0.6844 (t0) REVERT: G 515 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8526 (mm-30) REVERT: G 551 ASP cc_start: 0.8933 (t0) cc_final: 0.7912 (p0) REVERT: G 596 PHE cc_start: 0.9244 (m-80) cc_final: 0.9023 (m-80) REVERT: G 602 ASN cc_start: 0.8437 (m-40) cc_final: 0.8080 (m110) REVERT: G 727 PHE cc_start: 0.8279 (t80) cc_final: 0.7674 (t80) REVERT: H 74 TYR cc_start: 0.7803 (t80) cc_final: 0.7490 (t80) REVERT: H 117 HIS cc_start: 0.5973 (m90) cc_final: 0.5530 (m-70) REVERT: H 168 GLN cc_start: 0.9408 (tm-30) cc_final: 0.9203 (tm-30) REVERT: H 170 PHE cc_start: 0.9361 (t80) cc_final: 0.8730 (t80) REVERT: H 174 LEU cc_start: 0.9660 (mt) cc_final: 0.9363 (mt) REVERT: H 217 PHE cc_start: 0.8855 (t80) cc_final: 0.8426 (t80) REVERT: H 234 GLN cc_start: 0.8998 (mt0) cc_final: 0.8450 (mp10) REVERT: H 259 LEU cc_start: 0.9435 (mm) cc_final: 0.9210 (mm) REVERT: H 261 ASP cc_start: 0.9148 (t0) cc_final: 0.8942 (t0) REVERT: H 281 TRP cc_start: 0.8636 (t60) cc_final: 0.7968 (t60) REVERT: H 390 GLN cc_start: 0.8862 (mp10) cc_final: 0.8618 (mp10) REVERT: H 441 MET cc_start: 0.8219 (tmm) cc_final: 0.7668 (tmm) REVERT: H 484 MET cc_start: 0.8353 (mpp) cc_final: 0.7902 (mpp) REVERT: H 499 LEU cc_start: 0.8733 (mp) cc_final: 0.7726 (mp) REVERT: H 521 LEU cc_start: 0.9617 (mm) cc_final: 0.9035 (mm) REVERT: H 584 THR cc_start: 0.7686 (t) cc_final: 0.7310 (p) REVERT: H 586 ASN cc_start: 0.9344 (t0) cc_final: 0.9136 (t0) REVERT: H 605 GLU cc_start: 0.9340 (mt-10) cc_final: 0.8830 (pt0) REVERT: H 611 GLN cc_start: 0.8097 (tp-100) cc_final: 0.7836 (tp40) REVERT: H 628 ARG cc_start: 0.8490 (mtm110) cc_final: 0.8040 (ptp90) REVERT: H 736 PHE cc_start: 0.8925 (t80) cc_final: 0.8466 (t80) REVERT: H 737 PHE cc_start: 0.9058 (m-80) cc_final: 0.8523 (m-80) REVERT: H 744 MET cc_start: 0.9188 (ptt) cc_final: 0.8974 (ptt) REVERT: H 745 HIS cc_start: 0.8894 (m-70) cc_final: 0.8511 (m90) REVERT: I 35 HIS cc_start: 0.7602 (m90) cc_final: 0.7274 (m90) REVERT: I 108 TYR cc_start: 0.8262 (m-10) cc_final: 0.7965 (m-10) REVERT: I 149 TYR cc_start: 0.9163 (t80) cc_final: 0.8908 (t80) REVERT: I 156 SER cc_start: 0.8978 (t) cc_final: 0.8713 (p) REVERT: I 205 PHE cc_start: 0.8296 (m-80) cc_final: 0.7939 (m-10) REVERT: I 230 ARG cc_start: 0.8602 (ttm-80) cc_final: 0.8088 (ttm170) REVERT: I 263 ARG cc_start: 0.9411 (mmp80) cc_final: 0.9191 (mmm160) REVERT: I 264 MET cc_start: 0.8923 (pmm) cc_final: 0.8407 (pmm) REVERT: I 267 ARG cc_start: 0.9269 (ptp90) cc_final: 0.8959 (ptt-90) REVERT: I 268 TYR cc_start: 0.8790 (t80) cc_final: 0.8387 (t80) REVERT: I 440 ASN cc_start: 0.7822 (m-40) cc_final: 0.7447 (m-40) REVERT: I 441 MET cc_start: 0.7065 (tmm) cc_final: 0.5987 (tmm) REVERT: J 64 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8716 (mm-30) REVERT: J 174 LEU cc_start: 0.8898 (mt) cc_final: 0.8633 (mt) REVERT: J 201 PHE cc_start: 0.8830 (m-80) cc_final: 0.8202 (m-80) REVERT: J 205 PHE cc_start: 0.8945 (m-80) cc_final: 0.8304 (m-80) REVERT: J 217 PHE cc_start: 0.9181 (t80) cc_final: 0.8579 (t80) REVERT: J 221 PHE cc_start: 0.8946 (t80) cc_final: 0.8404 (t80) REVERT: J 223 TYR cc_start: 0.8725 (m-80) cc_final: 0.8397 (m-80) REVERT: J 247 PHE cc_start: 0.9166 (m-80) cc_final: 0.8598 (m-10) REVERT: J 277 HIS cc_start: 0.9013 (t-90) cc_final: 0.8748 (t-90) REVERT: J 411 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8494 (pt0) REVERT: J 436 TYR cc_start: 0.6909 (m-10) cc_final: 0.6570 (m-80) outliers start: 0 outliers final: 0 residues processed: 901 average time/residue: 0.2321 time to fit residues: 343.2496 Evaluate side-chains 763 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 763 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 217 optimal weight: 6.9990 chunk 369 optimal weight: 6.9990 chunk 452 optimal weight: 0.9990 chunk 302 optimal weight: 8.9990 chunk 432 optimal weight: 3.9990 chunk 169 optimal weight: 0.4980 chunk 340 optimal weight: 0.9980 chunk 483 optimal weight: 9.9990 chunk 176 optimal weight: 0.0770 chunk 376 optimal weight: 2.9990 chunk 48 optimal weight: 30.0000 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 ASN C 602 ASN C 705 ASN ** D 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 HIS ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN E 553 ASN E 556 GLN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 594 ASN H 638 ASN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 HIS J 248 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.158298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.099158 restraints weight = 100575.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.104382 restraints weight = 58067.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.106614 restraints weight = 32255.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.107037 restraints weight = 25277.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.107349 restraints weight = 23981.946| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 42867 Z= 0.129 Angle : 0.601 8.966 58454 Z= 0.314 Chirality : 0.046 0.236 6899 Planarity : 0.005 0.108 7709 Dihedral : 4.650 24.429 6111 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.11), residues: 5708 helix: 0.22 (0.13), residues: 1583 sheet: -0.23 (0.16), residues: 1058 loop : -0.62 (0.11), residues: 3067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 391 TYR 0.032 0.001 TYR I 167 PHE 0.020 0.001 PHE J 241 TRP 0.019 0.001 TRP A 346 HIS 0.007 0.001 HIS G 211 Details of bonding type rmsd covalent geometry : bond 0.00286 (42867) covalent geometry : angle 0.60055 (58454) hydrogen bonds : bond 0.03485 ( 1503) hydrogen bonds : angle 5.14812 ( 4329) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1018 time to evaluate : 1.422 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: 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: 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 190 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 192 TYR cc_start: 0.8939 (p90) cc_final: 0.8613 (p90) REVERT: A 200 ARG cc_start: 0.7518 (mpt-90) cc_final: 0.6506 (mpt180) REVERT: A 225 LYS cc_start: 0.9095 (ttmt) cc_final: 0.8624 (ttpt) REVERT: A 250 GLU cc_start: 0.8929 (mp0) cc_final: 0.8619 (tp30) REVERT: A 391 LEU cc_start: 0.9169 (mm) cc_final: 0.8910 (mm) REVERT: A 436 TYR cc_start: 0.8955 (t80) cc_final: 0.8613 (t80) REVERT: A 453 ASP cc_start: 0.8741 (p0) cc_final: 0.8351 (p0) REVERT: A 465 GLU cc_start: 0.8660 (mp0) cc_final: 0.8317 (mp0) REVERT: A 479 GLU cc_start: 0.9322 (mp0) cc_final: 0.8981 (mp0) REVERT: A 496 LYS cc_start: 0.9413 (mmtt) cc_final: 0.9040 (mmtt) REVERT: A 512 ASP cc_start: 0.7909 (t0) cc_final: 0.7470 (t0) REVERT: A 525 GLU cc_start: 0.9359 (mp0) cc_final: 0.9018 (pm20) REVERT: A 552 PHE cc_start: 0.9214 (m-80) cc_final: 0.8901 (m-80) REVERT: A 727 PHE cc_start: 0.9034 (t80) cc_final: 0.8542 (t80) REVERT: B 185 ASP cc_start: 0.8502 (p0) cc_final: 0.7904 (p0) REVERT: B 192 TYR cc_start: 0.9182 (p90) cc_final: 0.8248 (p90) REVERT: B 236 PHE cc_start: 0.9178 (t80) cc_final: 0.8944 (t80) REVERT: B 243 ILE cc_start: 0.9165 (tt) cc_final: 0.8595 (pt) REVERT: B 244 ASP cc_start: 0.8568 (t70) cc_final: 0.7562 (t0) REVERT: B 246 ASN cc_start: 0.9105 (m110) cc_final: 0.8607 (m110) REVERT: B 439 PHE cc_start: 0.9353 (t80) cc_final: 0.9147 (t80) REVERT: B 456 TYR cc_start: 0.7564 (m-10) cc_final: 0.7198 (m-10) REVERT: B 470 ARG cc_start: 0.8017 (ptp90) cc_final: 0.7540 (ttp80) REVERT: B 476 ASN cc_start: 0.8783 (t0) cc_final: 0.8496 (t0) REVERT: B 479 GLU cc_start: 0.8364 (pt0) cc_final: 0.7944 (tt0) REVERT: B 512 ASP cc_start: 0.8211 (t0) cc_final: 0.7971 (t0) REVERT: B 524 LYS cc_start: 0.9052 (ptmm) cc_final: 0.8588 (pttm) REVERT: B 553 ASN cc_start: 0.6512 (m-40) cc_final: 0.5819 (m-40) REVERT: B 561 ASN cc_start: 0.9031 (m110) cc_final: 0.8699 (m110) REVERT: B 727 PHE cc_start: 0.8529 (t80) cc_final: 0.8110 (t80) REVERT: C 195 ASP cc_start: 0.8217 (t0) cc_final: 0.7814 (t0) REVERT: C 243 ILE cc_start: 0.9389 (tp) cc_final: 0.9131 (tp) REVERT: C 246 ASN cc_start: 0.9112 (m-40) cc_final: 0.8678 (m-40) REVERT: C 297 ARG cc_start: 0.8674 (tpt170) cc_final: 0.8281 (tpp-160) REVERT: C 326 ASN cc_start: 0.8156 (p0) cc_final: 0.7729 (p0) REVERT: C 336 HIS cc_start: 0.9114 (p-80) cc_final: 0.8600 (p-80) REVERT: C 368 ASN cc_start: 0.8657 (t0) cc_final: 0.8401 (t0) REVERT: C 408 ASN cc_start: 0.9247 (t0) cc_final: 0.9027 (t0) REVERT: C 434 MET cc_start: 0.9132 (ppp) cc_final: 0.8884 (ppp) REVERT: C 439 PHE cc_start: 0.9432 (t80) cc_final: 0.9074 (t80) REVERT: C 462 TYR cc_start: 0.8980 (t80) cc_final: 0.8770 (t80) REVERT: C 486 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8629 (tm-30) REVERT: C 528 LYS cc_start: 0.9136 (ttmm) cc_final: 0.8600 (mmtt) REVERT: C 550 PHE cc_start: 0.9404 (m-80) cc_final: 0.9113 (m-80) REVERT: C 551 ASP cc_start: 0.8714 (t0) cc_final: 0.8496 (t70) REVERT: C 552 PHE cc_start: 0.8665 (m-80) cc_final: 0.8292 (m-80) REVERT: C 553 ASN cc_start: 0.8691 (t0) cc_final: 0.8216 (t0) REVERT: C 575 TYR cc_start: 0.7733 (m-80) cc_final: 0.7349 (m-80) REVERT: C 590 LEU cc_start: 0.9396 (tt) cc_final: 0.9035 (tt) REVERT: C 636 ARG cc_start: 0.8917 (ptt-90) cc_final: 0.8651 (ptp90) REVERT: C 727 PHE cc_start: 0.7910 (t80) cc_final: 0.7552 (t80) REVERT: D 190 GLU cc_start: 0.8793 (tp30) cc_final: 0.8441 (tp30) REVERT: D 192 TYR cc_start: 0.9246 (p90) cc_final: 0.8646 (p90) REVERT: D 195 ASP cc_start: 0.8716 (t0) cc_final: 0.8331 (t70) REVERT: D 246 ASN cc_start: 0.9216 (m110) cc_final: 0.8891 (m110) REVERT: D 265 ASP cc_start: 0.8741 (t70) cc_final: 0.8514 (t70) REVERT: D 299 HIS cc_start: 0.8903 (t-90) cc_final: 0.8541 (t-90) REVERT: D 365 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7215 (tpp-160) REVERT: D 408 ASN cc_start: 0.9246 (t0) cc_final: 0.8945 (t0) REVERT: D 411 TYR cc_start: 0.8052 (t80) cc_final: 0.7771 (t80) REVERT: D 441 GLU cc_start: 0.8944 (tp30) cc_final: 0.8571 (tp30) REVERT: D 447 GLN cc_start: 0.8568 (pp30) cc_final: 0.8046 (pp30) REVERT: D 449 ARG cc_start: 0.8391 (ptp-170) cc_final: 0.7901 (ptp90) REVERT: D 456 TYR cc_start: 0.9093 (m-80) cc_final: 0.8836 (m-80) REVERT: D 483 GLN cc_start: 0.8562 (mp10) cc_final: 0.8154 (mp10) REVERT: D 501 VAL cc_start: 0.9357 (t) cc_final: 0.9096 (p) REVERT: D 525 GLU cc_start: 0.9222 (mp0) cc_final: 0.8890 (mp0) REVERT: D 565 GLN cc_start: 0.9471 (mm-40) cc_final: 0.9099 (mt0) REVERT: D 638 ILE cc_start: 0.9149 (pt) cc_final: 0.8770 (pt) REVERT: D 703 LYS cc_start: 0.9600 (mppt) cc_final: 0.9347 (mmtm) REVERT: E 240 THR cc_start: 0.9323 (m) cc_final: 0.8911 (t) REVERT: E 391 LEU cc_start: 0.9512 (mm) cc_final: 0.9179 (mm) REVERT: E 434 MET cc_start: 0.8364 (tmm) cc_final: 0.8098 (ppp) REVERT: E 436 TYR cc_start: 0.8785 (t80) cc_final: 0.8138 (t80) REVERT: E 438 GLN cc_start: 0.8667 (mt0) cc_final: 0.8325 (mm-40) REVERT: E 439 PHE cc_start: 0.9463 (t80) cc_final: 0.9152 (t80) REVERT: E 470 ARG cc_start: 0.8119 (tmm-80) cc_final: 0.7727 (tmm160) REVERT: E 483 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8834 (mm110) REVERT: E 509 ASN cc_start: 0.9207 (t0) cc_final: 0.8867 (t0) REVERT: E 512 ASP cc_start: 0.8303 (t0) cc_final: 0.7935 (t0) REVERT: E 518 LYS cc_start: 0.9425 (ptmt) cc_final: 0.9215 (ptmm) REVERT: E 553 ASN cc_start: 0.8631 (m-40) cc_final: 0.8217 (m-40) REVERT: E 616 HIS cc_start: 0.9002 (m90) cc_final: 0.8666 (p-80) REVERT: E 635 ILE cc_start: 0.9699 (mm) cc_final: 0.9481 (pt) REVERT: F 176 PRO cc_start: 0.8537 (Cg_exo) cc_final: 0.8267 (Cg_endo) REVERT: F 190 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8226 (tm-30) REVERT: F 223 PRO cc_start: 0.9420 (Cg_endo) cc_final: 0.9056 (Cg_exo) REVERT: F 226 TRP cc_start: 0.9347 (t60) cc_final: 0.9109 (t60) REVERT: F 261 ILE cc_start: 0.9688 (mm) cc_final: 0.9462 (mm) REVERT: F 265 ASP cc_start: 0.8906 (t0) cc_final: 0.8297 (p0) REVERT: F 326 ASN cc_start: 0.7927 (m-40) cc_final: 0.7363 (m-40) REVERT: F 366 TYR cc_start: 0.8728 (m-10) cc_final: 0.8404 (m-10) REVERT: F 439 PHE cc_start: 0.9532 (t80) cc_final: 0.9160 (t80) REVERT: F 453 ASP cc_start: 0.8829 (p0) cc_final: 0.8607 (p0) REVERT: F 464 PHE cc_start: 0.8299 (t80) cc_final: 0.8092 (t80) REVERT: F 501 VAL cc_start: 0.9119 (t) cc_final: 0.8823 (p) REVERT: F 523 LEU cc_start: 0.9430 (tp) cc_final: 0.9160 (tp) REVERT: F 551 ASP cc_start: 0.7644 (t0) cc_final: 0.6967 (p0) REVERT: F 602 ASN cc_start: 0.9251 (m-40) cc_final: 0.8940 (m-40) REVERT: G 231 ASP cc_start: 0.8881 (p0) cc_final: 0.8564 (p0) REVERT: G 238 LYS cc_start: 0.9331 (mmmm) cc_final: 0.8885 (mmmm) REVERT: G 242 ARG cc_start: 0.8647 (mtt90) cc_final: 0.8121 (mmm-85) REVERT: G 266 MET cc_start: 0.8739 (ttt) cc_final: 0.8205 (ttt) REVERT: G 299 HIS cc_start: 0.8694 (t-90) cc_final: 0.8286 (t-90) REVERT: G 325 SER cc_start: 0.8714 (t) cc_final: 0.8447 (p) REVERT: G 440 LEU cc_start: 0.9215 (mt) cc_final: 0.8921 (mt) REVERT: G 448 LEU cc_start: 0.9542 (mm) cc_final: 0.9315 (mm) REVERT: G 512 ASP cc_start: 0.8288 (t0) cc_final: 0.6725 (t0) REVERT: G 514 LEU cc_start: 0.9592 (tt) cc_final: 0.9065 (tt) REVERT: G 515 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8444 (mm-30) REVERT: G 550 PHE cc_start: 0.8381 (m-80) cc_final: 0.7529 (m-80) REVERT: G 551 ASP cc_start: 0.8815 (t0) cc_final: 0.7601 (p0) REVERT: G 596 PHE cc_start: 0.9169 (m-80) cc_final: 0.8953 (m-80) REVERT: G 602 ASN cc_start: 0.8589 (m-40) cc_final: 0.8004 (m110) REVERT: G 727 PHE cc_start: 0.8252 (t80) cc_final: 0.7644 (t80) REVERT: H 65 LYS cc_start: 0.9547 (mmpt) cc_final: 0.9278 (mmtm) REVERT: H 74 TYR cc_start: 0.7841 (t80) cc_final: 0.7483 (t80) REVERT: H 117 HIS cc_start: 0.5786 (m90) cc_final: 0.5322 (m-70) REVERT: H 170 PHE cc_start: 0.9326 (t80) cc_final: 0.8710 (t80) REVERT: H 174 LEU cc_start: 0.9598 (mt) cc_final: 0.9378 (mt) REVERT: H 217 PHE cc_start: 0.8724 (t80) cc_final: 0.8100 (t80) REVERT: H 234 GLN cc_start: 0.8918 (mt0) cc_final: 0.8384 (mp10) REVERT: H 259 LEU cc_start: 0.9461 (mm) cc_final: 0.9254 (mm) REVERT: H 281 TRP cc_start: 0.8614 (t60) cc_final: 0.7795 (t60) REVERT: H 390 GLN cc_start: 0.8826 (mp10) cc_final: 0.8624 (mp10) REVERT: H 484 MET cc_start: 0.8441 (mpp) cc_final: 0.7813 (mpp) REVERT: H 486 VAL cc_start: 0.8817 (m) cc_final: 0.8552 (p) REVERT: H 499 LEU cc_start: 0.8750 (mp) cc_final: 0.7991 (mp) REVERT: H 521 LEU cc_start: 0.9585 (mm) cc_final: 0.9001 (mm) REVERT: H 527 LEU cc_start: 0.8352 (mt) cc_final: 0.8127 (mm) REVERT: H 586 ASN cc_start: 0.9335 (t0) cc_final: 0.9093 (t0) REVERT: H 611 GLN cc_start: 0.8144 (tp-100) cc_final: 0.7910 (tp40) REVERT: H 630 VAL cc_start: 0.9197 (t) cc_final: 0.8927 (m) REVERT: H 736 PHE cc_start: 0.8854 (t80) cc_final: 0.8528 (t80) REVERT: H 737 PHE cc_start: 0.9074 (m-80) cc_final: 0.8491 (m-80) REVERT: I 139 GLU cc_start: 0.8046 (tt0) cc_final: 0.7772 (tt0) REVERT: I 149 TYR cc_start: 0.9112 (t80) cc_final: 0.8847 (t80) REVERT: I 157 ARG cc_start: 0.8792 (ttp-110) cc_final: 0.8522 (tmm-80) REVERT: I 205 PHE cc_start: 0.8271 (m-80) cc_final: 0.7830 (m-80) REVERT: I 230 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.7845 (ttm170) REVERT: I 264 MET cc_start: 0.9006 (pmm) cc_final: 0.8138 (pmm) REVERT: I 267 ARG cc_start: 0.9257 (ptp90) cc_final: 0.8974 (ptt-90) REVERT: I 441 MET cc_start: 0.5998 (tmm) cc_final: 0.5504 (tmm) REVERT: J 64 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8755 (mm-30) REVERT: J 201 PHE cc_start: 0.8744 (m-80) cc_final: 0.7872 (m-80) REVERT: J 221 PHE cc_start: 0.8879 (t80) cc_final: 0.8435 (t80) REVERT: J 223 TYR cc_start: 0.8634 (m-80) cc_final: 0.8234 (m-80) REVERT: J 241 PHE cc_start: 0.9021 (t80) cc_final: 0.8819 (t80) REVERT: J 243 TYR cc_start: 0.8571 (t80) cc_final: 0.8030 (t80) REVERT: J 244 MET cc_start: 0.9260 (tpt) cc_final: 0.9060 (tpp) REVERT: J 277 HIS cc_start: 0.8979 (t-90) cc_final: 0.8730 (t-90) REVERT: J 411 GLN cc_start: 0.8858 (tp-100) cc_final: 0.8484 (pt0) REVERT: J 436 TYR cc_start: 0.6881 (m-10) cc_final: 0.6592 (m-80) outliers start: 0 outliers final: 0 residues processed: 1018 average time/residue: 0.2273 time to fit residues: 380.4996 Evaluate side-chains 844 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 844 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 374 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 chunk 415 optimal weight: 10.0000 chunk 316 optimal weight: 1.9990 chunk 469 optimal weight: 0.0970 chunk 405 optimal weight: 5.9990 chunk 363 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 215 optimal weight: 0.4980 chunk 314 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN B 485 GLN C 299 HIS ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** D 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 HIS ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN E 553 ASN E 556 GLN F 483 GLN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 594 ASN H 638 ASN H 642 GLN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 HIS J 248 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.161196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101284 restraints weight = 98026.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106755 restraints weight = 55077.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108179 restraints weight = 32591.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109621 restraints weight = 24636.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.110056 restraints weight = 21955.933| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 42867 Z= 0.115 Angle : 0.594 10.308 58454 Z= 0.310 Chirality : 0.045 0.208 6899 Planarity : 0.004 0.103 7709 Dihedral : 4.490 25.468 6111 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.11), residues: 5708 helix: 0.24 (0.13), residues: 1627 sheet: -0.12 (0.16), residues: 1049 loop : -0.57 (0.11), residues: 3032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 391 TYR 0.026 0.001 TYR J 243 PHE 0.031 0.001 PHE J 217 TRP 0.016 0.001 TRP H 271 HIS 0.006 0.001 HIS F 253 Details of bonding type rmsd covalent geometry : bond 0.00255 (42867) covalent geometry : angle 0.59449 (58454) hydrogen bonds : bond 0.03344 ( 1503) hydrogen bonds : angle 5.07143 ( 4329) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1063 time to evaluate : 1.353 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: 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: 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 190 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8174 (tm-30) REVERT: A 192 TYR cc_start: 0.8881 (p90) cc_final: 0.8590 (p90) REVERT: A 225 LYS cc_start: 0.9088 (ttmt) cc_final: 0.8617 (ttpt) REVERT: A 250 GLU cc_start: 0.8885 (mp0) cc_final: 0.8550 (tp30) REVERT: A 391 LEU cc_start: 0.9151 (mm) cc_final: 0.8846 (mm) REVERT: A 415 ASN cc_start: 0.8822 (m110) cc_final: 0.8564 (m110) REVERT: A 436 TYR cc_start: 0.8952 (t80) cc_final: 0.8610 (t80) REVERT: A 453 ASP cc_start: 0.8735 (p0) cc_final: 0.8330 (p0) REVERT: A 465 GLU cc_start: 0.8620 (mp0) cc_final: 0.8290 (mp0) REVERT: A 486 GLU cc_start: 0.8726 (tt0) cc_final: 0.8478 (tm-30) REVERT: A 496 LYS cc_start: 0.9416 (mmtt) cc_final: 0.8992 (mmtt) REVERT: A 512 ASP cc_start: 0.7671 (t0) cc_final: 0.7204 (t0) REVERT: A 525 GLU cc_start: 0.9308 (mp0) cc_final: 0.8960 (pm20) REVERT: A 551 ASP cc_start: 0.8313 (t0) cc_final: 0.8085 (p0) REVERT: A 552 PHE cc_start: 0.9238 (m-80) cc_final: 0.8759 (m-10) REVERT: A 590 LEU cc_start: 0.9350 (tt) cc_final: 0.9089 (tt) REVERT: A 727 PHE cc_start: 0.9036 (t80) cc_final: 0.8566 (t80) REVERT: B 192 TYR cc_start: 0.9201 (p90) cc_final: 0.8155 (p90) REVERT: B 244 ASP cc_start: 0.8576 (t70) cc_final: 0.7912 (t0) REVERT: B 246 ASN cc_start: 0.9131 (m110) cc_final: 0.8614 (m110) REVERT: B 297 ARG cc_start: 0.8088 (tmm160) cc_final: 0.7855 (ttp80) REVERT: B 328 ASN cc_start: 0.7903 (t0) cc_final: 0.7261 (t0) REVERT: B 378 LEU cc_start: 0.9009 (tp) cc_final: 0.8386 (tt) REVERT: B 411 TYR cc_start: 0.8567 (t80) cc_final: 0.8027 (t80) REVERT: B 439 PHE cc_start: 0.9354 (t80) cc_final: 0.9134 (t80) REVERT: B 470 ARG cc_start: 0.7856 (ptp90) cc_final: 0.7414 (ttp80) REVERT: B 487 THR cc_start: 0.9672 (t) cc_final: 0.9468 (t) REVERT: B 500 LEU cc_start: 0.9353 (mm) cc_final: 0.9008 (mm) REVERT: B 553 ASN cc_start: 0.6328 (m-40) cc_final: 0.5388 (m-40) REVERT: B 557 GLN cc_start: 0.7770 (tp40) cc_final: 0.7264 (tp40) REVERT: B 560 GLN cc_start: 0.9324 (tm-30) cc_final: 0.9055 (tm-30) REVERT: B 561 ASN cc_start: 0.9059 (m110) cc_final: 0.8314 (m110) REVERT: B 565 GLN cc_start: 0.9033 (mt0) cc_final: 0.8585 (tt0) REVERT: B 590 LEU cc_start: 0.9022 (tp) cc_final: 0.8399 (tp) REVERT: B 727 PHE cc_start: 0.8535 (t80) cc_final: 0.8156 (t80) REVERT: C 195 ASP cc_start: 0.8158 (t0) cc_final: 0.7695 (t0) REVERT: C 225 LYS cc_start: 0.9381 (tttt) cc_final: 0.8974 (tttm) REVERT: C 242 ARG cc_start: 0.9222 (mtm-85) cc_final: 0.8800 (mtm-85) REVERT: C 243 ILE cc_start: 0.9362 (tp) cc_final: 0.9097 (tp) REVERT: C 246 ASN cc_start: 0.9089 (m-40) cc_final: 0.8680 (m-40) REVERT: C 297 ARG cc_start: 0.8714 (tpt170) cc_final: 0.8425 (tpp-160) REVERT: C 326 ASN cc_start: 0.8163 (p0) cc_final: 0.7746 (p0) REVERT: C 336 HIS cc_start: 0.9116 (p-80) cc_final: 0.8573 (p-80) REVERT: C 368 ASN cc_start: 0.8653 (t0) cc_final: 0.8392 (t0) REVERT: C 408 ASN cc_start: 0.9257 (t0) cc_final: 0.9034 (t0) REVERT: C 434 MET cc_start: 0.8716 (ppp) cc_final: 0.8339 (ppp) REVERT: C 439 PHE cc_start: 0.9410 (t80) cc_final: 0.8883 (t80) REVERT: C 462 TYR cc_start: 0.8932 (t80) cc_final: 0.8598 (t80) REVERT: C 512 ASP cc_start: 0.8762 (t0) cc_final: 0.7691 (t70) REVERT: C 550 PHE cc_start: 0.9452 (m-80) cc_final: 0.9142 (m-80) REVERT: C 551 ASP cc_start: 0.8707 (t0) cc_final: 0.8464 (t70) REVERT: C 552 PHE cc_start: 0.8661 (m-80) cc_final: 0.8323 (m-80) REVERT: C 553 ASN cc_start: 0.8617 (t0) cc_final: 0.8263 (t0) REVERT: C 575 TYR cc_start: 0.7753 (m-80) cc_final: 0.7419 (m-80) REVERT: C 590 LEU cc_start: 0.9318 (tt) cc_final: 0.8980 (tt) REVERT: C 595 ARG cc_start: 0.8802 (ttm110) cc_final: 0.8567 (ttp-110) REVERT: C 636 ARG cc_start: 0.8893 (ptt-90) cc_final: 0.8622 (ptp90) REVERT: C 727 PHE cc_start: 0.7978 (t80) cc_final: 0.7750 (t80) REVERT: D 190 GLU cc_start: 0.8750 (tp30) cc_final: 0.8460 (tp30) REVERT: D 192 TYR cc_start: 0.9260 (p90) cc_final: 0.8755 (p90) REVERT: D 195 ASP cc_start: 0.8720 (t0) cc_final: 0.8338 (t70) REVERT: D 238 LYS cc_start: 0.9407 (tptp) cc_final: 0.9130 (tptm) REVERT: D 246 ASN cc_start: 0.9215 (m110) cc_final: 0.8916 (m110) REVERT: D 299 HIS cc_start: 0.8860 (t-90) cc_final: 0.8454 (t-90) REVERT: D 365 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7231 (tpp-160) REVERT: D 384 VAL cc_start: 0.9061 (p) cc_final: 0.8801 (p) REVERT: D 408 ASN cc_start: 0.9226 (t0) cc_final: 0.8913 (t0) REVERT: D 411 TYR cc_start: 0.7910 (t80) cc_final: 0.7664 (t80) REVERT: D 447 GLN cc_start: 0.8518 (pp30) cc_final: 0.8011 (pp30) REVERT: D 449 ARG cc_start: 0.8388 (ptp-170) cc_final: 0.7955 (ptp90) REVERT: D 456 TYR cc_start: 0.9070 (m-80) cc_final: 0.8847 (m-80) REVERT: D 483 GLN cc_start: 0.8513 (mp10) cc_final: 0.8122 (mp10) REVERT: D 501 VAL cc_start: 0.9287 (t) cc_final: 0.9003 (p) REVERT: D 525 GLU cc_start: 0.9177 (mp0) cc_final: 0.8770 (mp0) REVERT: D 553 ASN cc_start: 0.8001 (m110) cc_final: 0.7466 (m-40) REVERT: D 565 GLN cc_start: 0.9448 (mm-40) cc_final: 0.9091 (mt0) REVERT: E 202 PHE cc_start: 0.8539 (t80) cc_final: 0.8103 (t80) REVERT: E 216 LEU cc_start: 0.9250 (mt) cc_final: 0.9041 (mt) REVERT: E 240 THR cc_start: 0.9339 (m) cc_final: 0.8980 (t) REVERT: E 385 LEU cc_start: 0.7743 (pt) cc_final: 0.7300 (pt) REVERT: E 389 GLN cc_start: 0.8930 (mp10) cc_final: 0.8578 (mp10) REVERT: E 391 LEU cc_start: 0.9428 (mm) cc_final: 0.9196 (mm) REVERT: E 436 TYR cc_start: 0.8782 (t80) cc_final: 0.8143 (t80) REVERT: E 439 PHE cc_start: 0.9433 (t80) cc_final: 0.9192 (t80) REVERT: E 483 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8918 (mm110) REVERT: E 509 ASN cc_start: 0.9191 (t0) cc_final: 0.8797 (t0) REVERT: E 512 ASP cc_start: 0.8151 (t0) cc_final: 0.7799 (t0) REVERT: E 553 ASN cc_start: 0.8546 (m110) cc_final: 0.8250 (m-40) REVERT: E 602 ASN cc_start: 0.8594 (m-40) cc_final: 0.8280 (m-40) REVERT: E 616 HIS cc_start: 0.8966 (m90) cc_final: 0.8663 (p-80) REVERT: E 635 ILE cc_start: 0.9681 (mm) cc_final: 0.9420 (pt) REVERT: F 176 PRO cc_start: 0.8629 (Cg_exo) cc_final: 0.8353 (Cg_endo) REVERT: F 190 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8231 (tm-30) REVERT: F 223 PRO cc_start: 0.9448 (Cg_endo) cc_final: 0.9121 (Cg_exo) REVERT: F 226 TRP cc_start: 0.9337 (t60) cc_final: 0.9009 (t60) REVERT: F 261 ILE cc_start: 0.9681 (mm) cc_final: 0.9472 (mm) REVERT: F 265 ASP cc_start: 0.8927 (t0) cc_final: 0.8266 (p0) REVERT: F 326 ASN cc_start: 0.7944 (m-40) cc_final: 0.6370 (m-40) REVERT: F 366 TYR cc_start: 0.8672 (m-10) cc_final: 0.8350 (m-10) REVERT: F 439 PHE cc_start: 0.9515 (t80) cc_final: 0.9270 (t80) REVERT: F 453 ASP cc_start: 0.8824 (p0) cc_final: 0.8598 (p0) REVERT: F 486 GLU cc_start: 0.8156 (mp0) cc_final: 0.7885 (mp0) REVERT: F 490 ARG cc_start: 0.8353 (ttt180) cc_final: 0.7926 (ttp80) REVERT: F 501 VAL cc_start: 0.9067 (t) cc_final: 0.8766 (p) REVERT: F 512 ASP cc_start: 0.7548 (m-30) cc_final: 0.7256 (m-30) REVERT: F 523 LEU cc_start: 0.9418 (tp) cc_final: 0.9118 (tp) REVERT: F 551 ASP cc_start: 0.7528 (t0) cc_final: 0.6831 (p0) REVERT: F 590 LEU cc_start: 0.7822 (mt) cc_final: 0.7590 (mt) REVERT: F 602 ASN cc_start: 0.9271 (m-40) cc_final: 0.9004 (m-40) REVERT: G 211 HIS cc_start: 0.8991 (m90) cc_final: 0.8790 (m90) REVERT: G 238 LYS cc_start: 0.9277 (mmmm) cc_final: 0.8932 (mmmm) REVERT: G 242 ARG cc_start: 0.8588 (mtt90) cc_final: 0.8064 (mmm-85) REVERT: G 266 MET cc_start: 0.8658 (ttt) cc_final: 0.8141 (ttt) REVERT: G 299 HIS cc_start: 0.8731 (t-90) cc_final: 0.8377 (t-90) REVERT: G 325 SER cc_start: 0.8641 (t) cc_final: 0.8325 (p) REVERT: G 440 LEU cc_start: 0.9231 (mt) cc_final: 0.8903 (mt) REVERT: G 448 LEU cc_start: 0.9541 (mm) cc_final: 0.9316 (mm) REVERT: G 453 ASP cc_start: 0.8974 (p0) cc_final: 0.8646 (p0) REVERT: G 512 ASP cc_start: 0.8317 (t0) cc_final: 0.6677 (t0) REVERT: G 514 LEU cc_start: 0.9561 (tt) cc_final: 0.9101 (tt) REVERT: G 515 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8398 (mm-30) REVERT: G 550 PHE cc_start: 0.8320 (m-80) cc_final: 0.7420 (m-10) REVERT: G 551 ASP cc_start: 0.8848 (t0) cc_final: 0.7847 (p0) REVERT: G 602 ASN cc_start: 0.8606 (m-40) cc_final: 0.8045 (m110) REVERT: G 727 PHE cc_start: 0.8294 (t80) cc_final: 0.7714 (t80) REVERT: H 74 TYR cc_start: 0.7831 (t80) cc_final: 0.7445 (t80) REVERT: H 117 HIS cc_start: 0.6005 (m90) cc_final: 0.5529 (m90) REVERT: H 150 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8434 (mm-30) REVERT: H 158 ASP cc_start: 0.9269 (t0) cc_final: 0.9025 (m-30) REVERT: H 170 PHE cc_start: 0.9394 (t80) cc_final: 0.8736 (t80) REVERT: H 174 LEU cc_start: 0.9643 (mt) cc_final: 0.9352 (mt) REVERT: H 201 PHE cc_start: 0.8925 (m-80) cc_final: 0.8200 (m-80) REVERT: H 217 PHE cc_start: 0.8646 (t80) cc_final: 0.8070 (t80) REVERT: H 234 GLN cc_start: 0.8924 (mt0) cc_final: 0.8395 (mp10) REVERT: H 259 LEU cc_start: 0.9453 (mm) cc_final: 0.9236 (mm) REVERT: H 281 TRP cc_start: 0.8695 (t60) cc_final: 0.7770 (t60) REVERT: H 441 MET cc_start: 0.8151 (tmm) cc_final: 0.7547 (tmm) REVERT: H 486 VAL cc_start: 0.8843 (m) cc_final: 0.8569 (p) REVERT: H 499 LEU cc_start: 0.8860 (mp) cc_final: 0.8000 (mp) REVERT: H 521 LEU cc_start: 0.9598 (mm) cc_final: 0.9313 (mm) REVERT: H 586 ASN cc_start: 0.9305 (t0) cc_final: 0.9053 (t0) REVERT: H 611 GLN cc_start: 0.8172 (tp-100) cc_final: 0.7937 (tp40) REVERT: H 630 VAL cc_start: 0.9183 (t) cc_final: 0.8880 (m) REVERT: H 736 PHE cc_start: 0.8931 (t80) cc_final: 0.8488 (t80) REVERT: H 737 PHE cc_start: 0.9094 (m-80) cc_final: 0.8514 (m-80) REVERT: H 772 PHE cc_start: 0.8782 (m-10) cc_final: 0.8494 (m-80) REVERT: I 35 HIS cc_start: 0.7528 (m90) cc_final: 0.7274 (m90) REVERT: I 108 TYR cc_start: 0.8229 (m-10) cc_final: 0.7954 (m-80) REVERT: I 157 ARG cc_start: 0.8715 (ttp-110) cc_final: 0.7846 (ttp-110) REVERT: I 158 ASP cc_start: 0.8752 (m-30) cc_final: 0.8289 (m-30) REVERT: I 205 PHE cc_start: 0.8228 (m-80) cc_final: 0.7787 (m-80) REVERT: I 230 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.7906 (ttm110) REVERT: I 254 LEU cc_start: 0.8555 (pp) cc_final: 0.8182 (mm) REVERT: I 267 ARG cc_start: 0.9247 (ptp90) cc_final: 0.8976 (ptt-90) REVERT: I 392 LEU cc_start: 0.8450 (mt) cc_final: 0.8162 (tp) REVERT: I 440 ASN cc_start: 0.7517 (m-40) cc_final: 0.7083 (m110) REVERT: I 441 MET cc_start: 0.6141 (tmm) cc_final: 0.5643 (tmm) REVERT: I 597 GLU cc_start: 0.7255 (mp0) cc_final: 0.6700 (mp0) REVERT: J 217 PHE cc_start: 0.8571 (m-80) cc_final: 0.8244 (m-80) REVERT: J 221 PHE cc_start: 0.8910 (t80) cc_final: 0.8376 (t80) REVERT: J 223 TYR cc_start: 0.8670 (m-80) cc_final: 0.8079 (m-80) REVERT: J 277 HIS cc_start: 0.8978 (t-90) cc_final: 0.8738 (t-90) REVERT: J 411 GLN cc_start: 0.8860 (tp-100) cc_final: 0.8500 (pt0) REVERT: J 436 TYR cc_start: 0.6817 (m-10) cc_final: 0.6511 (m-80) REVERT: J 502 ARG cc_start: 0.7469 (mpp-170) cc_final: 0.7135 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 1063 average time/residue: 0.2301 time to fit residues: 403.5129 Evaluate side-chains 860 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 860 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 279 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 397 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 379 optimal weight: 1.9990 chunk 558 optimal weight: 50.0000 chunk 426 optimal weight: 0.0570 chunk 175 optimal weight: 4.9990 chunk 430 optimal weight: 5.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 HIS B 263 HIS B 485 GLN ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 HIS E 409 ASN E 553 ASN E 556 GLN G 198 ASN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 594 ASN H 638 ASN H 690 HIS ** I 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 HIS J 248 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.157956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.099446 restraints weight = 99129.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.103353 restraints weight = 52885.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.105929 restraints weight = 35468.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.107574 restraints weight = 27116.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.108643 restraints weight = 22805.759| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 42867 Z= 0.181 Angle : 0.626 10.150 58454 Z= 0.328 Chirality : 0.046 0.245 6899 Planarity : 0.005 0.115 7709 Dihedral : 4.636 25.666 6111 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.02 % Allowed : 1.01 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.11), residues: 5708 helix: 0.33 (0.13), residues: 1604 sheet: -0.18 (0.16), residues: 1036 loop : -0.62 (0.11), residues: 3068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 391 TYR 0.038 0.002 TYR I 149 PHE 0.037 0.002 PHE J 217 TRP 0.019 0.001 TRP H 271 HIS 0.005 0.001 HIS F 253 Details of bonding type rmsd covalent geometry : bond 0.00397 (42867) covalent geometry : angle 0.62565 (58454) hydrogen bonds : bond 0.03520 ( 1503) hydrogen bonds : angle 5.04426 ( 4329) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 961 time to evaluate : 1.598 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: 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: symmetry clash REVERT: A 190 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8160 (tm-30) REVERT: A 192 TYR cc_start: 0.8958 (p90) cc_final: 0.8714 (p90) REVERT: A 225 LYS cc_start: 0.9000 (ttmt) cc_final: 0.8570 (ttpt) REVERT: A 250 GLU cc_start: 0.8885 (mp0) cc_final: 0.8555 (tp30) REVERT: A 391 LEU cc_start: 0.9219 (mm) cc_final: 0.8949 (mm) REVERT: A 415 ASN cc_start: 0.8829 (m110) cc_final: 0.8512 (m110) REVERT: A 436 TYR cc_start: 0.8956 (t80) cc_final: 0.8616 (t80) REVERT: A 453 ASP cc_start: 0.8819 (p0) cc_final: 0.8341 (p0) REVERT: A 465 GLU cc_start: 0.8577 (mp0) cc_final: 0.8280 (mp0) REVERT: A 512 ASP cc_start: 0.7906 (t0) cc_final: 0.7407 (t0) REVERT: A 525 GLU cc_start: 0.9309 (mp0) cc_final: 0.8982 (pm20) REVERT: A 551 ASP cc_start: 0.8383 (t0) cc_final: 0.8076 (p0) REVERT: A 552 PHE cc_start: 0.9242 (m-80) cc_final: 0.8992 (m-10) REVERT: A 590 LEU cc_start: 0.9303 (tt) cc_final: 0.9062 (tt) REVERT: A 727 PHE cc_start: 0.8999 (t80) cc_final: 0.8573 (t80) REVERT: B 192 TYR cc_start: 0.9222 (p90) cc_final: 0.8456 (p90) REVERT: B 225 LYS cc_start: 0.9398 (tttt) cc_final: 0.9148 (tttm) REVERT: B 243 ILE cc_start: 0.9193 (tt) cc_final: 0.8582 (pt) REVERT: B 244 ASP cc_start: 0.8598 (t70) cc_final: 0.7530 (t0) REVERT: B 246 ASN cc_start: 0.9096 (m110) cc_final: 0.8609 (m110) REVERT: B 265 ASP cc_start: 0.8508 (t0) cc_final: 0.8198 (t0) REVERT: B 468 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7872 (mmm-85) REVERT: B 470 ARG cc_start: 0.7978 (ptp90) cc_final: 0.7502 (ttp80) REVERT: B 476 ASN cc_start: 0.8689 (t0) cc_final: 0.8027 (t0) REVERT: B 478 SER cc_start: 0.9294 (m) cc_final: 0.8846 (p) REVERT: B 486 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8497 (tm-30) REVERT: B 487 THR cc_start: 0.9639 (t) cc_final: 0.9250 (t) REVERT: B 500 LEU cc_start: 0.9413 (mm) cc_final: 0.9213 (mm) REVERT: B 512 ASP cc_start: 0.8284 (t0) cc_final: 0.7872 (t0) REVERT: B 553 ASN cc_start: 0.6696 (m-40) cc_final: 0.6401 (m-40) REVERT: B 557 GLN cc_start: 0.7737 (tp40) cc_final: 0.7170 (tp40) REVERT: B 560 GLN cc_start: 0.9286 (tm-30) cc_final: 0.8997 (tm-30) REVERT: B 561 ASN cc_start: 0.8984 (m110) cc_final: 0.8141 (m110) REVERT: B 565 GLN cc_start: 0.9001 (mt0) cc_final: 0.8581 (tt0) REVERT: B 584 ASN cc_start: 0.8683 (t0) cc_final: 0.8470 (t0) REVERT: B 590 LEU cc_start: 0.8998 (tp) cc_final: 0.8696 (tp) REVERT: B 727 PHE cc_start: 0.8519 (t80) cc_final: 0.8203 (t80) REVERT: C 195 ASP cc_start: 0.8129 (t0) cc_final: 0.7674 (t0) REVERT: C 225 LYS cc_start: 0.9386 (tttt) cc_final: 0.9009 (tttm) REVERT: C 243 ILE cc_start: 0.9411 (tp) cc_final: 0.9052 (tp) REVERT: C 246 ASN cc_start: 0.9059 (m-40) cc_final: 0.8583 (m-40) REVERT: C 265 ASP cc_start: 0.8944 (t0) cc_final: 0.7776 (p0) REVERT: C 266 MET cc_start: 0.8157 (tpt) cc_final: 0.7207 (tpt) REVERT: C 297 ARG cc_start: 0.8733 (tpt170) cc_final: 0.8344 (tpp-160) REVERT: C 326 ASN cc_start: 0.8105 (p0) cc_final: 0.7752 (p0) REVERT: C 336 HIS cc_start: 0.9080 (p-80) cc_final: 0.8532 (p-80) REVERT: C 378 LEU cc_start: 0.9344 (tp) cc_final: 0.8801 (tt) REVERT: C 408 ASN cc_start: 0.9244 (t0) cc_final: 0.9024 (t0) REVERT: C 434 MET cc_start: 0.8876 (ppp) cc_final: 0.8604 (ppp) REVERT: C 439 PHE cc_start: 0.9374 (t80) cc_final: 0.9137 (t80) REVERT: C 497 ASP cc_start: 0.8133 (p0) cc_final: 0.7878 (p0) REVERT: C 512 ASP cc_start: 0.8821 (t0) cc_final: 0.7945 (t70) REVERT: C 528 LYS cc_start: 0.9120 (ttmm) cc_final: 0.8624 (mmtt) REVERT: C 552 PHE cc_start: 0.8705 (m-80) cc_final: 0.8349 (m-80) REVERT: C 553 ASN cc_start: 0.8723 (t0) cc_final: 0.8427 (t0) REVERT: C 575 TYR cc_start: 0.7848 (m-80) cc_final: 0.7504 (m-80) REVERT: C 590 LEU cc_start: 0.9358 (tt) cc_final: 0.9041 (tt) REVERT: C 596 PHE cc_start: 0.9158 (m-80) cc_final: 0.8933 (m-80) REVERT: C 727 PHE cc_start: 0.7955 (t80) cc_final: 0.7605 (t80) REVERT: D 190 GLU cc_start: 0.8835 (tp30) cc_final: 0.8528 (tp30) REVERT: D 192 TYR cc_start: 0.9321 (p90) cc_final: 0.8697 (p90) REVERT: D 195 ASP cc_start: 0.8581 (t0) cc_final: 0.8264 (t70) REVERT: D 197 LYS cc_start: 0.8917 (tptt) cc_final: 0.8324 (tptp) REVERT: D 244 ASP cc_start: 0.9088 (t0) cc_final: 0.8693 (t70) REVERT: D 246 ASN cc_start: 0.9157 (m110) cc_final: 0.8918 (m110) REVERT: D 265 ASP cc_start: 0.8601 (t70) cc_final: 0.8365 (t70) REVERT: D 297 ARG cc_start: 0.8390 (ttp80) cc_final: 0.7885 (ttp80) REVERT: D 353 ASN cc_start: 0.9268 (t0) cc_final: 0.9049 (t0) REVERT: D 365 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7369 (tpp-160) REVERT: D 367 VAL cc_start: 0.9424 (t) cc_final: 0.9110 (p) REVERT: D 408 ASN cc_start: 0.9216 (t0) cc_final: 0.8873 (t0) REVERT: D 411 TYR cc_start: 0.8114 (t80) cc_final: 0.7873 (t80) REVERT: D 437 ASN cc_start: 0.9592 (m-40) cc_final: 0.9201 (m-40) REVERT: D 447 GLN cc_start: 0.8617 (pp30) cc_final: 0.8182 (pp30) REVERT: D 449 ARG cc_start: 0.8373 (ptp-170) cc_final: 0.8132 (ptp90) REVERT: D 483 GLN cc_start: 0.8594 (mp10) cc_final: 0.8179 (mp10) REVERT: D 501 VAL cc_start: 0.9362 (t) cc_final: 0.9103 (p) REVERT: D 525 GLU cc_start: 0.9178 (mp0) cc_final: 0.8743 (mp0) REVERT: D 565 GLN cc_start: 0.9420 (mm-40) cc_final: 0.9173 (mt0) REVERT: D 587 MET cc_start: 0.9384 (ptp) cc_final: 0.8584 (mpp) REVERT: E 202 PHE cc_start: 0.8471 (t80) cc_final: 0.8116 (t80) REVERT: E 385 LEU cc_start: 0.8074 (pt) cc_final: 0.7284 (pp) REVERT: E 389 GLN cc_start: 0.9024 (mp10) cc_final: 0.8465 (mp10) REVERT: E 434 MET cc_start: 0.8604 (ppp) cc_final: 0.8115 (ppp) REVERT: E 436 TYR cc_start: 0.8716 (t80) cc_final: 0.8244 (t80) REVERT: E 438 GLN cc_start: 0.8773 (mt0) cc_final: 0.8315 (mm-40) REVERT: E 439 PHE cc_start: 0.9345 (t80) cc_final: 0.9055 (t80) REVERT: E 502 GLU cc_start: 0.7850 (tp30) cc_final: 0.7384 (tp30) REVERT: E 509 ASN cc_start: 0.9101 (t0) cc_final: 0.8784 (t0) REVERT: E 512 ASP cc_start: 0.8507 (t0) cc_final: 0.7371 (t0) REVERT: E 553 ASN cc_start: 0.8741 (m-40) cc_final: 0.8395 (m-40) REVERT: E 602 ASN cc_start: 0.8690 (m-40) cc_final: 0.8288 (m-40) REVERT: E 635 ILE cc_start: 0.9678 (mm) cc_final: 0.9395 (pt) REVERT: E 639 LEU cc_start: 0.9453 (mm) cc_final: 0.9097 (tp) REVERT: F 176 PRO cc_start: 0.9121 (Cg_exo) cc_final: 0.8905 (Cg_endo) REVERT: F 190 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8206 (tm-30) REVERT: F 195 ASP cc_start: 0.8862 (t0) cc_final: 0.8358 (t0) REVERT: F 219 TYR cc_start: 0.8757 (m-80) cc_final: 0.8475 (m-80) REVERT: F 223 PRO cc_start: 0.9388 (Cg_endo) cc_final: 0.9007 (Cg_exo) REVERT: F 226 TRP cc_start: 0.9382 (t60) cc_final: 0.9134 (t-100) REVERT: F 242 ARG cc_start: 0.7617 (mtp180) cc_final: 0.6575 (mtp180) REVERT: F 261 ILE cc_start: 0.9644 (mm) cc_final: 0.9415 (mm) REVERT: F 265 ASP cc_start: 0.8909 (t0) cc_final: 0.8249 (p0) REVERT: F 326 ASN cc_start: 0.7965 (m-40) cc_final: 0.7417 (m-40) REVERT: F 366 TYR cc_start: 0.8914 (m-10) cc_final: 0.8524 (m-10) REVERT: F 439 PHE cc_start: 0.9485 (t80) cc_final: 0.9173 (t80) REVERT: F 453 ASP cc_start: 0.8821 (p0) cc_final: 0.8534 (p0) REVERT: F 462 TYR cc_start: 0.7794 (t80) cc_final: 0.6864 (t80) REVERT: F 497 ASP cc_start: 0.8833 (p0) cc_final: 0.8474 (p0) REVERT: F 501 VAL cc_start: 0.9113 (t) cc_final: 0.8818 (p) REVERT: F 512 ASP cc_start: 0.7607 (m-30) cc_final: 0.7194 (m-30) REVERT: F 523 LEU cc_start: 0.9472 (tp) cc_final: 0.9225 (tp) REVERT: F 551 ASP cc_start: 0.7500 (t0) cc_final: 0.6901 (p0) REVERT: F 590 LEU cc_start: 0.7837 (mt) cc_final: 0.7609 (mt) REVERT: F 602 ASN cc_start: 0.9235 (m-40) cc_final: 0.8906 (m-40) REVERT: G 202 PHE cc_start: 0.8137 (p90) cc_final: 0.7934 (p90) REVERT: G 231 ASP cc_start: 0.8940 (p0) cc_final: 0.8649 (p0) REVERT: G 238 LYS cc_start: 0.9301 (mmmm) cc_final: 0.8923 (mmmm) REVERT: G 242 ARG cc_start: 0.8696 (mtt90) cc_final: 0.8159 (mmm-85) REVERT: G 266 MET cc_start: 0.8622 (ttt) cc_final: 0.8145 (ttt) REVERT: G 299 HIS cc_start: 0.8567 (t-90) cc_final: 0.8289 (t-90) REVERT: G 325 SER cc_start: 0.8693 (t) cc_final: 0.8439 (p) REVERT: G 448 LEU cc_start: 0.9494 (mm) cc_final: 0.9268 (mm) REVERT: G 453 ASP cc_start: 0.8955 (p0) cc_final: 0.8622 (p0) REVERT: G 479 GLU cc_start: 0.8974 (mp0) cc_final: 0.8523 (mp0) REVERT: G 496 LYS cc_start: 0.9407 (tppt) cc_final: 0.9202 (mmtm) REVERT: G 550 PHE cc_start: 0.8393 (m-80) cc_final: 0.7574 (m-80) REVERT: G 551 ASP cc_start: 0.8875 (t0) cc_final: 0.8008 (p0) REVERT: G 602 ASN cc_start: 0.8697 (m-40) cc_final: 0.8068 (m110) REVERT: G 727 PHE cc_start: 0.8300 (t80) cc_final: 0.7670 (t80) REVERT: H 74 TYR cc_start: 0.7763 (t80) cc_final: 0.7336 (t80) REVERT: H 117 HIS cc_start: 0.6168 (m90) cc_final: 0.5688 (m90) REVERT: H 170 PHE cc_start: 0.9322 (t80) cc_final: 0.8663 (t80) REVERT: H 174 LEU cc_start: 0.9634 (mt) cc_final: 0.9323 (mt) REVERT: H 217 PHE cc_start: 0.8764 (t80) cc_final: 0.8202 (t80) REVERT: H 234 GLN cc_start: 0.8949 (mt0) cc_final: 0.8453 (mp10) REVERT: H 235 LEU cc_start: 0.9307 (mm) cc_final: 0.9051 (mm) REVERT: H 259 LEU cc_start: 0.9438 (mm) cc_final: 0.9190 (mm) REVERT: H 281 TRP cc_start: 0.8698 (t60) cc_final: 0.7808 (t60) REVERT: H 390 GLN cc_start: 0.8730 (mp10) cc_final: 0.8494 (mp10) REVERT: H 441 MET cc_start: 0.8130 (tmm) cc_final: 0.7530 (tmm) REVERT: H 484 MET cc_start: 0.8430 (mpp) cc_final: 0.8104 (mpp) REVERT: H 499 LEU cc_start: 0.8860 (mp) cc_final: 0.7929 (mp) REVERT: H 521 LEU cc_start: 0.9611 (mm) cc_final: 0.9070 (mm) REVERT: H 582 LEU cc_start: 0.8735 (pp) cc_final: 0.8150 (tt) REVERT: H 583 ILE cc_start: 0.9131 (mp) cc_final: 0.8698 (pt) REVERT: H 584 THR cc_start: 0.7750 (p) cc_final: 0.7547 (p) REVERT: H 586 ASN cc_start: 0.9275 (t0) cc_final: 0.9003 (t0) REVERT: H 605 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8833 (pt0) REVERT: H 611 GLN cc_start: 0.8147 (tp-100) cc_final: 0.7946 (tp40) REVERT: H 628 ARG cc_start: 0.8377 (mtm110) cc_final: 0.8082 (ptp90) REVERT: H 630 VAL cc_start: 0.9130 (t) cc_final: 0.8823 (m) REVERT: H 736 PHE cc_start: 0.8905 (t80) cc_final: 0.8551 (t80) REVERT: H 737 PHE cc_start: 0.9030 (m-80) cc_final: 0.8665 (m-80) REVERT: H 739 GLU cc_start: 0.8791 (mp0) cc_final: 0.8499 (mp0) REVERT: I 108 TYR cc_start: 0.8137 (m-10) cc_final: 0.7863 (m-80) REVERT: I 149 TYR cc_start: 0.9071 (t80) cc_final: 0.8824 (t80) REVERT: I 157 ARG cc_start: 0.8751 (ttp-110) cc_final: 0.8286 (ttp80) REVERT: I 205 PHE cc_start: 0.8131 (m-80) cc_final: 0.7790 (m-10) REVERT: I 230 ARG cc_start: 0.8456 (ttm-80) cc_final: 0.8025 (ttm170) REVERT: I 244 MET cc_start: 0.9512 (tpt) cc_final: 0.9297 (tpt) REVERT: I 264 MET cc_start: 0.8735 (pmm) cc_final: 0.7982 (pmm) REVERT: I 267 ARG cc_start: 0.9278 (ptp90) cc_final: 0.8979 (ptt-90) REVERT: I 268 TYR cc_start: 0.8966 (m-80) cc_final: 0.8552 (m-80) REVERT: I 440 ASN cc_start: 0.7607 (m-40) cc_final: 0.7186 (m110) REVERT: I 441 MET cc_start: 0.6500 (tmm) cc_final: 0.5661 (tmm) REVERT: J 153 LYS cc_start: 0.9229 (ttmm) cc_final: 0.8979 (ptpp) REVERT: J 217 PHE cc_start: 0.8550 (m-80) cc_final: 0.8119 (m-80) REVERT: J 221 PHE cc_start: 0.8773 (t80) cc_final: 0.8251 (t80) REVERT: J 223 TYR cc_start: 0.8714 (m-80) cc_final: 0.8499 (m-80) REVERT: J 277 HIS cc_start: 0.8933 (t-90) cc_final: 0.8690 (t-90) REVERT: J 411 GLN cc_start: 0.8839 (tp-100) cc_final: 0.8476 (pt0) REVERT: J 436 TYR cc_start: 0.6841 (m-10) cc_final: 0.6523 (m-80) REVERT: J 590 ARG cc_start: 0.7104 (mmp80) cc_final: 0.6628 (mmp80) outliers start: 1 outliers final: 0 residues processed: 962 average time/residue: 0.2328 time to fit residues: 366.7842 Evaluate side-chains 810 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 810 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 13 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 288 optimal weight: 3.9990 chunk 488 optimal weight: 10.0000 chunk 269 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 431 optimal weight: 20.0000 chunk 406 optimal weight: 10.0000 chunk 529 optimal weight: 8.9990 chunk 322 optimal weight: 20.0000 chunk 439 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 HIS B 485 GLN ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 ASN C 556 GLN C 602 ASN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 HIS ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN E 556 GLN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 543 GLN H 440 ASN H 594 ASN H 638 ASN I 563 GLN ** J 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.151523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.092893 restraints weight = 100413.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.097755 restraints weight = 57209.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.099480 restraints weight = 34469.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.100821 restraints weight = 25553.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.100920 restraints weight = 24163.567| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.181 42867 Z= 0.389 Angle : 0.815 14.616 58454 Z= 0.429 Chirality : 0.049 0.235 6899 Planarity : 0.006 0.130 7709 Dihedral : 5.352 24.725 6111 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.02 % Allowed : 1.23 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.11), residues: 5708 helix: 0.01 (0.13), residues: 1611 sheet: -0.51 (0.15), residues: 1066 loop : -0.90 (0.11), residues: 3031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 468 TYR 0.037 0.003 TYR G 411 PHE 0.038 0.003 PHE G 596 TRP 0.029 0.003 TRP A 346 HIS 0.011 0.002 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00831 (42867) covalent geometry : angle 0.81505 (58454) hydrogen bonds : bond 0.04271 ( 1503) hydrogen bonds : angle 5.53211 ( 4329) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 870 time to evaluate : 1.585 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: 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: 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: symmetry clash REVERT: A 190 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8216 (tm-30) REVERT: A 192 TYR cc_start: 0.9103 (p90) cc_final: 0.8831 (p90) REVERT: A 225 LYS cc_start: 0.8992 (ttmt) cc_final: 0.8585 (ttpt) REVERT: A 415 ASN cc_start: 0.8874 (m110) cc_final: 0.8578 (m110) REVERT: A 436 TYR cc_start: 0.8983 (t80) cc_final: 0.8602 (t80) REVERT: A 439 PHE cc_start: 0.9370 (t80) cc_final: 0.9121 (t80) REVERT: A 453 ASP cc_start: 0.8825 (p0) cc_final: 0.8367 (p0) REVERT: A 512 ASP cc_start: 0.8221 (t0) cc_final: 0.7649 (t0) REVERT: A 525 GLU cc_start: 0.9324 (mp0) cc_final: 0.8977 (pm20) REVERT: A 630 ASN cc_start: 0.9257 (m110) cc_final: 0.9001 (m110) REVERT: A 631 ILE cc_start: 0.9151 (mp) cc_final: 0.8598 (tp) REVERT: A 727 PHE cc_start: 0.9072 (t80) cc_final: 0.8644 (t80) REVERT: B 190 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8230 (tm-30) REVERT: B 192 TYR cc_start: 0.9143 (p90) cc_final: 0.8574 (p90) REVERT: B 225 LYS cc_start: 0.9425 (ttpt) cc_final: 0.9117 (tttt) REVERT: B 244 ASP cc_start: 0.8679 (t70) cc_final: 0.8061 (t70) REVERT: B 246 ASN cc_start: 0.9141 (m110) cc_final: 0.8711 (m110) REVERT: B 265 ASP cc_start: 0.8475 (t0) cc_final: 0.8250 (t0) REVERT: B 297 ARG cc_start: 0.8208 (tmm160) cc_final: 0.7663 (ttp80) REVERT: B 328 ASN cc_start: 0.7922 (t0) cc_final: 0.6775 (t0) REVERT: B 456 TYR cc_start: 0.7878 (m-10) cc_final: 0.7620 (m-10) REVERT: B 470 ARG cc_start: 0.8233 (ptp90) cc_final: 0.8027 (ptp90) REVERT: B 476 ASN cc_start: 0.8750 (t0) cc_final: 0.8189 (t0) REVERT: B 478 SER cc_start: 0.9501 (m) cc_final: 0.9003 (p) REVERT: B 486 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8629 (tm-30) REVERT: B 500 LEU cc_start: 0.9431 (mm) cc_final: 0.9193 (mm) REVERT: B 512 ASP cc_start: 0.8755 (t0) cc_final: 0.8304 (t0) REVERT: B 553 ASN cc_start: 0.7044 (m-40) cc_final: 0.6053 (m-40) REVERT: B 561 ASN cc_start: 0.8965 (m110) cc_final: 0.8619 (m110) REVERT: B 584 ASN cc_start: 0.8828 (t0) cc_final: 0.8551 (t0) REVERT: B 590 LEU cc_start: 0.9072 (tp) cc_final: 0.8466 (tp) REVERT: B 727 PHE cc_start: 0.8291 (t80) cc_final: 0.7996 (t80) REVERT: C 195 ASP cc_start: 0.8173 (t0) cc_final: 0.7639 (t0) REVERT: C 225 LYS cc_start: 0.9400 (tttt) cc_final: 0.9038 (ttmm) REVERT: C 233 TYR cc_start: 0.8318 (m-10) cc_final: 0.7908 (m-10) REVERT: C 243 ILE cc_start: 0.9488 (tp) cc_final: 0.8807 (tp) REVERT: C 246 ASN cc_start: 0.9133 (m-40) cc_final: 0.8882 (m-40) REVERT: C 297 ARG cc_start: 0.8718 (tpt170) cc_final: 0.8303 (tpp-160) REVERT: C 336 HIS cc_start: 0.9179 (p-80) cc_final: 0.8523 (p-80) REVERT: C 368 ASN cc_start: 0.8851 (t0) cc_final: 0.8573 (t0) REVERT: C 408 ASN cc_start: 0.9321 (t0) cc_final: 0.9052 (t0) REVERT: C 434 MET cc_start: 0.8780 (ppp) cc_final: 0.8577 (ppp) REVERT: C 439 PHE cc_start: 0.9417 (t80) cc_final: 0.9184 (t80) REVERT: C 497 ASP cc_start: 0.8239 (p0) cc_final: 0.7929 (p0) REVERT: C 528 LYS cc_start: 0.9113 (ttmm) cc_final: 0.8670 (mmtt) REVERT: C 552 PHE cc_start: 0.8728 (m-80) cc_final: 0.8293 (m-80) REVERT: C 575 TYR cc_start: 0.7882 (m-80) cc_final: 0.7438 (m-80) REVERT: C 590 LEU cc_start: 0.9394 (tt) cc_final: 0.9070 (tt) REVERT: C 596 PHE cc_start: 0.9129 (m-80) cc_final: 0.8135 (m-80) REVERT: C 636 ARG cc_start: 0.8850 (ptt-90) cc_final: 0.8578 (ptp90) REVERT: C 727 PHE cc_start: 0.7879 (t80) cc_final: 0.7513 (t80) REVERT: D 190 GLU cc_start: 0.8979 (tp30) cc_final: 0.8718 (tp30) REVERT: D 195 ASP cc_start: 0.8565 (t0) cc_final: 0.8220 (t70) REVERT: D 197 LYS cc_start: 0.9005 (tptt) cc_final: 0.8719 (tptt) REVERT: D 263 HIS cc_start: 0.8381 (p-80) cc_final: 0.8173 (p-80) REVERT: D 265 ASP cc_start: 0.8573 (t70) cc_final: 0.8260 (t0) REVERT: D 365 ARG cc_start: 0.8332 (ttm-80) cc_final: 0.7455 (tpp-160) REVERT: D 367 VAL cc_start: 0.9497 (t) cc_final: 0.9114 (m) REVERT: D 394 ILE cc_start: 0.9246 (mp) cc_final: 0.9034 (mp) REVERT: D 405 LEU cc_start: 0.9226 (tp) cc_final: 0.8814 (tp) REVERT: D 441 GLU cc_start: 0.9038 (pt0) cc_final: 0.8669 (tp30) REVERT: D 449 ARG cc_start: 0.8371 (ptp-170) cc_final: 0.8147 (ptp90) REVERT: D 525 GLU cc_start: 0.9184 (mp0) cc_final: 0.8701 (mp0) REVERT: D 565 GLN cc_start: 0.9435 (mm-40) cc_final: 0.9115 (mt0) REVERT: D 587 MET cc_start: 0.9396 (ptp) cc_final: 0.8520 (mpp) REVERT: E 202 PHE cc_start: 0.8609 (t80) cc_final: 0.8177 (t80) REVERT: E 385 LEU cc_start: 0.7921 (pt) cc_final: 0.7357 (pp) REVERT: E 389 GLN cc_start: 0.9028 (mp10) cc_final: 0.8567 (mp10) REVERT: E 421 LEU cc_start: 0.9438 (mt) cc_final: 0.9228 (mt) REVERT: E 434 MET cc_start: 0.8519 (ppp) cc_final: 0.8126 (ppp) REVERT: E 436 TYR cc_start: 0.8705 (t80) cc_final: 0.8426 (t80) REVERT: E 439 PHE cc_start: 0.9403 (t80) cc_final: 0.9122 (t80) REVERT: E 502 GLU cc_start: 0.7726 (tp30) cc_final: 0.7400 (tp30) REVERT: E 590 LEU cc_start: 0.9029 (mt) cc_final: 0.8821 (mm) REVERT: E 616 HIS cc_start: 0.8939 (m90) cc_final: 0.8452 (p-80) REVERT: E 639 LEU cc_start: 0.9486 (mm) cc_final: 0.9177 (tp) REVERT: F 176 PRO cc_start: 0.9116 (Cg_exo) cc_final: 0.8675 (Cg_endo) REVERT: F 190 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8243 (tm-30) REVERT: F 192 TYR cc_start: 0.8529 (p90) cc_final: 0.8016 (p90) REVERT: F 195 ASP cc_start: 0.8953 (t0) cc_final: 0.8502 (t0) REVERT: F 265 ASP cc_start: 0.8932 (t0) cc_final: 0.8258 (p0) REVERT: F 266 MET cc_start: 0.9249 (ttt) cc_final: 0.9043 (ttt) REVERT: F 326 ASN cc_start: 0.8055 (m-40) cc_final: 0.7504 (m-40) REVERT: F 366 TYR cc_start: 0.9134 (m-10) cc_final: 0.8811 (m-10) REVERT: F 439 PHE cc_start: 0.9499 (t80) cc_final: 0.9218 (t80) REVERT: F 454 GLN cc_start: 0.8412 (mp10) cc_final: 0.8068 (mp10) REVERT: F 479 GLU cc_start: 0.9288 (mp0) cc_final: 0.8879 (mp0) REVERT: F 480 VAL cc_start: 0.8393 (t) cc_final: 0.7968 (m) REVERT: F 501 VAL cc_start: 0.9122 (t) cc_final: 0.8854 (p) REVERT: F 512 ASP cc_start: 0.7611 (m-30) cc_final: 0.7361 (m-30) REVERT: F 523 LEU cc_start: 0.9500 (tp) cc_final: 0.9291 (tp) REVERT: F 551 ASP cc_start: 0.7551 (t0) cc_final: 0.6999 (p0) REVERT: G 192 TYR cc_start: 0.8001 (p90) cc_final: 0.7178 (p90) REVERT: G 224 GLU cc_start: 0.8765 (tp30) cc_final: 0.8536 (tp30) REVERT: G 238 LYS cc_start: 0.9332 (mmmm) cc_final: 0.8994 (mmmm) REVERT: G 242 ARG cc_start: 0.8839 (mtt90) cc_final: 0.8467 (mmm-85) REVERT: G 299 HIS cc_start: 0.8647 (t-90) cc_final: 0.8402 (t-90) REVERT: G 448 LEU cc_start: 0.9539 (mm) cc_final: 0.9271 (mm) REVERT: G 551 ASP cc_start: 0.8943 (t0) cc_final: 0.8110 (p0) REVERT: G 561 ASN cc_start: 0.9490 (t0) cc_final: 0.9209 (m110) REVERT: G 596 PHE cc_start: 0.9248 (m-80) cc_final: 0.8974 (m-80) REVERT: G 727 PHE cc_start: 0.8291 (t80) cc_final: 0.7679 (t80) REVERT: H 74 TYR cc_start: 0.7805 (t80) cc_final: 0.7422 (t80) REVERT: H 170 PHE cc_start: 0.9372 (t80) cc_final: 0.8722 (t80) REVERT: H 174 LEU cc_start: 0.9667 (mt) cc_final: 0.9392 (mt) REVERT: H 217 PHE cc_start: 0.8835 (t80) cc_final: 0.8460 (t80) REVERT: H 234 GLN cc_start: 0.8966 (mt0) cc_final: 0.8475 (mp10) REVERT: H 244 MET cc_start: 0.9275 (tpt) cc_final: 0.8529 (tpt) REVERT: H 259 LEU cc_start: 0.9486 (mm) cc_final: 0.9272 (mm) REVERT: H 281 TRP cc_start: 0.8752 (t60) cc_final: 0.8126 (t60) REVERT: H 441 MET cc_start: 0.8126 (tmm) cc_final: 0.7558 (tmm) REVERT: H 484 MET cc_start: 0.8282 (mpp) cc_final: 0.7776 (mpp) REVERT: H 485 ILE cc_start: 0.9494 (mm) cc_final: 0.9179 (tp) REVERT: H 499 LEU cc_start: 0.8795 (mp) cc_final: 0.7712 (mp) REVERT: H 521 LEU cc_start: 0.9663 (mm) cc_final: 0.9249 (mm) REVERT: H 582 LEU cc_start: 0.8754 (pp) cc_final: 0.8301 (tt) REVERT: H 583 ILE cc_start: 0.9130 (mp) cc_final: 0.8885 (mm) REVERT: H 591 TYR cc_start: 0.8211 (t80) cc_final: 0.8011 (t80) REVERT: H 605 GLU cc_start: 0.9331 (mt-10) cc_final: 0.8984 (mt-10) REVERT: H 611 GLN cc_start: 0.8172 (tp-100) cc_final: 0.7897 (tp-100) REVERT: H 630 VAL cc_start: 0.9174 (t) cc_final: 0.8880 (m) REVERT: H 631 PHE cc_start: 0.9338 (m-80) cc_final: 0.9004 (m-80) REVERT: H 736 PHE cc_start: 0.8893 (t80) cc_final: 0.8596 (t80) REVERT: H 737 PHE cc_start: 0.9101 (m-80) cc_final: 0.8764 (m-80) REVERT: H 744 MET cc_start: 0.9107 (ptt) cc_final: 0.8877 (ptt) REVERT: H 745 HIS cc_start: 0.8845 (m-70) cc_final: 0.8546 (m90) REVERT: I 108 TYR cc_start: 0.8340 (m-10) cc_final: 0.8052 (m-80) REVERT: I 157 ARG cc_start: 0.8761 (ttp-110) cc_final: 0.8525 (ttp80) REVERT: I 205 PHE cc_start: 0.8341 (m-80) cc_final: 0.7993 (m-10) REVERT: I 230 ARG cc_start: 0.8487 (ttm-80) cc_final: 0.7651 (tpp80) REVERT: I 244 MET cc_start: 0.9532 (tpt) cc_final: 0.9173 (tpt) REVERT: I 247 PHE cc_start: 0.9686 (t80) cc_final: 0.9418 (t80) REVERT: I 264 MET cc_start: 0.8671 (pmm) cc_final: 0.8074 (pmm) REVERT: I 268 TYR cc_start: 0.9008 (m-80) cc_final: 0.8574 (m-80) REVERT: I 440 ASN cc_start: 0.7719 (m-40) cc_final: 0.7329 (m-40) REVERT: I 441 MET cc_start: 0.7056 (tmm) cc_final: 0.6069 (tmm) REVERT: I 499 LEU cc_start: 0.9131 (mp) cc_final: 0.8898 (mp) REVERT: J 153 LYS cc_start: 0.9200 (ttmm) cc_final: 0.8911 (mtmm) REVERT: J 157 ARG cc_start: 0.8825 (ptt-90) cc_final: 0.8556 (ptt-90) REVERT: J 221 PHE cc_start: 0.8812 (t80) cc_final: 0.8311 (t80) REVERT: J 260 LYS cc_start: 0.8694 (mptt) cc_final: 0.8492 (pptt) REVERT: J 277 HIS cc_start: 0.8933 (t-90) cc_final: 0.8732 (t-90) REVERT: J 411 GLN cc_start: 0.8864 (tp-100) cc_final: 0.8495 (pm20) REVERT: J 436 TYR cc_start: 0.6780 (m-10) cc_final: 0.6515 (m-80) outliers start: 1 outliers final: 0 residues processed: 871 average time/residue: 0.2304 time to fit residues: 327.0296 Evaluate side-chains 742 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 742 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 525 optimal weight: 5.9990 chunk 376 optimal weight: 1.9990 chunk 427 optimal weight: 5.9990 chunk 297 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 460 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 437 optimal weight: 1.9990 chunk 221 optimal weight: 8.9990 chunk 295 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 HIS ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 556 GLN F 616 HIS ** G 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 563 GLN H 594 ASN H 620 ASN H 638 ASN ** I 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.157477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.099810 restraints weight = 98197.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.103691 restraints weight = 52170.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.106264 restraints weight = 34754.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.107911 restraints weight = 26544.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.108850 restraints weight = 22302.445| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 42867 Z= 0.162 Angle : 0.655 9.448 58454 Z= 0.344 Chirality : 0.047 0.233 6899 Planarity : 0.005 0.131 7709 Dihedral : 4.928 24.891 6111 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.02 % Allowed : 0.37 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.11), residues: 5708 helix: 0.17 (0.13), residues: 1620 sheet: -0.57 (0.16), residues: 939 loop : -0.73 (0.11), residues: 3149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 592 TYR 0.062 0.002 TYR I 167 PHE 0.028 0.002 PHE G 596 TRP 0.027 0.002 TRP A 346 HIS 0.009 0.001 HIS F 253 Details of bonding type rmsd covalent geometry : bond 0.00359 (42867) covalent geometry : angle 0.65518 (58454) hydrogen bonds : bond 0.03627 ( 1503) hydrogen bonds : angle 5.23607 ( 4329) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 973 time to evaluate : 1.470 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: 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: 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 190 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8168 (tm-30) REVERT: A 192 TYR cc_start: 0.8916 (p90) cc_final: 0.8682 (p90) REVERT: A 225 LYS cc_start: 0.9012 (ttmt) cc_final: 0.8600 (ttpt) REVERT: A 250 GLU cc_start: 0.8928 (mp0) cc_final: 0.8718 (tp30) REVERT: A 391 LEU cc_start: 0.9257 (mm) cc_final: 0.9025 (mm) REVERT: A 415 ASN cc_start: 0.8828 (m110) cc_final: 0.8530 (m110) REVERT: A 436 TYR cc_start: 0.8953 (t80) cc_final: 0.8635 (t80) REVERT: A 453 ASP cc_start: 0.8805 (p0) cc_final: 0.8338 (p0) REVERT: A 512 ASP cc_start: 0.8080 (t0) cc_final: 0.7607 (t0) REVERT: A 525 GLU cc_start: 0.9300 (mp0) cc_final: 0.8937 (pm20) REVERT: A 551 ASP cc_start: 0.8509 (t0) cc_final: 0.8122 (p0) REVERT: A 590 LEU cc_start: 0.9286 (tt) cc_final: 0.9075 (tt) REVERT: A 631 ILE cc_start: 0.9078 (mp) cc_final: 0.8559 (tp) REVERT: A 727 PHE cc_start: 0.9024 (t80) cc_final: 0.8618 (t80) REVERT: B 192 TYR cc_start: 0.9128 (p90) cc_final: 0.8394 (p90) REVERT: B 225 LYS cc_start: 0.9356 (ttpt) cc_final: 0.9067 (tttp) REVERT: B 244 ASP cc_start: 0.8534 (t70) cc_final: 0.7905 (t0) REVERT: B 246 ASN cc_start: 0.9139 (m110) cc_final: 0.8654 (m110) REVERT: B 265 ASP cc_start: 0.8427 (t0) cc_final: 0.8112 (t0) REVERT: B 328 ASN cc_start: 0.7800 (t0) cc_final: 0.7456 (t0) REVERT: B 439 PHE cc_start: 0.9233 (t80) cc_final: 0.9026 (t80) REVERT: B 456 TYR cc_start: 0.7753 (m-10) cc_final: 0.7448 (m-10) REVERT: B 470 ARG cc_start: 0.8130 (ptp90) cc_final: 0.7821 (ptp90) REVERT: B 476 ASN cc_start: 0.8708 (t0) cc_final: 0.8013 (t0) REVERT: B 478 SER cc_start: 0.9408 (m) cc_final: 0.8883 (p) REVERT: B 486 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8478 (tm-30) REVERT: B 487 THR cc_start: 0.9651 (t) cc_final: 0.9172 (t) REVERT: B 500 LEU cc_start: 0.9403 (mm) cc_final: 0.9183 (mm) REVERT: B 512 ASP cc_start: 0.8623 (t0) cc_final: 0.8080 (t0) REVERT: B 553 ASN cc_start: 0.6478 (m-40) cc_final: 0.5784 (m-40) REVERT: B 561 ASN cc_start: 0.9004 (m110) cc_final: 0.8652 (m110) REVERT: B 584 ASN cc_start: 0.8674 (t0) cc_final: 0.8444 (t0) REVERT: B 590 LEU cc_start: 0.9080 (tp) cc_final: 0.8599 (tp) REVERT: B 727 PHE cc_start: 0.8336 (t80) cc_final: 0.8000 (t80) REVERT: C 195 ASP cc_start: 0.8206 (t0) cc_final: 0.7742 (t0) REVERT: C 225 LYS cc_start: 0.9465 (tttt) cc_final: 0.8996 (ttmm) REVERT: C 265 ASP cc_start: 0.8952 (t0) cc_final: 0.7696 (p0) REVERT: C 266 MET cc_start: 0.8156 (tpt) cc_final: 0.7340 (tpt) REVERT: C 336 HIS cc_start: 0.9118 (p-80) cc_final: 0.8425 (p-80) REVERT: C 368 ASN cc_start: 0.8822 (t0) cc_final: 0.8575 (t0) REVERT: C 408 ASN cc_start: 0.9268 (t0) cc_final: 0.9034 (t0) REVERT: C 434 MET cc_start: 0.8834 (ppp) cc_final: 0.8544 (ppp) REVERT: C 439 PHE cc_start: 0.9342 (t80) cc_final: 0.8840 (t80) REVERT: C 497 ASP cc_start: 0.8170 (p0) cc_final: 0.7940 (p0) REVERT: C 512 ASP cc_start: 0.8815 (t0) cc_final: 0.7991 (t70) REVERT: C 528 LYS cc_start: 0.9115 (ttmm) cc_final: 0.8632 (mmtt) REVERT: C 551 ASP cc_start: 0.8611 (t0) cc_final: 0.8396 (t0) REVERT: C 553 ASN cc_start: 0.8721 (t0) cc_final: 0.8456 (t0) REVERT: C 590 LEU cc_start: 0.9367 (tt) cc_final: 0.9076 (tt) REVERT: C 636 ARG cc_start: 0.8832 (ptt-90) cc_final: 0.8534 (ptp90) REVERT: C 727 PHE cc_start: 0.7984 (t80) cc_final: 0.7762 (t80) REVERT: D 192 TYR cc_start: 0.9302 (p90) cc_final: 0.8678 (p90) REVERT: D 195 ASP cc_start: 0.8551 (t0) cc_final: 0.8307 (t70) REVERT: D 197 LYS cc_start: 0.8939 (tptt) cc_final: 0.8396 (tptm) REVERT: D 244 ASP cc_start: 0.9088 (t0) cc_final: 0.8767 (t70) REVERT: D 246 ASN cc_start: 0.9252 (m110) cc_final: 0.9037 (m110) REVERT: D 297 ARG cc_start: 0.8537 (tmm160) cc_final: 0.7634 (tmm160) REVERT: D 365 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7450 (tpp-160) REVERT: D 384 VAL cc_start: 0.9120 (p) cc_final: 0.8859 (p) REVERT: D 408 ASN cc_start: 0.9273 (t0) cc_final: 0.8952 (t0) REVERT: D 449 ARG cc_start: 0.8328 (ptp-170) cc_final: 0.7832 (ptp90) REVERT: D 454 GLN cc_start: 0.8752 (mp10) cc_final: 0.8468 (mp10) REVERT: D 483 GLN cc_start: 0.8548 (mp10) cc_final: 0.8051 (mp10) REVERT: D 486 GLU cc_start: 0.8627 (tt0) cc_final: 0.8392 (tt0) REVERT: D 525 GLU cc_start: 0.9015 (mp0) cc_final: 0.8753 (mp0) REVERT: D 565 GLN cc_start: 0.9404 (mm-40) cc_final: 0.9120 (mt0) REVERT: D 587 MET cc_start: 0.9348 (ptp) cc_final: 0.8570 (mpp) REVERT: E 202 PHE cc_start: 0.8683 (t80) cc_final: 0.8172 (t80) REVERT: E 224 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8181 (mm-30) REVERT: E 225 LYS cc_start: 0.9090 (mmmm) cc_final: 0.8644 (mtpp) REVERT: E 385 LEU cc_start: 0.8017 (pt) cc_final: 0.7259 (pp) REVERT: E 389 GLN cc_start: 0.9056 (mp10) cc_final: 0.8530 (mp10) REVERT: E 434 MET cc_start: 0.8509 (ppp) cc_final: 0.7931 (ppp) REVERT: E 436 TYR cc_start: 0.8649 (t80) cc_final: 0.8242 (t80) REVERT: E 438 GLN cc_start: 0.8736 (mt0) cc_final: 0.8456 (mm110) REVERT: E 439 PHE cc_start: 0.9324 (t80) cc_final: 0.9036 (t80) REVERT: E 502 GLU cc_start: 0.7555 (tp30) cc_final: 0.7257 (tp30) REVERT: E 512 ASP cc_start: 0.8288 (t0) cc_final: 0.7896 (t0) REVERT: E 553 ASN cc_start: 0.8825 (m-40) cc_final: 0.8427 (m-40) REVERT: E 580 LYS cc_start: 0.9587 (mmpt) cc_final: 0.9356 (mmmt) REVERT: E 616 HIS cc_start: 0.8894 (m90) cc_final: 0.8510 (p-80) REVERT: E 635 ILE cc_start: 0.9673 (mm) cc_final: 0.9386 (pt) REVERT: E 639 LEU cc_start: 0.9390 (mm) cc_final: 0.9136 (tp) REVERT: F 176 PRO cc_start: 0.8854 (Cg_exo) cc_final: 0.8582 (Cg_endo) REVERT: F 190 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8286 (tm-30) REVERT: F 195 ASP cc_start: 0.8859 (t0) cc_final: 0.8393 (t0) REVERT: F 219 TYR cc_start: 0.8625 (m-80) cc_final: 0.8420 (m-80) REVERT: F 223 PRO cc_start: 0.9403 (Cg_endo) cc_final: 0.9017 (Cg_exo) REVERT: F 265 ASP cc_start: 0.8902 (t0) cc_final: 0.8239 (p0) REVERT: F 326 ASN cc_start: 0.7865 (m-40) cc_final: 0.7381 (m-40) REVERT: F 366 TYR cc_start: 0.8919 (m-10) cc_final: 0.8538 (m-10) REVERT: F 439 PHE cc_start: 0.9468 (t80) cc_final: 0.9130 (t80) REVERT: F 453 ASP cc_start: 0.8759 (p0) cc_final: 0.8516 (p0) REVERT: F 480 VAL cc_start: 0.8560 (t) cc_final: 0.8169 (m) REVERT: F 486 GLU cc_start: 0.8504 (mp0) cc_final: 0.8218 (mp0) REVERT: F 490 ARG cc_start: 0.8318 (ttt180) cc_final: 0.7569 (ttp-170) REVERT: F 497 ASP cc_start: 0.8584 (p0) cc_final: 0.7885 (p0) REVERT: F 501 VAL cc_start: 0.9062 (t) cc_final: 0.8674 (p) REVERT: F 512 ASP cc_start: 0.7504 (m-30) cc_final: 0.7191 (m-30) REVERT: F 523 LEU cc_start: 0.9467 (tp) cc_final: 0.9196 (tp) REVERT: F 551 ASP cc_start: 0.7503 (t0) cc_final: 0.6955 (p0) REVERT: F 590 LEU cc_start: 0.7936 (mt) cc_final: 0.7697 (mt) REVERT: F 636 ARG cc_start: 0.8568 (ptp90) cc_final: 0.8296 (ptp90) REVERT: G 238 LYS cc_start: 0.9297 (mmmm) cc_final: 0.8965 (mmmm) REVERT: G 242 ARG cc_start: 0.8649 (mtt90) cc_final: 0.8379 (mmm-85) REVERT: G 266 MET cc_start: 0.8631 (ttt) cc_final: 0.8114 (ttt) REVERT: G 299 HIS cc_start: 0.8566 (t-90) cc_final: 0.8351 (t-90) REVERT: G 448 LEU cc_start: 0.9512 (mm) cc_final: 0.9270 (mm) REVERT: G 479 GLU cc_start: 0.9026 (mp0) cc_final: 0.8539 (mp0) REVERT: G 512 ASP cc_start: 0.8455 (t0) cc_final: 0.7927 (t0) REVERT: G 551 ASP cc_start: 0.8864 (t0) cc_final: 0.8102 (p0) REVERT: G 635 ILE cc_start: 0.9385 (tp) cc_final: 0.9181 (mm) REVERT: G 638 ILE cc_start: 0.9086 (pt) cc_final: 0.8866 (pt) REVERT: G 727 PHE cc_start: 0.8249 (t80) cc_final: 0.7648 (t80) REVERT: H 74 TYR cc_start: 0.7821 (t80) cc_final: 0.7418 (t80) REVERT: H 170 PHE cc_start: 0.9279 (t80) cc_final: 0.8554 (t80) REVERT: H 174 LEU cc_start: 0.9617 (mt) cc_final: 0.9356 (mt) REVERT: H 217 PHE cc_start: 0.8773 (t80) cc_final: 0.8194 (t80) REVERT: H 234 GLN cc_start: 0.8939 (mt0) cc_final: 0.8417 (mp10) REVERT: H 281 TRP cc_start: 0.8698 (t60) cc_final: 0.8079 (t60) REVERT: H 390 GLN cc_start: 0.8708 (mp10) cc_final: 0.8502 (mp10) REVERT: H 441 MET cc_start: 0.8128 (tmm) cc_final: 0.7891 (tmm) REVERT: H 484 MET cc_start: 0.8385 (mpp) cc_final: 0.7854 (mpp) REVERT: H 485 ILE cc_start: 0.9463 (mm) cc_final: 0.9126 (tp) REVERT: H 488 ILE cc_start: 0.8497 (tt) cc_final: 0.8241 (tt) REVERT: H 499 LEU cc_start: 0.8885 (mp) cc_final: 0.8191 (mp) REVERT: H 521 LEU cc_start: 0.9643 (mm) cc_final: 0.9145 (mm) REVERT: H 582 LEU cc_start: 0.8698 (pp) cc_final: 0.8170 (tt) REVERT: H 586 ASN cc_start: 0.9245 (t0) cc_final: 0.9019 (t0) REVERT: H 605 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8831 (pt0) REVERT: H 611 GLN cc_start: 0.8139 (tp-100) cc_final: 0.7874 (tp40) REVERT: H 736 PHE cc_start: 0.8928 (t80) cc_final: 0.8495 (t80) REVERT: H 737 PHE cc_start: 0.9071 (m-80) cc_final: 0.8604 (m-80) REVERT: H 739 GLU cc_start: 0.8924 (mp0) cc_final: 0.8620 (mp0) REVERT: H 744 MET cc_start: 0.9107 (ptt) cc_final: 0.8871 (ptt) REVERT: H 745 HIS cc_start: 0.8829 (m-70) cc_final: 0.8512 (m90) REVERT: I 75 LYS cc_start: 0.9116 (pptt) cc_final: 0.8861 (pttm) REVERT: I 108 TYR cc_start: 0.8175 (m-10) cc_final: 0.7929 (m-80) REVERT: I 149 TYR cc_start: 0.9103 (t80) cc_final: 0.8751 (t80) REVERT: I 158 ASP cc_start: 0.8793 (m-30) cc_final: 0.8452 (m-30) REVERT: I 205 PHE cc_start: 0.8211 (m-80) cc_final: 0.7856 (m-10) REVERT: I 228 GLN cc_start: 0.8857 (mp-120) cc_final: 0.8451 (mp10) REVERT: I 230 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.7379 (tpp80) REVERT: I 244 MET cc_start: 0.9525 (tpt) cc_final: 0.9180 (tpt) REVERT: I 254 LEU cc_start: 0.9041 (pp) cc_final: 0.8563 (mm) REVERT: I 264 MET cc_start: 0.8713 (pmm) cc_final: 0.7907 (pmm) REVERT: I 267 ARG cc_start: 0.9249 (ptp90) cc_final: 0.8978 (ptt-90) REVERT: I 268 TYR cc_start: 0.8959 (m-80) cc_final: 0.8484 (m-80) REVERT: I 440 ASN cc_start: 0.7663 (m-40) cc_final: 0.7267 (m110) REVERT: I 441 MET cc_start: 0.7049 (tmm) cc_final: 0.6090 (tmm) REVERT: J 153 LYS cc_start: 0.9233 (ttmm) cc_final: 0.8934 (mtmm) REVERT: J 157 ARG cc_start: 0.8832 (ptt-90) cc_final: 0.8505 (ptt-90) REVERT: J 221 PHE cc_start: 0.8768 (t80) cc_final: 0.8262 (t80) REVERT: J 223 TYR cc_start: 0.8621 (m-80) cc_final: 0.8395 (m-80) REVERT: J 260 LYS cc_start: 0.8649 (mptt) cc_final: 0.8397 (pttm) REVERT: J 411 GLN cc_start: 0.8837 (tp-100) cc_final: 0.8487 (pm20) REVERT: J 436 TYR cc_start: 0.6705 (m-10) cc_final: 0.6439 (m-80) outliers start: 1 outliers final: 0 residues processed: 974 average time/residue: 0.2277 time to fit residues: 364.0894 Evaluate side-chains 790 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 790 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 289 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 535 optimal weight: 0.2980 chunk 297 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 467 optimal weight: 50.0000 chunk 533 optimal weight: 50.0000 chunk 158 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 161 optimal weight: 0.4980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 HIS B 588 ASN C 246 ASN E 483 GLN E 541 GLN ** G 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 ASN H 563 GLN ** H 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 594 ASN H 638 ASN ** I 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.158955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.100943 restraints weight = 98087.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.105009 restraints weight = 51642.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.107610 restraints weight = 34193.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109302 restraints weight = 26074.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.110324 restraints weight = 21864.867| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 42867 Z= 0.139 Angle : 0.648 9.699 58454 Z= 0.340 Chirality : 0.046 0.233 6899 Planarity : 0.005 0.077 7709 Dihedral : 4.739 24.660 6111 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.05 % Allowed : 0.37 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.11), residues: 5708 helix: 0.32 (0.13), residues: 1582 sheet: -0.55 (0.16), residues: 960 loop : -0.65 (0.11), residues: 3166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 468 TYR 0.061 0.002 TYR I 167 PHE 0.030 0.001 PHE I 471 TRP 0.024 0.002 TRP A 346 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00310 (42867) covalent geometry : angle 0.64774 (58454) hydrogen bonds : bond 0.03493 ( 1503) hydrogen bonds : angle 5.14597 ( 4329) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9062.44 seconds wall clock time: 156 minutes 32.82 seconds (9392.82 seconds total)