Starting phenix.real_space_refine on Sat Mar 7 11:18:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zxk_11523/03_2026/6zxk_11523.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zxk_11523/03_2026/6zxk_11523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zxk_11523/03_2026/6zxk_11523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zxk_11523/03_2026/6zxk_11523.map" model { file = "/net/cci-nas-00/data/ceres_data/6zxk_11523/03_2026/6zxk_11523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zxk_11523/03_2026/6zxk_11523.cif" } resolution = 3.8 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= 0.031 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 26530 2.51 5 N 7357 2.21 5 O 8365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 193 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: 42292 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3984 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASN:plan1': 8, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 8, 'ARG:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 111 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: 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: "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: 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: "H" Number of atoms: 5401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5401 Classifications: {'peptide': 699} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 680} Chain breaks: 1 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 419 Unresolved non-hydrogen dihedrals: 297 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 13, 'GLN:plan1': 9, 'TYR:plan': 2, 'ASP:plan': 7, 'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 172 Chain: "I" Number of atoms: 4734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 4734 Classifications: {'peptide': 710} Incomplete info: {'truncation_to_alanine': 310} Link IDs: {'PTRANS': 18, 'TRANS': 691} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1138 Unresolved non-hydrogen angles: 1430 Unresolved non-hydrogen dihedrals: 932 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 19, 'GLU:plan': 39, 'ASP:plan': 29, 'TYR:plan': 11, 'ASN:plan1': 20, 'ARG:plan': 14, 'HIS:plan': 9, 'PHE:plan': 12, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 652 Chain: "J" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 4318 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 16, 'TRANS': 644} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1159 Unresolved non-hydrogen angles: 1439 Unresolved non-hydrogen dihedrals: 960 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'ASP:plan': 24, 'GLU:plan': 41, 'TYR:plan': 11, 'ASN:plan1': 22, 'GLN:plan1': 20, 'ARG:plan': 16, 'HIS:plan': 8, 'PHE:plan': 11, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 654 Time building chain proxies: 9.92, per 1000 atoms: 0.23 Number of scatterers: 42292 At special positions: 0 Unit cell: (181.9, 180.83, 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 8365 8.00 N 7357 7.00 C 26530 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: 3.78 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: 216 helices and 80 sheets defined 35.4% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.525A pdb=" N HIS A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 3.949A 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: 3.705A pdb=" N VAL A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.938A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.556A 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: 3.970A pdb=" N THR A 517 " --> pdb=" O PRO A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.561A pdb=" N LEU A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 4.500A pdb=" N ASP A 579 " --> pdb=" O THR A 576 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 581 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.509A pdb=" N VAL A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 637 removed outlier: 3.505A 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: 3.557A pdb=" N LEU A 663 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN A 664 " --> pdb=" O ASP A 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 660 through 664' Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.866A 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: 3.726A pdb=" N GLU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 removed outlier: 3.768A pdb=" N VAL B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.843A 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: 4.006A pdb=" N THR B 517 " --> pdb=" O PRO B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 531 Processing helix chain 'B' and resid 555 through 568 Processing helix chain 'B' and resid 576 through 581 removed outlier: 4.494A pdb=" N ASP B 579 " --> pdb=" O THR B 576 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 581 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 removed outlier: 3.623A pdb=" N GLU B 614 " --> pdb=" O SER B 610 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 615 " --> pdb=" O VAL B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 637 removed outlier: 3.531A 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 212 removed outlier: 3.849A pdb=" N GLU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 234 through 241 removed outlier: 3.815A pdb=" N VAL C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 253 removed outlier: 4.013A 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: 3.587A 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 removed outlier: 3.504A pdb=" N THR C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 518 Processing helix chain 'C' and resid 522 through 532 removed outlier: 3.598A 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: 4.457A pdb=" N ASP C 579 " --> pdb=" O THR C 576 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 581 " --> pdb=" O LEU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 615 Processing helix chain 'C' and resid 634 through 638 Processing helix chain 'C' and resid 702 through 706 Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 207 through 213 removed outlier: 3.606A pdb=" N GLU D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS D 213 " --> pdb=" O ASN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 241 removed outlier: 3.627A pdb=" N VAL D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.866A 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: 3.674A 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 Processing helix chain 'D' and resid 555 through 568 Processing helix chain 'D' and resid 576 through 581 removed outlier: 4.246A pdb=" N ASP D 579 " --> pdb=" O THR D 576 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 581 " --> pdb=" O LEU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 615 removed outlier: 3.517A pdb=" N VAL D 612 " --> pdb=" O ASP D 608 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 614 " --> pdb=" O SER D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 637 removed outlier: 3.516A pdb=" N LYS D 637 " --> pdb=" O ASP D 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 634 through 637' Processing helix chain 'D' and resid 704 through 706 No H-bonds generated for 'chain 'D' and resid 704 through 706' Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 207 through 213 removed outlier: 3.843A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS E 213 " --> pdb=" O ASN E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 241 removed outlier: 3.630A pdb=" N VAL E 239 " --> pdb=" O ASP E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.922A 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 480 through 486 Processing helix chain 'E' and resid 512 through 517 removed outlier: 3.844A pdb=" N THR E 517 " --> pdb=" O PRO E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 532 removed outlier: 3.541A pdb=" N PHE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY E 532 " --> pdb=" O LYS E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 568 Processing helix chain 'E' and resid 576 through 581 removed outlier: 4.541A pdb=" N ASP E 579 " --> pdb=" O THR E 576 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE E 581 " --> pdb=" O LEU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 615 removed outlier: 3.535A pdb=" N VAL E 612 " --> pdb=" O ASP E 608 " (cutoff:3.500A) Processing helix 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 212 removed outlier: 4.022A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 234 through 241 removed outlier: 3.575A pdb=" N VAL F 239 " --> pdb=" O ASP F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 253 removed outlier: 3.966A 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 570 removed outlier: 3.699A pdb=" N ASN F 564 " --> pdb=" O GLN F 560 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN F 565 " --> pdb=" O ASN F 561 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 569 " --> pdb=" O GLN F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 576 through 581 removed outlier: 4.447A pdb=" N ASP F 579 " --> pdb=" O THR F 576 " (cutoff:3.500A) removed outlier: 3.547A 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 'G' and resid 184 through 191 Processing helix chain 'G' and resid 207 through 212 removed outlier: 4.089A 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 Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.932A 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: 3.595A 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: 3.825A pdb=" N THR G 517 " --> pdb=" O PRO G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 532 removed outlier: 3.663A 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: 4.576A pdb=" N ASP G 579 " --> pdb=" O THR G 576 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE G 581 " --> pdb=" O LEU G 578 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 615 removed outlier: 3.520A pdb=" N VAL G 612 " --> pdb=" O ASP G 608 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU G 614 " --> pdb=" O SER G 610 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 638 removed outlier: 3.531A pdb=" N LYS G 637 " --> pdb=" O ASP G 634 " (cutoff:3.500A) Processing helix chain 'G' and resid 702 through 706 Processing helix chain 'H' and resid 53 through 65 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: 4.212A pdb=" N ASN H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) removed outlier: 3.826A 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: 4.039A pdb=" N VAL H 173 " --> pdb=" O LYS H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 removed outlier: 3.643A pdb=" N ASP H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 196 Processing helix chain 'H' and resid 202 through 209 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: 3.995A pdb=" N LEU H 254 " --> pdb=" O GLN H 250 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU H 257 " --> pdb=" O ASN H 253 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU H 259 " --> pdb=" O SER H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 278 removed outlier: 3.696A pdb=" N GLN H 276 " --> pdb=" O GLU H 272 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N HIS H 277 " --> pdb=" O LYS H 273 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR H 278 " --> pdb=" O ILE H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 284 Processing helix chain 'H' and resid 286 through 298 Processing helix chain 'H' and resid 303 through 312 removed outlier: 3.635A pdb=" N ILE H 307 " --> pdb=" O LYS H 303 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER H 312 " --> pdb=" O ILE H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 321 removed outlier: 3.908A pdb=" N ARG H 321 " --> pdb=" O GLU H 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 345 Processing helix chain 'H' and resid 371 through 381 removed outlier: 4.023A pdb=" N PHE H 375 " --> pdb=" O LYS H 371 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS H 378 " --> pdb=" O GLU H 374 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU H 381 " --> pdb=" O LYS H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 396 removed outlier: 3.847A pdb=" N GLN H 393 " --> pdb=" O ASN H 389 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP H 394 " --> pdb=" O GLN H 390 " (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 removed outlier: 3.577A pdb=" N ALA H 452 " --> pdb=" O ALA H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 464 through 474 removed outlier: 3.791A pdb=" N GLU H 470 " --> pdb=" O GLY H 466 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN H 474 " --> pdb=" O GLU H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 551 through 575 removed outlier: 3.716A pdb=" N ILE H 555 " --> pdb=" O PRO H 551 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS H 558 " --> pdb=" O LYS H 554 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS H 572 " --> pdb=" O GLN H 568 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 573 " --> pdb=" O GLU H 569 " (cutoff:3.500A) Processing helix chain 'H' and resid 591 through 610 removed outlier: 3.687A pdb=" N ILE H 595 " --> pdb=" O TYR H 591 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR H 600 " --> pdb=" O VAL H 596 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU H 601 " --> pdb=" O GLU H 597 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN H 604 " --> pdb=" O TYR H 600 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN H 609 " --> pdb=" O GLU H 605 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE H 610 " --> pdb=" O TRP H 606 " (cutoff:3.500A) Processing helix chain 'H' and resid 611 through 624 removed outlier: 3.541A 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: 3.766A pdb=" N THR H 644 " --> pdb=" O ALA H 640 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS H 645 " --> pdb=" O GLU H 641 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN H 646 " --> pdb=" O GLN H 642 " (cutoff:3.500A) Processing helix chain 'H' and resid 679 through 701 removed outlier: 3.856A pdb=" N GLY H 683 " --> pdb=" O ASN H 679 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP H 694 " --> pdb=" O HIS H 690 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU H 700 " --> pdb=" O ALA H 696 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP H 701 " --> pdb=" O GLY H 697 " (cutoff:3.500A) Processing helix chain 'H' and resid 711 through 721 removed outlier: 4.003A pdb=" N ASP H 716 " --> pdb=" O LYS H 712 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE H 717 " --> pdb=" O LYS H 713 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU H 720 " --> pdb=" O ASP H 716 " (cutoff:3.500A) Processing helix chain 'H' and resid 728 through 731 Processing helix chain 'H' and resid 732 through 745 removed outlier: 3.582A pdb=" N LEU H 743 " --> pdb=" O GLU H 739 " (cutoff:3.500A) Processing helix chain 'H' and resid 748 through 759 removed outlier: 3.522A pdb=" N ARG H 752 " --> pdb=" O ASP H 748 " (cutoff:3.500A) Processing helix chain 'H' and resid 759 through 770 removed outlier: 3.634A pdb=" N GLN H 764 " --> pdb=" O PRO H 760 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN H 767 " --> pdb=" O PHE H 763 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 44 removed outlier: 4.245A pdb=" N LYS I 37 " --> pdb=" O GLU I 33 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU I 38 " --> pdb=" O GLU I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 65 removed outlier: 3.537A pdb=" N LYS I 56 " --> pdb=" O GLU I 52 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS I 65 " --> pdb=" O LYS I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 77 removed outlier: 3.970A pdb=" N LEU I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 4.081A pdb=" N ALA I 96 " --> pdb=" O ILE I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 159 removed outlier: 3.706A pdb=" N ASN I 146 " --> pdb=" O GLU I 142 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL I 147 " --> pdb=" O LYS I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 163 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.536A pdb=" N LYS I 178 " --> pdb=" O LEU I 174 " (cutoff:3.500A) removed outlier: 3.635A 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: 3.631A pdb=" N GLU I 196 " --> pdb=" O GLN I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 209 removed outlier: 3.645A pdb=" N LEU I 206 " --> pdb=" O SER I 202 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU I 207 " --> pdb=" O VAL I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 226 Processing helix chain 'I' and resid 226 through 237 removed outlier: 4.303A pdb=" N ASP I 231 " --> pdb=" O PRO I 227 " (cutoff:3.500A) removed outlier: 4.869A 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: 3.781A pdb=" N TYR I 278 " --> pdb=" O ILE I 274 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N HIS I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TRP I 281 " --> pdb=" O HIS I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 298 removed outlier: 4.013A pdb=" N LEU I 292 " --> pdb=" O GLU I 288 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU I 293 " --> pdb=" O GLY I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 312 removed outlier: 3.823A pdb=" N SER I 312 " --> pdb=" O ILE I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 321 removed outlier: 4.076A pdb=" N GLU I 317 " --> pdb=" O GLN I 313 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG I 321 " --> pdb=" O GLU I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 323 through 327 removed outlier: 3.862A 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: 3.904A pdb=" N LEU I 376 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS I 377 " --> pdb=" O LYS I 373 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU I 381 " --> pdb=" O LYS I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 396 Processing helix chain 'I' and resid 405 through 421 removed outlier: 3.575A pdb=" N GLN I 411 " --> pdb=" O ASP I 407 " (cutoff:3.500A) 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: 3.747A 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 572 removed outlier: 3.611A pdb=" N LYS I 558 " --> pdb=" O LYS I 554 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU I 561 " --> pdb=" O THR I 557 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA I 562 " --> pdb=" O LYS I 558 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS I 572 " --> pdb=" O GLN I 568 " (cutoff:3.500A) Processing helix chain 'I' and resid 591 through 608 removed outlier: 3.550A pdb=" N ILE I 595 " --> pdb=" O TYR I 591 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR I 600 " --> pdb=" O VAL I 596 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU I 601 " --> pdb=" O GLU I 597 " (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: 3.910A pdb=" N HIS I 690 " --> pdb=" O HIS I 686 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA I 691 " --> pdb=" O GLU I 687 " (cutoff:3.500A) Processing helix chain 'I' and resid 707 through 721 removed outlier: 4.171A pdb=" N LYS I 712 " --> pdb=" O VAL I 708 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS I 713 " --> pdb=" O THR I 709 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP I 716 " --> pdb=" O LYS I 712 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE I 717 " --> pdb=" O LYS I 713 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU I 720 " --> pdb=" O ASP I 716 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU I 721 " --> pdb=" O ILE I 717 " (cutoff:3.500A) Processing helix chain 'I' and resid 722 through 725 removed outlier: 3.703A pdb=" N LEU I 725 " --> pdb=" O GLY I 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 722 through 725' Processing helix chain 'I' and resid 732 through 745 Processing helix chain 'I' and resid 748 through 759 removed outlier: 3.632A pdb=" N VAL I 755 " --> pdb=" O GLU I 751 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN I 756 " --> pdb=" O ARG I 752 " (cutoff:3.500A) Processing helix chain 'I' and resid 759 through 772 removed outlier: 4.217A pdb=" N GLN I 764 " --> pdb=" O PRO I 760 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE I 765 " --> pdb=" O LYS I 761 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS I 771 " --> pdb=" O ASN I 767 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE I 772 " --> pdb=" O ASP I 768 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 65 removed outlier: 3.540A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 77 removed outlier: 3.992A pdb=" N LEU J 71 " --> pdb=" O PRO J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 96 removed outlier: 4.020A pdb=" N ALA J 96 " --> pdb=" O ILE J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 158 removed outlier: 3.787A 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: 3.632A pdb=" N LYS J 178 " --> pdb=" O LEU J 174 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN J 179 " --> pdb=" O ASN J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 193 through 197 removed outlier: 3.577A pdb=" N GLU J 196 " --> pdb=" O GLN J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 209 removed outlier: 3.716A pdb=" N LEU J 206 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU J 207 " --> pdb=" O VAL J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 226 removed outlier: 3.509A pdb=" N GLU J 226 " --> pdb=" O ALA J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 237 removed outlier: 4.161A pdb=" N ASP J 231 " --> pdb=" O PRO J 227 " (cutoff:3.500A) removed outlier: 4.733A 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 Processing helix chain 'J' and resid 263 through 285 removed outlier: 3.692A pdb=" N HIS J 277 " --> pdb=" O LYS J 273 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR J 278 " --> pdb=" O ILE J 274 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N HIS J 280 " --> pdb=" O GLN J 276 " (cutoff:3.500A) removed outlier: 5.244A 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: 4.016A 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: 3.803A pdb=" N LEU J 376 " --> pdb=" O GLU J 372 " (cutoff:3.500A) Processing helix chain 'J' and resid 388 through 396 Processing helix chain 'J' and resid 406 through 421 removed outlier: 3.691A pdb=" N LYS J 410 " --> pdb=" O LEU J 406 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN J 411 " --> pdb=" O ASP J 407 " (cutoff:3.500A) Processing helix chain 'J' and resid 444 through 446 No H-bonds generated for 'chain 'J' and resid 444 through 446' Processing helix chain 'J' and resid 447 through 452 removed outlier: 3.680A pdb=" N ALA J 452 " --> pdb=" O ALA J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 464 through 473 removed outlier: 3.710A pdb=" N GLU J 470 " --> pdb=" O GLY J 466 " (cutoff:3.500A) Processing helix chain 'J' and resid 551 through 572 removed outlier: 3.506A pdb=" N LYS J 558 " --> pdb=" O LYS J 554 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU J 561 " --> pdb=" O THR J 557 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS J 572 " --> pdb=" O GLN J 568 " (cutoff:3.500A) Processing helix chain 'J' and resid 591 through 610 removed outlier: 3.661A pdb=" N ILE J 595 " --> pdb=" O TYR J 591 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR J 600 " --> pdb=" O VAL J 596 " (cutoff:3.500A) removed outlier: 3.723A 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: 4.763A 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: 3.959A pdb=" N HIS J 690 " --> pdb=" O HIS J 686 " (cutoff:3.500A) Processing helix chain 'J' and resid 707 through 721 removed outlier: 4.271A pdb=" N LYS J 712 " --> pdb=" O VAL J 708 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS J 713 " --> pdb=" O THR J 709 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP J 716 " --> pdb=" O LYS J 712 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE J 717 " --> pdb=" O LYS J 713 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU J 721 " --> pdb=" O ILE J 717 " (cutoff:3.500A) Processing helix chain 'J' and resid 722 through 725 removed outlier: 3.698A 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: 3.518A pdb=" N VAL J 755 " --> pdb=" O GLU J 751 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN J 756 " --> pdb=" O ARG J 752 " (cutoff:3.500A) Processing helix chain 'J' and resid 759 through 772 removed outlier: 4.108A pdb=" N GLN J 764 " --> pdb=" O PRO J 760 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE J 765 " --> pdb=" O LYS J 761 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE J 770 " --> pdb=" O ILE J 766 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS J 771 " --> pdb=" O ASN J 767 " (cutoff:3.500A) removed outlier: 3.538A 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: 3.620A pdb=" N ASP A 195 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 202 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 360 removed outlier: 3.516A pdb=" N SER A 272 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN A 368 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN A 409 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 389 through 394 removed outlier: 5.041A pdb=" N THR A 390 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 385 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 392 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR A 381 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 451 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLU A 267 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR A 295 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASP A 265 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ARG A 297 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N HIS A 263 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 364 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 3.624A 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: 4.306A 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: 8.716A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ASP A 593 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 592 " --> pdb=" O ASP A 551 " (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: 6.590A pdb=" N HIS A 597 " --> pdb=" O VAL A 605 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 627 through 629 removed outlier: 3.525A pdb=" N LEU A 627 " --> pdb=" O ILE A 676 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.648A pdb=" N GLY A 641 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ALA A 700 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 5.472A 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: 3.626A pdb=" N ASP B 195 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 4.011A 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: 5.038A pdb=" N THR B 390 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 385 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 392 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR B 381 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN B 328 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 294 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLU B 267 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR B 295 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ASP B 265 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ARG B 297 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N HIS B 263 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE B 269 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASN B 361 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU B 271 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG B 359 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN B 368 " --> pdb=" O ASN B 409 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN B 409 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 389 through 394 removed outlier: 5.038A pdb=" N THR B 390 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 385 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 392 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR B 381 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN B 328 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 294 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLU B 267 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR B 295 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ASP B 265 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ARG B 297 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N HIS B 263 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE B 269 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASN B 361 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU B 271 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 6.726A 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: 4.178A 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 removed outlier: 3.714A pdb=" N ARG B 592 " --> pdb=" O ASP B 551 " (cutoff:3.500A) 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 removed outlier: 6.663A pdb=" N HIS B 597 " --> pdb=" O VAL B 605 " (cutoff:3.500A) 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: 3.570A pdb=" N GLY B 641 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 645 " --> pdb=" O ASN B 697 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN B 697 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA B 700 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 5.835A 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: 7.196A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C 368 " --> pdb=" O ASN C 409 " (cutoff:3.500A) removed outlier: 3.979A 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: 7.267A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 448 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N SER C 329 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLU C 267 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR C 295 " --> pdb=" O ASP C 265 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP C 265 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ARG C 297 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N HIS C 263 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 7.196A 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: 4.283A pdb=" N ILE C 459 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 501 through 506 removed outlier: 8.514A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.583A 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 removed outlier: 6.394A pdb=" N HIS C 597 " --> pdb=" O VAL C 605 " (cutoff:3.500A) 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: 3.530A pdb=" N ASN C 697 " --> pdb=" O GLU C 645 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL C 696 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 728 " --> pdb=" O VAL C 696 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL C 698 " --> pdb=" O ILE C 726 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 192 through 197 removed outlier: 3.576A pdb=" N ASP D 195 " --> pdb=" O PHE D 202 " (cutoff:3.500A) removed outlier: 4.029A 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: 7.238A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG D 359 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 262 through 273 removed outlier: 7.238A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.723A 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 297 removed outlier: 3.511A pdb=" N LEU D 448 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR D 381 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA D 392 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU D 385 " --> pdb=" O THR D 390 " (cutoff:3.500A) removed outlier: 5.047A 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: 4.303A pdb=" N ILE D 459 " --> pdb=" O ASP D 472 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 501 through 506 removed outlier: 8.573A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (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: 5.917A pdb=" N VAL D 696 " --> pdb=" O SER D 728 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER D 728 " --> pdb=" O VAL D 696 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL D 698 " --> pdb=" O ILE D 726 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 192 through 197 removed outlier: 3.673A pdb=" N PHE E 202 " --> pdb=" O ASP E 195 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 389 through 394 removed outlier: 7.075A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E 384 " --> pdb=" O ARG E 449 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER E 294 " --> pdb=" O ALA E 333 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU E 267 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N THR E 295 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASP E 265 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ARG E 297 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 10.400A pdb=" N HIS E 263 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE E 269 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASN E 361 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU E 271 " --> pdb=" O ARG E 359 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ARG E 359 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.707A 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: 7.075A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E 384 " --> pdb=" O ARG E 449 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER E 294 " --> pdb=" O ALA E 333 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU E 267 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N THR E 295 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASP E 265 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ARG E 297 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 10.400A pdb=" N HIS E 263 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE E 269 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASN E 361 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU E 271 " --> pdb=" O ARG E 359 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ARG E 359 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE E 364 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE E 419 " --> pdb=" O ILE E 364 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 458 through 462 removed outlier: 4.204A pdb=" N ILE E 459 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 501 through 506 removed outlier: 8.575A pdb=" N ILE E 589 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG E 490 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE E 591 " --> pdb=" O ARG E 490 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE E 492 " --> pdb=" O ILE E 591 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ASP E 593 " --> pdb=" O ILE E 492 " (cutoff:3.500A) removed outlier: 3.570A 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: 6.548A 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: 5.952A pdb=" N ALA E 700 " --> pdb=" O LEU E 725 " (cutoff:3.500A) removed outlier: 5.420A 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 Processing sheet with id=AF3, first strand: chain 'F' and resid 358 through 360 removed outlier: 6.650A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN F 409 " --> pdb=" O ASN F 368 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 389 through 394 removed outlier: 5.012A pdb=" N THR F 390 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU F 385 " --> pdb=" O THR F 390 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA F 392 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR F 381 " --> pdb=" O ILE F 394 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP F 451 " --> pdb=" O SER F 382 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL F 384 " --> pdb=" O ARG F 449 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG F 449 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN F 328 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER F 294 " --> pdb=" O ALA F 333 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLU F 267 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR F 295 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ASP F 265 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N ARG F 297 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N HIS F 263 " --> pdb=" O ARG F 297 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE F 364 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE F 419 " --> pdb=" O ILE F 364 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 458 through 462 removed outlier: 4.326A pdb=" N ILE F 459 " --> pdb=" O ASP F 472 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 501 through 506 removed outlier: 8.576A pdb=" N ILE F 589 " --> pdb=" O THR F 488 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG F 490 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE F 591 " --> pdb=" O ARG F 490 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE F 492 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASP F 593 " --> pdb=" O ILE F 492 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG F 592 " --> pdb=" O ASP F 551 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=AF8, first strand: chain 'F' and resid 596 through 598 removed outlier: 6.854A pdb=" N HIS F 597 " --> pdb=" O VAL F 605 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 628 through 629 Processing sheet with id=AG1, first strand: chain 'F' and resid 654 through 655 removed outlier: 3.816A 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: 3.819A pdb=" N SER F 728 " --> pdb=" O VAL F 696 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL F 698 " --> pdb=" O ILE F 726 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 192 through 196 Processing sheet with id=AG3, first strand: chain 'G' and resid 389 through 394 removed outlier: 4.946A pdb=" N THR G 390 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU G 385 " --> pdb=" O THR G 390 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA G 392 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR G 381 " --> pdb=" O ILE G 394 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP G 451 " --> pdb=" O SER G 382 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU G 448 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN G 328 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU G 267 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR G 295 " --> pdb=" O ASP G 265 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASP G 265 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ARG G 297 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N HIS G 263 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE G 269 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASN G 361 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU G 271 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG G 359 " --> pdb=" O LEU G 271 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN G 368 " --> pdb=" O ASN G 409 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 389 through 394 removed outlier: 4.946A pdb=" N THR G 390 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU G 385 " --> pdb=" O THR G 390 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA G 392 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR G 381 " --> pdb=" O ILE G 394 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP G 451 " --> pdb=" O SER G 382 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU G 448 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN G 328 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU G 267 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR G 295 " --> pdb=" O ASP G 265 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASP G 265 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ARG G 297 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N HIS G 263 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE G 269 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASN G 361 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU G 271 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG G 359 " --> pdb=" O LEU G 271 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 458 through 462 removed outlier: 4.495A pdb=" N ILE G 459 " --> pdb=" O ASP G 472 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 501 through 506 Processing sheet with id=AG7, first strand: chain 'G' and resid 541 through 542 Processing sheet with id=AG8, first strand: chain 'G' and resid 596 through 598 Processing sheet with id=AG9, first strand: chain 'G' and resid 628 through 629 Processing sheet with id=AH1, first strand: chain 'G' and resid 654 through 655 removed outlier: 6.293A pdb=" N VAL G 696 " --> pdb=" O SER G 728 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER G 728 " --> pdb=" O VAL G 696 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL G 698 " --> pdb=" O ILE G 726 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE G 724 " --> pdb=" O ALA G 700 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 80 through 82 Processing sheet with id=AH3, first strand: chain 'H' and resid 436 through 441 removed outlier: 3.614A pdb=" N GLU H 439 " --> pdb=" O TRP H 501 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS H 548 " --> pdb=" O GLU H 528 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU H 528 " --> pdb=" O LYS H 548 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY H 526 " --> pdb=" O VAL H 550 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 436 through 441 removed outlier: 3.614A pdb=" N GLU H 439 " --> pdb=" O TRP H 501 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 485 through 486 Processing sheet with id=AH6, first strand: chain 'H' and resid 630 through 632 removed outlier: 3.547A pdb=" N LEU H 658 " --> pdb=" O LEU H 667 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 82 through 84 removed outlier: 3.855A pdb=" N ILE I 131 " --> pdb=" O TYR I 82 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL I 128 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 103 through 105 removed outlier: 3.525A pdb=" N ILE I 104 " --> pdb=" O ALA I 112 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 436 through 442 removed outlier: 3.697A pdb=" N LEU I 437 " --> pdb=" O ILE I 503 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ARG I 498 " --> pdb=" O ILE I 543 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE I 545 " --> pdb=" O ARG I 498 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LYS I 500 " --> pdb=" O ILE I 545 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA I 547 " --> pdb=" O LYS I 500 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ARG I 502 " --> pdb=" O ALA I 547 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL I 549 " --> pdb=" O ARG I 502 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN I 504 " --> pdb=" O VAL I 549 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP I 531 " --> pdb=" O ASP I 546 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS I 548 " --> pdb=" O ILE I 529 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE I 529 " --> pdb=" O LYS I 548 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL I 550 " --> pdb=" O LEU I 527 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU I 527 " --> pdb=" O VAL I 550 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 485 through 487 removed outlier: 3.869A pdb=" N LYS I 518 " --> pdb=" O LEU I 514 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 583 through 586 removed outlier: 3.619A pdb=" N PHE I 631 " --> pdb=" O THR I 584 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 83 through 84 removed outlier: 3.527A pdb=" N VAL J 128 " --> pdb=" O LYS J 122 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 103 through 105 Processing sheet with id=AI5, first strand: chain 'J' and resid 436 through 442 removed outlier: 3.947A pdb=" N LEU J 437 " --> pdb=" O ILE J 503 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE J 503 " --> pdb=" O LEU J 437 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU J 499 " --> pdb=" O MET J 441 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG J 498 " --> pdb=" O ILE J 543 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE J 545 " --> pdb=" O ARG J 498 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LYS J 500 " --> pdb=" O ILE J 545 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA J 547 " --> pdb=" O LYS J 500 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ARG J 502 " --> pdb=" O ALA J 547 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL J 549 " --> pdb=" O ARG J 502 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN J 504 " --> pdb=" O VAL J 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP J 531 " --> pdb=" O ASP J 546 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS J 548 " --> pdb=" O ILE J 529 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE J 529 " --> pdb=" O LYS J 548 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL J 550 " --> pdb=" O LEU J 527 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU J 527 " --> pdb=" O VAL J 550 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 455 through 456 removed outlier: 6.064A pdb=" N LYS J 462 " --> pdb=" O ASP J 456 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'J' and resid 485 through 487 Processing sheet with id=AI8, first strand: chain 'J' and resid 583 through 585 removed outlier: 4.748A pdb=" N THR J 584 " --> pdb=" O PHE J 629 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE J 631 " --> pdb=" O THR J 584 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG J 628 " --> pdb=" O ILE J 666 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU J 668 " --> pdb=" O ARG J 628 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL J 630 " --> pdb=" O LEU J 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 1639 hydrogen bonds defined for protein. 4500 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: 12.47 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8548 1.32 - 1.44: 9866 1.44 - 1.57: 24498 1.57 - 1.69: 2 1.69 - 1.81: 80 Bond restraints: 42994 Sorted by residual: bond pdb=" C PRO D 176 " pdb=" O PRO D 176 " ideal model delta sigma weight residual 1.233 1.199 0.034 9.90e-03 1.02e+04 1.17e+01 bond pdb=" CD LYS B 291 " pdb=" CE LYS B 291 " ideal model delta sigma weight residual 1.520 1.421 0.099 3.00e-02 1.11e+03 1.09e+01 bond pdb=" N VAL A 175 " pdb=" CA VAL A 175 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.23e-02 6.61e+03 1.06e+01 bond pdb=" N ILE J 83 " pdb=" CA ILE J 83 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.20e-02 6.94e+03 1.02e+01 bond pdb=" N ILE H 298 " pdb=" CA ILE H 298 " ideal model delta sigma weight residual 1.462 1.493 -0.032 1.01e-02 9.80e+03 9.87e+00 ... (remaining 42989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.07: 58498 7.07 - 14.14: 108 14.14 - 21.21: 10 21.21 - 28.28: 0 28.28 - 35.35: 1 Bond angle restraints: 58617 Sorted by residual: angle pdb=" C ILE H 88 " pdb=" N THR H 89 " pdb=" CA THR H 89 " ideal model delta sigma weight residual 122.20 157.55 -35.35 3.42e+00 8.55e-02 1.07e+02 angle pdb=" CB MET F 587 " pdb=" CG MET F 587 " pdb=" SD MET F 587 " ideal model delta sigma weight residual 112.70 93.31 19.39 3.00e+00 1.11e-01 4.18e+01 angle pdb=" CA PRO J 67 " pdb=" N PRO J 67 " pdb=" CD PRO J 67 " ideal model delta sigma weight residual 112.00 103.25 8.75 1.40e+00 5.10e-01 3.91e+01 angle pdb=" N PRO J 67 " pdb=" CD PRO J 67 " pdb=" CG PRO J 67 " ideal model delta sigma weight residual 103.20 94.79 8.41 1.50e+00 4.44e-01 3.14e+01 angle pdb=" CA MET A 434 " pdb=" CB MET A 434 " pdb=" CG MET A 434 " ideal model delta sigma weight residual 114.10 125.04 -10.94 2.00e+00 2.50e-01 2.99e+01 ... (remaining 58612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 24179 17.35 - 34.71: 1502 34.71 - 52.06: 231 52.06 - 69.42: 44 69.42 - 86.77: 25 Dihedral angle restraints: 25981 sinusoidal: 8998 harmonic: 16983 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 36.40 -36.40 0 5.00e+00 4.00e-02 5.30e+01 dihedral pdb=" C TYR J 579 " pdb=" N TYR J 579 " pdb=" CA TYR J 579 " pdb=" CB TYR J 579 " ideal model delta harmonic sigma weight residual -122.60 -136.09 13.49 0 2.50e+00 1.60e-01 2.91e+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 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 25978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 5993 0.095 - 0.190: 829 0.190 - 0.284: 77 0.284 - 0.379: 4 0.379 - 0.474: 3 Chirality restraints: 6906 Sorted by residual: chirality pdb=" CA TYR J 579 " pdb=" N TYR J 579 " pdb=" C TYR J 579 " pdb=" CB TYR J 579 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CB VAL J 550 " pdb=" CA VAL J 550 " pdb=" CG1 VAL J 550 " pdb=" CG2 VAL J 550 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CB VAL A 175 " pdb=" CA VAL A 175 " pdb=" CG1 VAL A 175 " pdb=" CG2 VAL A 175 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 6903 not shown) Planarity restraints: 7726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN I 384 " -0.100 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO I 385 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO I 385 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO I 385 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 66 " -0.086 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO J 67 " 0.215 5.00e-02 4.00e+02 pdb=" CA PRO J 67 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO J 67 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 486 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C GLU F 486 " 0.072 2.00e-02 2.50e+03 pdb=" O GLU F 486 " -0.027 2.00e-02 2.50e+03 pdb=" N THR F 487 " -0.025 2.00e-02 2.50e+03 ... (remaining 7723 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 437 2.54 - 3.13: 37996 3.13 - 3.72: 62631 3.72 - 4.31: 85575 4.31 - 4.90: 135891 Nonbonded interactions: 322530 Sorted by model distance: nonbonded pdb=" OE1 GLU A 486 " pdb=" NZ LYS A 586 " model vdw 1.950 3.120 nonbonded pdb=" CG PRO D 176 " pdb=" OD2 ASP D 185 " model vdw 1.969 3.440 nonbonded pdb=" NH2 ARG G 592 " pdb=" OD1 ASN G 602 " model vdw 2.018 3.120 nonbonded pdb=" O ILE A 210 " pdb=" NZ LYS A 214 " model vdw 2.026 3.120 nonbonded pdb=" OD1 ASN F 561 " pdb=" NE2 GLN F 565 " model vdw 2.062 3.120 ... (remaining 322525 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 274 or (resid 287 and (name N or name CA or na \ me C or name O or name CB )) or resid 288 through 659 or (resid 660 through 665 \ and (name N or name CA or name C or name O or name CB )) or resid 666 through 66 \ 7 or (resid 668 through 671 and (name N or name CA or name C or name O or name C \ B )) or resid 672 through 680 or (resid 681 through 685 and (name N or name CA o \ r name C or name O or name CB )) or resid 686 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 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 or (resid 123 and (name \ N or name CA or name C or name O or name CB )) or resid 124 or (resid 125 throug \ h 126 and (name N or name CA or name C or name O or name CB )) or resid 127 thro \ ugh 161 or (resid 162 and (name N or name CA or name C or name O or name CB )) o \ r resid 163 or (resid 164 through 165 and (name N or name CA or name C or name O \ or name CB )) or 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 19 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 194 or (resi \ d 195 and (name N or name CA or name C or name O or name CB )) or resid 196 thro \ ugh 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 262 or (resid 263 through 270 and (name N or nam \ e CA or name C or name O or name CB )) or resid 271 through 272 or (resid 273 th \ rough 276 and (name 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 name 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 n \ ame CA or name C or name O or name CB )) or (resid 332 through 338 and (name N o \ r name CA or name 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 (resi \ d 388 through 391 and (name N or name CA or name C or name O or name CB )) or re \ sid 392 or (resid 393 through 395 and (name N or name CA or name C or name O or \ name CB )) or resid 396 through 397 or (resid 405 through 407 and (name N or nam \ e CA or name C or name O or name CB )) or resid 408 or (resid 409 through 414 an \ d (name N or name CA or name C or name O or name CB )) or resid 415 or (resid 41 \ 6 through 417 and (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 na \ me O or name CB )) or resid 428 or (resid 433 through 436 and (name N or name CA \ or name C or name O or name CB )) or resid 437 through 445 or (resid 446 throug \ h 450 and (name N or name CA or name C or name O or name CB )) or (resid 451 thr \ ough 453 and (name N or name CA or name C or name O or name CB )) or resid 454 t \ hrough 456 or (resid 457 through 459 and (name N or name CA or name C or name O \ or name CB )) or resid 460 through 463 or (resid 464 through 465 and (name N or \ name CA or 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 4 \ 74 or (resid 475 through 476 and (name N or name CA or name C or name O or name \ CB )) or resid 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 (name N or name CA or name C or name O or name CB )) or resid 488 or (r \ esid 489 through 491 and (name N or name CA or name C or name O or name CB )) or \ resid 492 through 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 507 or (resid 508 through 511 and \ (name N or name CA or name C or name O or name CB )) or resid 512 through 513 o \ r (resid 514 through 516 and (name N or name CA or name C or name O or name CB ) \ ) or resid 517 or (resid 518 through 525 and (name N or name CA or name C or nam \ e O or name CB )) or resid 526 or (resid 527 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 (na \ me N or name CA or name C or name O or name CB )) or resid 538 through 540 or (r \ esid 541 through 542 and (name N or name CA or name C or name O or name CB )) or \ resid 543 through 547 or (resid 548 and (name N or name CA or name C or name O \ or name CB )) or resid 549 or (resid 550 and (name N or name CA or name C or nam \ e 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 through \ 563 and (name N or name CA or name C or name O or name CB )) or resid 564 or (r \ esid 565 and (name N or name CA or name C or name O or name CB )) or resid 566 o \ r (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 nam \ e O or name CB )) or resid 575 through 577 or (resid 578 through 579 and (name N \ or name CA or name C or name O or name CB )) or resid 580 or (resid 581 through \ 582 and (name N or name CA or name C or name O or name CB )) or resid 583 throu \ gh 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 name \ 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 resid 6 \ 05 or (resid 606 through 614 and (name N or name CA or name C or name O or name \ 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 through 619 or (resid 620 through 621 and (na \ me N or name CA or name C or name O or name CB )) or resid 622 or (resid 623 thr \ ough 624 and (name N or name CA or name C or name O or name CB )) or resid 625 t \ hrough 627 or (resid 628 and (name N or name CA or name C or name O or name CB ) \ ) or resid 629 through 630 or (resid 631 through 636 and (name N or name CA or n \ ame 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 name C or name O or name CB )) or resid 670 or (r \ esid 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 through 684 or (resid 685 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 name C or name O or name CB )) or res \ id 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 resid 729 or (resid 730 through 759 and \ (name N or name CA or name C or name O or name 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 7 \ 64 through 765 or (resid 766 through 767 and (name N or name CA or name C or nam \ e O or name CB )) or resid 768 through 769 or (resid 770 and (name N or name CA \ or name C or name O or name CB )) or resid 771 through 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 463 or (resid 464 through 465 and (name N or name CA or na \ me 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 resi \ d 477 through 490 or (resid 491 and (name N or name CA or name C or name O or na \ me CB )) or resid 492 through 494 or (resid 495 through 498 and (name N or name \ CA or name C or name O or name CB )) or resid 499 or (resid 500 and (name N or n \ ame CA or name C or name O or name CB )) or resid 501 through 515 or (resid 516 \ and (name N or name CA or name C or name 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 (res \ id 526 through 533 and (name N or name CA or name C or name O or name CB )) or r \ esid 534 through 536 or (resid 537 and (name N or name CA or name C or name O or \ name CB )) or resid 538 through 539 or (resid 540 through 542 and (name N or na \ me CA or name C or name O or name CB )) or resid 543 through 547 or (resid 548 a \ nd (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 resid \ 564 through 590 or (resid 591 through 592 and (name N or name CA or name C or n \ ame O or name CB )) or resid 593 through 596 or (resid 597 and (name N or name C \ A or name C or name O or name CB )) or resid 598 through 606 or (resid 607 throu \ gh 614 and (name N or name CA or name C or name O or name CB )) or resid 615 thr \ ough 620 or (resid 621 and (name N or name CA or name C or name O or name CB )) \ or resid 622 through 753 or (resid 754 through 759 and (name N or name CA or nam \ e C or name O or name CB )) or resid 760 through 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 79 or (resid 80 and (name N or nam \ e CA or name C or name O or name CB )) or resid 81 through 87 or (resid 88 throu \ gh 90 and (name N or name CA or name C or name O or name CB )) or resid 91 throu \ gh 124 or (resid 125 through 126 and (name N or name CA or name C or name O or n \ ame CB )) or resid 127 through 192 or (resid 193 and (name N or name CA or name \ 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 273 o \ r (resid 274 through 276 and (name N or name CA or name C or name O or name CB ) \ ) or resid 277 or (resid 278 through 280 and (name N or name CA or name C or nam \ e O or name CB )) or resid 281 through 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 338 and (nam \ e N or name CA or name C or name O or name CB )) or resid 369 through 389 or (re \ sid 390 through 391 and (name N or name CA or name C or name O or name CB )) or \ resid 392 through 393 or (resid 394 through 395 and (name N or name CA or name C \ or name O or name CB )) or resid 396 through 397 or (resid 405 through 407 and \ (name N or name 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 415 through 419 or (resid 420 through 427 and (name N or name CA or na \ me 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 name O or name CB )) or resid 437 through 501 or (resid \ 502 and (name N or name CA or name C or name O or name CB )) or resid 503 throug \ h 518 or (resid 519 through 525 and (name N or name CA or name C or name O or na \ me CB )) or resid 526 through 549 or (resid 550 and (name N or name CA or name C \ or name O or name CB )) or resid 551 through 578 or (resid 579 and (name N or n \ ame CA or name C or name O or name CB )) or resid 580 or (resid 581 through 582 \ and (name N or name CA or name C or name O or name CB )) or resid 583 through 58 \ 4 or (resid 585 and (name N or name CA or name C or name O or name CB )) or resi \ d 586 through 663 or (resid 664 through 669 and (name N or name CA or name C or \ name O or name CB )) or resid 670 through 689 or (resid 690 through 696 and (nam \ e N or name CA or name C or name O or name CB )) or resid 697 or (resid 698 thro \ ugh 710 and (name N or name CA or name C or name O or name CB )) or resid 711 th \ rough 746 or (resid 747 through 759 and (name N or name CA or name C or name O o \ r name CB )) or resid 760 through 769 or (resid 770 and (name N or name CA or na \ me C or name O or name 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.620 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 42.810 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 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 : 0.011 0.135 42994 Z= 0.502 Angle : 1.211 35.345 58617 Z= 0.670 Chirality : 0.065 0.474 6906 Planarity : 0.007 0.150 7726 Dihedral : 12.007 86.769 14943 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.94 % Favored : 91.65 % Rotamer: Outliers : 0.34 % Allowed : 0.93 % Favored : 98.73 % Cbeta Deviations : 0.04 % 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: -2.91 (0.10), residues: 5704 helix: -2.03 (0.11), residues: 1616 sheet: -1.01 (0.15), residues: 988 loop : -2.20 (0.10), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 252 TYR 0.061 0.004 TYR H 82 PHE 0.036 0.003 PHE A 554 TRP 0.056 0.004 TRP H 570 HIS 0.020 0.003 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.01119 (42994) covalent geometry : angle 1.21136 (58617) hydrogen bonds : bond 0.27398 ( 1540) hydrogen bonds : angle 9.14708 ( 4500) *********************** 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 1113 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1099 time to evaluate : 1.589 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: A 227 SER cc_start: 0.8389 (p) cc_final: 0.8161 (p) REVERT: A 243 ILE cc_start: 0.9554 (tt) cc_final: 0.9308 (tt) REVERT: A 261 ILE cc_start: 0.9278 (mt) cc_final: 0.8859 (pt) REVERT: A 368 ASN cc_start: 0.9000 (t0) cc_final: 0.8699 (t0) REVERT: A 434 MET cc_start: 0.8163 (tpt) cc_final: 0.7729 (tmm) REVERT: A 436 TYR cc_start: 0.8974 (t80) cc_final: 0.8664 (t80) REVERT: A 439 PHE cc_start: 0.9090 (t80) cc_final: 0.8544 (t80) REVERT: A 450 LEU cc_start: 0.8792 (mt) cc_final: 0.8278 (mp) REVERT: A 453 ASP cc_start: 0.8663 (p0) cc_final: 0.8429 (p0) REVERT: A 512 ASP cc_start: 0.8467 (t70) cc_final: 0.8172 (t70) REVERT: A 551 ASP cc_start: 0.7248 (m-30) cc_final: 0.6901 (m-30) REVERT: A 595 ARG cc_start: 0.8638 (mtm110) cc_final: 0.8404 (mtm110) REVERT: A 602 ASN cc_start: 0.8929 (m-40) cc_final: 0.8410 (m110) REVERT: A 633 LYS cc_start: 0.9565 (tmtt) cc_final: 0.9209 (tppt) REVERT: A 635 ILE cc_start: 0.9489 (tp) cc_final: 0.9150 (mm) REVERT: A 643 ILE cc_start: 0.8803 (mm) cc_final: 0.8344 (mm) REVERT: B 227 SER cc_start: 0.8394 (p) cc_final: 0.8135 (p) REVERT: B 243 ILE cc_start: 0.9344 (tt) cc_final: 0.8984 (tt) REVERT: B 265 ASP cc_start: 0.7931 (t0) cc_final: 0.7399 (t0) REVERT: B 328 ASN cc_start: 0.8670 (m-40) cc_final: 0.8467 (m-40) REVERT: B 368 ASN cc_start: 0.8988 (t0) cc_final: 0.8760 (t0) REVERT: B 394 ILE cc_start: 0.8290 (mm) cc_final: 0.8013 (mm) REVERT: B 414 LYS cc_start: 0.8868 (mptt) cc_final: 0.8590 (mmtm) REVERT: B 444 LYS cc_start: 0.9179 (pttm) cc_final: 0.8910 (ptpp) REVERT: B 450 LEU cc_start: 0.9325 (mt) cc_final: 0.8969 (mt) REVERT: B 453 ASP cc_start: 0.8793 (p0) cc_final: 0.8570 (p0) REVERT: B 459 ILE cc_start: 0.9099 (mt) cc_final: 0.8795 (mt) REVERT: B 486 GLU cc_start: 0.8065 (tp30) cc_final: 0.7686 (tp30) REVERT: B 522 THR cc_start: 0.8698 (p) cc_final: 0.8409 (p) REVERT: B 563 LYS cc_start: 0.9345 (mmmt) cc_final: 0.9064 (mmtm) REVERT: B 577 VAL cc_start: 0.8916 (m) cc_final: 0.8386 (p) REVERT: B 635 ILE cc_start: 0.9031 (mm) cc_final: 0.8780 (mm) REVERT: C 434 MET cc_start: 0.8113 (ppp) cc_final: 0.7601 (ppp) REVERT: C 444 LYS cc_start: 0.9377 (tptp) cc_final: 0.9109 (tppt) REVERT: C 462 TYR cc_start: 0.8899 (t80) cc_final: 0.8671 (t80) REVERT: C 486 GLU cc_start: 0.8020 (tp30) cc_final: 0.7716 (tp30) REVERT: C 525 GLU cc_start: 0.7578 (pt0) cc_final: 0.7038 (pt0) REVERT: C 551 ASP cc_start: 0.8424 (t0) cc_final: 0.8094 (t0) REVERT: C 602 ASN cc_start: 0.8850 (m-40) cc_final: 0.8406 (m110) REVERT: C 616 HIS cc_start: 0.8428 (m90) cc_final: 0.8013 (m90) REVERT: C 637 LYS cc_start: 0.9377 (mmmm) cc_final: 0.8847 (mmtm) REVERT: C 724 ILE cc_start: 0.9275 (mm) cc_final: 0.8917 (tt) REVERT: D 185 ASP cc_start: 0.8576 (p0) cc_final: 0.8311 (p0) REVERT: D 242 ARG cc_start: 0.8489 (mtt90) cc_final: 0.8086 (mtt90) REVERT: D 250 GLU cc_start: 0.8408 (pm20) cc_final: 0.7976 (mp0) REVERT: D 261 ILE cc_start: 0.9337 (mt) cc_final: 0.9115 (tp) REVERT: D 394 ILE cc_start: 0.9395 (mm) cc_final: 0.9153 (mp) REVERT: D 472 ASP cc_start: 0.8681 (t0) cc_final: 0.8152 (t0) REVERT: D 486 GLU cc_start: 0.8214 (tp30) cc_final: 0.7817 (tp30) REVERT: D 514 LEU cc_start: 0.8837 (tp) cc_final: 0.8524 (tt) REVERT: D 525 GLU cc_start: 0.8978 (tp30) cc_final: 0.8437 (tp30) REVERT: D 551 ASP cc_start: 0.8057 (m-30) cc_final: 0.7365 (m-30) REVERT: D 578 LEU cc_start: 0.9377 (tt) cc_final: 0.8980 (tt) REVERT: E 185 ASP cc_start: 0.9077 (p0) cc_final: 0.8702 (p0) REVERT: E 195 ASP cc_start: 0.8087 (t70) cc_final: 0.7822 (t0) REVERT: E 385 LEU cc_start: 0.8669 (mm) cc_final: 0.7656 (mm) REVERT: E 389 GLN cc_start: 0.8277 (mp10) cc_final: 0.7815 (mp10) REVERT: E 416 LEU cc_start: 0.9142 (mp) cc_final: 0.8933 (mp) REVERT: E 434 MET cc_start: 0.8737 (ppp) cc_final: 0.8387 (ppp) REVERT: E 472 ASP cc_start: 0.8746 (t0) cc_final: 0.8409 (t0) REVERT: E 485 GLN cc_start: 0.8867 (mt0) cc_final: 0.8651 (mt0) REVERT: E 541 GLN cc_start: 0.7905 (mt0) cc_final: 0.7246 (mm-40) REVERT: E 580 LYS cc_start: 0.9542 (mmmt) cc_final: 0.9298 (mmmm) REVERT: F 376 ASN cc_start: 0.8873 (m-40) cc_final: 0.8512 (t0) REVERT: F 440 LEU cc_start: 0.9338 (mt) cc_final: 0.8863 (mt) REVERT: F 444 LYS cc_start: 0.9082 (ptpp) cc_final: 0.8687 (ptpt) REVERT: F 470 ARG cc_start: 0.7964 (tmm-80) cc_final: 0.7702 (tmm-80) REVERT: F 472 ASP cc_start: 0.8199 (t0) cc_final: 0.7679 (t0) REVERT: F 590 LEU cc_start: 0.9035 (tp) cc_final: 0.8791 (tt) REVERT: F 608 ASP cc_start: 0.7081 (t70) cc_final: 0.6832 (t70) REVERT: F 616 HIS cc_start: 0.9353 (m90) cc_final: 0.9132 (m90) REVERT: F 633 LYS cc_start: 0.9058 (pptt) cc_final: 0.8808 (pptt) REVERT: G 190 GLU cc_start: 0.8590 (tp30) cc_final: 0.8301 (tm-30) REVERT: G 222 SER cc_start: 0.8884 (t) cc_final: 0.8551 (t) REVERT: G 250 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7571 (mm-30) REVERT: G 326 ASN cc_start: 0.8126 (m-40) cc_final: 0.7775 (m110) REVERT: G 383 LEU cc_start: 0.8828 (tp) cc_final: 0.8610 (tp) REVERT: G 439 PHE cc_start: 0.9442 (t80) cc_final: 0.9080 (t80) REVERT: G 465 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8083 (mp0) REVERT: G 525 GLU cc_start: 0.7911 (pt0) cc_final: 0.7457 (pt0) REVERT: G 589 ILE cc_start: 0.8996 (mt) cc_final: 0.8730 (mm) REVERT: G 593 ASP cc_start: 0.8999 (t70) cc_final: 0.8643 (t0) REVERT: G 595 ARG cc_start: 0.9058 (ttp80) cc_final: 0.8800 (ttp-110) REVERT: G 617 ARG cc_start: 0.8936 (ttp80) cc_final: 0.8508 (ttp80) REVERT: G 703 LYS cc_start: 0.8549 (ptpp) cc_final: 0.8347 (ptpp) REVERT: H 158 ASP cc_start: 0.8009 (t70) cc_final: 0.7514 (t70) REVERT: H 187 ASP cc_start: 0.8697 (m-30) cc_final: 0.8434 (m-30) REVERT: H 226 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8355 (tp30) REVERT: H 228 GLN cc_start: 0.8932 (mm110) cc_final: 0.8533 (mm-40) REVERT: H 246 LYS cc_start: 0.8788 (ptpp) cc_final: 0.8583 (mppt) REVERT: H 415 ASP cc_start: 0.8475 (m-30) cc_final: 0.8170 (m-30) REVERT: H 472 LYS cc_start: 0.9036 (pttm) cc_final: 0.8478 (pttm) REVERT: H 474 ASN cc_start: 0.7728 (m110) cc_final: 0.7459 (m-40) REVERT: H 499 LEU cc_start: 0.9049 (mp) cc_final: 0.8529 (mp) REVERT: H 533 GLN cc_start: 0.8412 (pm20) cc_final: 0.7965 (pm20) REVERT: H 541 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7948 (mt-10) REVERT: H 658 LEU cc_start: 0.8581 (tt) cc_final: 0.8313 (tt) REVERT: H 684 PHE cc_start: 0.8877 (t80) cc_final: 0.8667 (t80) REVERT: H 688 PHE cc_start: 0.9154 (t80) cc_final: 0.8810 (t80) REVERT: H 693 ASP cc_start: 0.8231 (t0) cc_final: 0.8022 (t0) REVERT: H 761 LYS cc_start: 0.9234 (mttt) cc_final: 0.8846 (pttp) REVERT: I 42 HIS cc_start: 0.8469 (m170) cc_final: 0.8223 (m-70) REVERT: I 61 LYS cc_start: 0.9166 (mmpt) cc_final: 0.8919 (mmtm) REVERT: I 153 LYS cc_start: 0.9121 (ttmm) cc_final: 0.8896 (ttmm) REVERT: I 158 ASP cc_start: 0.7996 (m-30) cc_final: 0.7746 (m-30) REVERT: I 171 LEU cc_start: 0.9318 (tp) cc_final: 0.9069 (tp) REVERT: I 184 ASP cc_start: 0.8409 (p0) cc_final: 0.8064 (p0) REVERT: I 243 TYR cc_start: 0.9154 (t80) cc_final: 0.8830 (t80) REVERT: I 256 LEU cc_start: 0.8717 (mp) cc_final: 0.8498 (mp) REVERT: I 277 HIS cc_start: 0.8753 (t-90) cc_final: 0.8006 (t-170) REVERT: I 467 ILE cc_start: 0.8307 (mp) cc_final: 0.7699 (mp) REVERT: I 544 ARG cc_start: 0.8221 (tpt90) cc_final: 0.7817 (tpt-90) REVERT: I 570 TRP cc_start: 0.5651 (m100) cc_final: 0.4939 (m100) REVERT: I 597 GLU cc_start: 0.7163 (mp0) cc_final: 0.6711 (mp0) REVERT: J 153 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8711 (mtmt) REVERT: J 190 PHE cc_start: 0.9045 (m-10) cc_final: 0.8777 (m-10) REVERT: J 207 GLU cc_start: 0.8847 (tt0) cc_final: 0.8645 (mm-30) REVERT: J 221 PHE cc_start: 0.9081 (t80) cc_final: 0.8139 (t80) REVERT: J 277 HIS cc_start: 0.7320 (t-90) cc_final: 0.7080 (t-90) REVERT: J 411 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8441 (tp-100) REVERT: J 581 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7502 (pptt) REVERT: J 582 LEU cc_start: 0.9440 (tp) cc_final: 0.9103 (tp) REVERT: J 584 THR cc_start: 0.7281 (p) cc_final: 0.6577 (p) REVERT: J 586 ASN cc_start: 0.8116 (m-40) cc_final: 0.7488 (m-40) REVERT: J 590 ARG cc_start: 0.8164 (mmm160) cc_final: 0.7662 (mmm-85) outliers start: 14 outliers final: 2 residues processed: 1106 average time/residue: 0.2623 time to fit residues: 469.1448 Evaluate side-chains 879 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 876 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain J residue 581 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 265 optimal weight: 0.9990 chunk 523 optimal weight: 8.9990 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 0.9980 chunk 310 optimal weight: 0.3980 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN B 328 ASN ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 GLN B 602 ASN C 458 ASN C 705 ASN ** D 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 HIS E 246 ASN E 328 ASN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 565 GLN E 602 ASN E 616 HIS F 458 ASN F 499 ASN F 553 ASN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 GLN G 553 ASN ** G 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN H 228 GLN ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 594 ASN I 35 HIS I 228 GLN I 262 GLN I 496 ASN ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.187068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108005 restraints weight = 73308.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112224 restraints weight = 36561.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.114899 restraints weight = 24502.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116425 restraints weight = 19411.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117485 restraints weight = 17013.946| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 42994 Z= 0.224 Angle : 0.766 17.234 58617 Z= 0.401 Chirality : 0.049 0.335 6906 Planarity : 0.005 0.082 7726 Dihedral : 5.007 46.316 6121 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.42 % Rotamer: Outliers : 2.40 % Allowed : 12.05 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.48 (0.11), residues: 5704 helix: -0.54 (0.12), residues: 1655 sheet: -0.55 (0.15), residues: 1054 loop : -1.37 (0.11), residues: 2995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 600 TYR 0.027 0.002 TYR I 513 PHE 0.027 0.002 PHE I 765 TRP 0.032 0.002 TRP H 570 HIS 0.007 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00502 (42994) covalent geometry : angle 0.76598 (58617) hydrogen bonds : bond 0.05587 ( 1540) hydrogen bonds : angle 5.97660 ( 4500) *********************** REFINEMENT MACRO_CYCLE 2 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 1103 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 1005 time to evaluate : 1.334 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: 0.8672 (p0) cc_final: 0.8428 (p0) REVERT: A 224 GLU cc_start: 0.8505 (tp30) cc_final: 0.7974 (mm-30) REVERT: A 227 SER cc_start: 0.8589 (p) cc_final: 0.8377 (p) REVERT: A 368 ASN cc_start: 0.9085 (t0) cc_final: 0.8794 (t0) REVERT: A 436 TYR cc_start: 0.8957 (t80) cc_final: 0.8615 (t80) REVERT: A 447 GLN cc_start: 0.8933 (tt0) cc_final: 0.8109 (tm-30) REVERT: A 470 ARG cc_start: 0.7540 (tpt-90) cc_final: 0.7288 (tpt-90) REVERT: A 549 GLU cc_start: 0.8802 (mp0) cc_final: 0.8450 (mp0) REVERT: A 551 ASP cc_start: 0.7403 (m-30) cc_final: 0.7014 (m-30) REVERT: A 602 ASN cc_start: 0.8729 (m-40) cc_final: 0.8292 (m110) REVERT: A 632 ASP cc_start: 0.9219 (p0) cc_final: 0.8688 (p0) REVERT: A 633 LYS cc_start: 0.9589 (tmtt) cc_final: 0.9297 (tppt) REVERT: A 635 ILE cc_start: 0.9442 (tp) cc_final: 0.9125 (mm) REVERT: A 703 LYS cc_start: 0.8063 (mmtm) cc_final: 0.7748 (mmtm) REVERT: B 190 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7660 (mt-10) REVERT: B 227 SER cc_start: 0.8663 (p) cc_final: 0.8378 (p) REVERT: B 265 ASP cc_start: 0.7778 (t0) cc_final: 0.7253 (t0) REVERT: B 267 GLU cc_start: 0.7235 (mp0) cc_final: 0.7008 (mp0) REVERT: B 368 ASN cc_start: 0.8972 (t0) cc_final: 0.8720 (t0) REVERT: B 403 GLN cc_start: 0.8186 (mp10) cc_final: 0.7897 (mp10) REVERT: B 414 LYS cc_start: 0.9090 (mptt) cc_final: 0.8865 (mmtp) REVERT: B 450 LEU cc_start: 0.9216 (mt) cc_final: 0.8976 (mt) REVERT: B 486 GLU cc_start: 0.8187 (tp30) cc_final: 0.7910 (tp30) REVERT: B 577 VAL cc_start: 0.8892 (m) cc_final: 0.8403 (p) REVERT: B 602 ASN cc_start: 0.8961 (m-40) cc_final: 0.8698 (m-40) REVERT: B 633 LYS cc_start: 0.9148 (pptt) cc_final: 0.8646 (pptt) REVERT: B 635 ILE cc_start: 0.9187 (mm) cc_final: 0.8884 (mm) REVERT: B 703 LYS cc_start: 0.8364 (mmtp) cc_final: 0.8108 (mmtp) REVERT: B 722 LYS cc_start: 0.9223 (tppt) cc_final: 0.8779 (tppt) REVERT: C 197 LYS cc_start: 0.7770 (tppt) cc_final: 0.7497 (tptp) REVERT: C 389 GLN cc_start: 0.7780 (mp10) cc_final: 0.7495 (mp10) REVERT: C 434 MET cc_start: 0.8142 (ppp) cc_final: 0.7445 (ppp) REVERT: C 444 LYS cc_start: 0.9443 (tptp) cc_final: 0.9176 (tppt) REVERT: C 551 ASP cc_start: 0.8221 (t0) cc_final: 0.7761 (t0) REVERT: C 583 LEU cc_start: 0.9328 (mt) cc_final: 0.8995 (mp) REVERT: C 587 MET cc_start: 0.8968 (mtp) cc_final: 0.8703 (mtt) REVERT: C 602 ASN cc_start: 0.8610 (m-40) cc_final: 0.8335 (m110) REVERT: C 616 HIS cc_start: 0.8476 (m90) cc_final: 0.8249 (m90) REVERT: C 632 ASP cc_start: 0.9002 (t0) cc_final: 0.8762 (p0) REVERT: C 637 LYS cc_start: 0.9407 (mmmm) cc_final: 0.9093 (mmmt) REVERT: D 250 GLU cc_start: 0.8282 (pm20) cc_final: 0.8061 (mp0) REVERT: D 261 ILE cc_start: 0.9328 (mt) cc_final: 0.9021 (tp) REVERT: D 324 PHE cc_start: 0.7049 (p90) cc_final: 0.6746 (p90) REVERT: D 444 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8631 (ptpt) REVERT: D 447 GLN cc_start: 0.8246 (tm-30) cc_final: 0.8027 (tm-30) REVERT: D 448 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8093 (tp) REVERT: D 468 ARG cc_start: 0.8587 (mmm-85) cc_final: 0.8359 (tpp80) REVERT: D 472 ASP cc_start: 0.8187 (t0) cc_final: 0.7485 (t0) REVERT: D 509 ASN cc_start: 0.9189 (t0) cc_final: 0.8978 (t0) REVERT: D 514 LEU cc_start: 0.8250 (tp) cc_final: 0.8013 (tt) REVERT: D 525 GLU cc_start: 0.8760 (tp30) cc_final: 0.8509 (pt0) REVERT: D 551 ASP cc_start: 0.7902 (m-30) cc_final: 0.7004 (p0) REVERT: D 587 MET cc_start: 0.9013 (ptp) cc_final: 0.8413 (ptp) REVERT: D 602 ASN cc_start: 0.8749 (m-40) cc_final: 0.8463 (m110) REVERT: D 614 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8181 (pm20) REVERT: E 185 ASP cc_start: 0.9043 (p0) cc_final: 0.8773 (p0) REVERT: E 195 ASP cc_start: 0.8101 (t70) cc_final: 0.7647 (t0) REVERT: E 202 PHE cc_start: 0.8731 (p90) cc_final: 0.8226 (p90) REVERT: E 220 LYS cc_start: 0.8339 (mmtt) cc_final: 0.7901 (mmmt) REVERT: E 359 ARG cc_start: 0.8041 (pmt170) cc_final: 0.7768 (ptt-90) REVERT: E 385 LEU cc_start: 0.8565 (mm) cc_final: 0.8196 (mm) REVERT: E 387 LYS cc_start: 0.9310 (mmmt) cc_final: 0.9083 (ptmm) REVERT: E 391 LEU cc_start: 0.9200 (mm) cc_final: 0.8819 (mm) REVERT: E 434 MET cc_start: 0.8966 (ppp) cc_final: 0.8534 (ppp) REVERT: E 444 LYS cc_start: 0.9237 (tppt) cc_final: 0.8996 (tppt) REVERT: E 470 ARG cc_start: 0.7720 (tmm-80) cc_final: 0.7482 (tmm-80) REVERT: E 472 ASP cc_start: 0.8599 (t0) cc_final: 0.8156 (t0) REVERT: E 488 THR cc_start: 0.9321 (p) cc_final: 0.8994 (t) REVERT: E 512 ASP cc_start: 0.7704 (t0) cc_final: 0.7065 (t0) REVERT: E 541 GLN cc_start: 0.7845 (mt0) cc_final: 0.7205 (mm-40) REVERT: E 580 LYS cc_start: 0.9555 (mmmt) cc_final: 0.9221 (mmmm) REVERT: E 593 ASP cc_start: 0.7194 (t0) cc_final: 0.6833 (t0) REVERT: F 245 LYS cc_start: 0.9316 (mmmm) cc_final: 0.9091 (mmtm) REVERT: F 326 ASN cc_start: 0.8456 (m-40) cc_final: 0.7318 (m-40) REVERT: F 376 ASN cc_start: 0.9009 (m-40) cc_final: 0.8490 (t0) REVERT: F 471 VAL cc_start: 0.8560 (m) cc_final: 0.8170 (t) REVERT: F 472 ASP cc_start: 0.8119 (t0) cc_final: 0.7354 (t0) REVERT: F 479 GLU cc_start: 0.8312 (mp0) cc_final: 0.8001 (mp0) REVERT: F 499 ASN cc_start: 0.8482 (m-40) cc_final: 0.7775 (m-40) REVERT: F 521 MET cc_start: 0.7893 (tpt) cc_final: 0.6497 (mmm) REVERT: F 551 ASP cc_start: 0.7167 (t0) cc_final: 0.6034 (p0) REVERT: F 599 ASP cc_start: 0.8729 (t0) cc_final: 0.8526 (t0) REVERT: F 601 ASN cc_start: 0.9295 (p0) cc_final: 0.8964 (p0) REVERT: F 616 HIS cc_start: 0.9322 (m90) cc_final: 0.8990 (m90) REVERT: F 633 LYS cc_start: 0.9206 (pptt) cc_final: 0.8904 (pptt) REVERT: F 636 ARG cc_start: 0.8418 (ptp90) cc_final: 0.8106 (ptp90) REVERT: G 250 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7439 (tp30) REVERT: G 326 ASN cc_start: 0.7746 (m-40) cc_final: 0.7422 (m-40) REVERT: G 439 PHE cc_start: 0.9400 (t80) cc_final: 0.9052 (t80) REVERT: G 444 LYS cc_start: 0.9267 (ptpp) cc_final: 0.9023 (pttm) REVERT: G 465 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8238 (mm-30) REVERT: G 515 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8176 (mm-30) REVERT: G 551 ASP cc_start: 0.7802 (t0) cc_final: 0.7451 (t0) REVERT: G 557 GLN cc_start: 0.9175 (tp-100) cc_final: 0.8946 (tp-100) REVERT: G 560 GLN cc_start: 0.9252 (tp-100) cc_final: 0.8870 (mm-40) REVERT: G 589 ILE cc_start: 0.8665 (mt) cc_final: 0.8404 (mm) REVERT: G 593 ASP cc_start: 0.9022 (t70) cc_final: 0.8540 (t0) REVERT: G 595 ARG cc_start: 0.9119 (ttp80) cc_final: 0.8919 (ttp-110) REVERT: G 617 ARG cc_start: 0.9006 (ttp80) cc_final: 0.8575 (ttp80) REVERT: H 65 LYS cc_start: 0.9186 (mmpt) cc_final: 0.8986 (mmmt) REVERT: H 118 TYR cc_start: 0.7275 (OUTLIER) cc_final: 0.5981 (p90) REVERT: H 158 ASP cc_start: 0.8128 (t70) cc_final: 0.7712 (t70) REVERT: H 184 ASP cc_start: 0.8783 (m-30) cc_final: 0.8398 (m-30) REVERT: H 186 GLN cc_start: 0.7977 (pt0) cc_final: 0.7324 (pm20) REVERT: H 187 ASP cc_start: 0.8603 (m-30) cc_final: 0.8216 (m-30) REVERT: H 201 PHE cc_start: 0.9007 (m-80) cc_final: 0.8641 (m-80) REVERT: H 215 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7889 (pt0) REVERT: H 236 TYR cc_start: 0.8149 (m-80) cc_final: 0.7921 (m-80) REVERT: H 393 GLN cc_start: 0.8546 (pm20) cc_final: 0.8091 (pm20) REVERT: H 415 ASP cc_start: 0.8257 (m-30) cc_final: 0.7926 (m-30) REVERT: H 472 LYS cc_start: 0.8962 (pttm) cc_final: 0.8719 (tttp) REVERT: H 510 ARG cc_start: 0.7298 (mmm-85) cc_final: 0.6806 (mmm-85) REVERT: H 548 LYS cc_start: 0.7434 (mmmt) cc_final: 0.7196 (tptp) REVERT: H 589 ASN cc_start: 0.7502 (m110) cc_final: 0.6898 (m110) REVERT: H 638 ASN cc_start: 0.8701 (m110) cc_final: 0.8072 (t0) REVERT: H 693 ASP cc_start: 0.8536 (t0) cc_final: 0.8208 (t0) REVERT: H 718 PHE cc_start: 0.7967 (t80) cc_final: 0.7630 (t80) REVERT: H 737 PHE cc_start: 0.8845 (m-80) cc_final: 0.8219 (m-10) REVERT: I 61 LYS cc_start: 0.9114 (mmpt) cc_final: 0.8715 (mttm) REVERT: I 72 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: I 137 TYR cc_start: 0.8437 (m-10) cc_final: 0.8186 (m-10) REVERT: I 158 ASP cc_start: 0.7993 (m-30) cc_final: 0.7762 (m-30) REVERT: I 184 ASP cc_start: 0.8246 (p0) cc_final: 0.7851 (p0) REVERT: I 243 TYR cc_start: 0.9170 (t80) cc_final: 0.8725 (t80) REVERT: I 277 HIS cc_start: 0.8642 (t-90) cc_final: 0.7983 (t-170) REVERT: I 531 ASP cc_start: 0.7604 (t0) cc_final: 0.6938 (t0) REVERT: I 537 GLN cc_start: 0.9049 (tp40) cc_final: 0.8393 (mp10) REVERT: I 542 TYR cc_start: 0.8358 (m-80) cc_final: 0.7960 (m-80) REVERT: I 769 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8436 (mm-40) REVERT: J 108 TYR cc_start: 0.7430 (m-80) cc_final: 0.7024 (m-80) REVERT: J 153 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8531 (mtpt) REVERT: J 217 PHE cc_start: 0.7969 (t80) cc_final: 0.7544 (t80) REVERT: J 221 PHE cc_start: 0.8883 (t80) cc_final: 0.8329 (t80) REVERT: J 250 GLN cc_start: 0.7421 (tm-30) cc_final: 0.7148 (tm-30) REVERT: J 277 HIS cc_start: 0.7525 (t-90) cc_final: 0.7278 (t-90) REVERT: J 411 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8651 (tp-100) REVERT: J 436 TYR cc_start: 0.6463 (m-10) cc_final: 0.6166 (m-10) REVERT: J 582 LEU cc_start: 0.9131 (tp) cc_final: 0.8733 (tp) REVERT: J 584 THR cc_start: 0.7378 (p) cc_final: 0.6977 (p) REVERT: J 586 ASN cc_start: 0.7739 (m-40) cc_final: 0.7470 (m-40) REVERT: J 629 PHE cc_start: 0.8471 (m-10) cc_final: 0.7879 (m-10) outliers start: 98 outliers final: 62 residues processed: 1047 average time/residue: 0.2414 time to fit residues: 413.2573 Evaluate side-chains 976 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 910 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 725 LEU Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 438 GLN Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 475 SER Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 607 LYS Chi-restraints excluded: chain H residue 708 VAL Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 115 HIS Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 579 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 315 optimal weight: 4.9990 chunk 405 optimal weight: 20.0000 chunk 548 optimal weight: 4.9990 chunk 533 optimal weight: 0.0670 chunk 236 optimal weight: 0.7980 chunk 263 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 412 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 368 optimal weight: 6.9990 overall best weight: 2.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN A 556 GLN A 557 GLN B 458 ASN B 494 ASN B 543 GLN B 553 ASN C 705 ASN D 246 ASN ** D 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN F 602 ASN G 483 GLN ** G 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 ASN ** H 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 767 ASN J 186 GLN ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.185945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106992 restraints weight = 73158.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.111164 restraints weight = 36651.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113779 restraints weight = 24602.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115363 restraints weight = 19517.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116310 restraints weight = 17064.717| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 42994 Z= 0.210 Angle : 0.684 14.660 58617 Z= 0.356 Chirality : 0.047 0.192 6906 Planarity : 0.005 0.062 7726 Dihedral : 4.835 50.137 6116 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.65 % Favored : 95.30 % Rotamer: Outliers : 3.28 % Allowed : 14.84 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.01 (0.11), residues: 5704 helix: -0.22 (0.13), residues: 1678 sheet: -0.30 (0.15), residues: 1072 loop : -1.03 (0.11), residues: 2954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 600 TYR 0.022 0.002 TYR F 462 PHE 0.026 0.002 PHE F 202 TRP 0.021 0.001 TRP I 570 HIS 0.010 0.001 HIS D 616 Details of bonding type rmsd covalent geometry : bond 0.00483 (42994) covalent geometry : angle 0.68447 (58617) hydrogen bonds : bond 0.04400 ( 1540) hydrogen bonds : angle 5.28468 ( 4500) *********************** REFINEMENT MACRO_CYCLE 3 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 1106 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 972 time to evaluate : 1.456 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: 0.8632 (p0) cc_final: 0.8367 (p0) REVERT: A 224 GLU cc_start: 0.8496 (tp30) cc_final: 0.7952 (mm-30) REVERT: A 265 ASP cc_start: 0.8199 (t0) cc_final: 0.7538 (p0) REVERT: A 446 LYS cc_start: 0.8658 (mttt) cc_final: 0.8386 (mmmt) REVERT: A 447 GLN cc_start: 0.8911 (tt0) cc_final: 0.8096 (tm-30) REVERT: A 470 ARG cc_start: 0.7500 (tpt-90) cc_final: 0.7254 (tpt-90) REVERT: A 479 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7602 (tt0) REVERT: A 551 ASP cc_start: 0.7506 (m-30) cc_final: 0.7101 (m-30) REVERT: A 557 GLN cc_start: 0.8900 (mm110) cc_final: 0.8599 (mm-40) REVERT: A 595 ARG cc_start: 0.8800 (mtm110) cc_final: 0.8506 (mtm110) REVERT: A 602 ASN cc_start: 0.8717 (m-40) cc_final: 0.8224 (m110) REVERT: A 632 ASP cc_start: 0.9274 (p0) cc_final: 0.8721 (p0) REVERT: A 633 LYS cc_start: 0.9591 (tmtt) cc_final: 0.9271 (tppt) REVERT: A 635 ILE cc_start: 0.9450 (tp) cc_final: 0.9106 (mm) REVERT: A 703 LYS cc_start: 0.8145 (mmtm) cc_final: 0.7873 (mmtm) REVERT: B 190 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7658 (mt-10) REVERT: B 227 SER cc_start: 0.8824 (p) cc_final: 0.8543 (p) REVERT: B 265 ASP cc_start: 0.7835 (t0) cc_final: 0.7354 (t0) REVERT: B 326 ASN cc_start: 0.8848 (p0) cc_final: 0.8524 (p0) REVERT: B 328 ASN cc_start: 0.8500 (m110) cc_final: 0.8276 (m110) REVERT: B 403 GLN cc_start: 0.8231 (mp10) cc_final: 0.7888 (mp10) REVERT: B 434 MET cc_start: 0.7809 (tmm) cc_final: 0.7506 (tmm) REVERT: B 450 LEU cc_start: 0.9204 (mt) cc_final: 0.8998 (mt) REVERT: B 453 ASP cc_start: 0.9026 (p0) cc_final: 0.8670 (p0) REVERT: B 459 ILE cc_start: 0.8825 (mt) cc_final: 0.8584 (mt) REVERT: B 486 GLU cc_start: 0.8268 (tp30) cc_final: 0.7977 (tp30) REVERT: B 577 VAL cc_start: 0.8909 (m) cc_final: 0.8469 (p) REVERT: B 587 MET cc_start: 0.7833 (mpp) cc_final: 0.7569 (mpp) REVERT: B 593 ASP cc_start: 0.7990 (t0) cc_final: 0.7307 (t0) REVERT: B 602 ASN cc_start: 0.8946 (m-40) cc_final: 0.8607 (m-40) REVERT: B 633 LYS cc_start: 0.9183 (pptt) cc_final: 0.8567 (pptt) REVERT: B 635 ILE cc_start: 0.9185 (mm) cc_final: 0.8835 (mm) REVERT: B 636 ARG cc_start: 0.8747 (ptt-90) cc_final: 0.8353 (ptt-90) REVERT: B 722 LYS cc_start: 0.9336 (tppt) cc_final: 0.9054 (tppt) REVERT: C 434 MET cc_start: 0.8275 (ppp) cc_final: 0.7585 (ppp) REVERT: C 444 LYS cc_start: 0.9504 (tptp) cc_final: 0.9258 (tppt) REVERT: C 462 TYR cc_start: 0.9042 (t80) cc_final: 0.8833 (t80) REVERT: C 525 GLU cc_start: 0.8099 (pt0) cc_final: 0.7890 (pt0) REVERT: C 551 ASP cc_start: 0.8293 (t0) cc_final: 0.7859 (t0) REVERT: C 555 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7588 (t70) REVERT: C 579 ASP cc_start: 0.8657 (t0) cc_final: 0.8445 (t0) REVERT: C 583 LEU cc_start: 0.9299 (mt) cc_final: 0.8887 (mp) REVERT: C 587 MET cc_start: 0.9026 (mtp) cc_final: 0.8683 (mtt) REVERT: C 602 ASN cc_start: 0.8708 (m-40) cc_final: 0.8373 (m110) REVERT: C 616 HIS cc_start: 0.8633 (m90) cc_final: 0.8314 (m90) REVERT: C 723 LYS cc_start: 0.9209 (mttp) cc_final: 0.8881 (mptt) REVERT: D 261 ILE cc_start: 0.9196 (mt) cc_final: 0.8969 (tp) REVERT: D 291 LYS cc_start: 0.8795 (mmtm) cc_final: 0.8417 (mptt) REVERT: D 335 ASP cc_start: 0.8518 (t0) cc_final: 0.8299 (t0) REVERT: D 437 ASN cc_start: 0.9126 (m-40) cc_final: 0.8238 (p0) REVERT: D 444 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8639 (mmtt) REVERT: D 448 LEU cc_start: 0.8593 (tp) cc_final: 0.8169 (tp) REVERT: D 470 ARG cc_start: 0.7694 (mmm160) cc_final: 0.7447 (mmm160) REVERT: D 472 ASP cc_start: 0.8079 (t0) cc_final: 0.7285 (t0) REVERT: D 486 GLU cc_start: 0.8600 (tp30) cc_final: 0.8250 (tp30) REVERT: D 509 ASN cc_start: 0.9165 (t0) cc_final: 0.8906 (t0) REVERT: D 514 LEU cc_start: 0.8202 (tp) cc_final: 0.7963 (tt) REVERT: D 551 ASP cc_start: 0.7778 (m-30) cc_final: 0.6762 (p0) REVERT: D 559 SER cc_start: 0.9063 (t) cc_final: 0.8833 (p) REVERT: D 602 ASN cc_start: 0.8920 (m-40) cc_final: 0.8614 (m110) REVERT: E 185 ASP cc_start: 0.8929 (p0) cc_final: 0.8661 (p0) REVERT: E 195 ASP cc_start: 0.8032 (t70) cc_final: 0.7705 (t0) REVERT: E 202 PHE cc_start: 0.8694 (p90) cc_final: 0.8397 (p90) REVERT: E 220 LYS cc_start: 0.8364 (mmtt) cc_final: 0.7907 (mmmt) REVERT: E 359 ARG cc_start: 0.8095 (pmt170) cc_final: 0.7788 (ptt-90) REVERT: E 385 LEU cc_start: 0.8744 (mm) cc_final: 0.8402 (mm) REVERT: E 387 LYS cc_start: 0.9307 (mmmt) cc_final: 0.9079 (ptmm) REVERT: E 391 LEU cc_start: 0.9218 (mm) cc_final: 0.8828 (mm) REVERT: E 434 MET cc_start: 0.8761 (ppp) cc_final: 0.8201 (ppp) REVERT: E 449 ARG cc_start: 0.9292 (mtm110) cc_final: 0.9080 (mtm110) REVERT: E 470 ARG cc_start: 0.7780 (tmm-80) cc_final: 0.7492 (tmm-80) REVERT: E 472 ASP cc_start: 0.8589 (t0) cc_final: 0.8152 (t0) REVERT: E 512 ASP cc_start: 0.7940 (t0) cc_final: 0.7098 (t0) REVERT: E 515 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8129 (mm-30) REVERT: E 525 GLU cc_start: 0.8075 (pt0) cc_final: 0.7815 (pp20) REVERT: E 541 GLN cc_start: 0.7940 (mt0) cc_final: 0.7269 (mm-40) REVERT: E 593 ASP cc_start: 0.7298 (t0) cc_final: 0.6885 (t0) REVERT: E 637 LYS cc_start: 0.8985 (mttp) cc_final: 0.8576 (mptt) REVERT: E 722 LYS cc_start: 0.8628 (tptt) cc_final: 0.8230 (tptp) REVERT: F 185 ASP cc_start: 0.8297 (p0) cc_final: 0.8094 (p0) REVERT: F 245 LYS cc_start: 0.9352 (mmmm) cc_final: 0.9145 (mmtm) REVERT: F 376 ASN cc_start: 0.9031 (m-40) cc_final: 0.8439 (t0) REVERT: F 389 GLN cc_start: 0.8648 (mp10) cc_final: 0.8374 (mp10) REVERT: F 438 GLN cc_start: 0.9384 (mt0) cc_final: 0.9054 (mt0) REVERT: F 444 LYS cc_start: 0.8967 (ptpp) cc_final: 0.8698 (pttm) REVERT: F 472 ASP cc_start: 0.8006 (t0) cc_final: 0.7181 (t0) REVERT: F 479 GLU cc_start: 0.8361 (mp0) cc_final: 0.8022 (mp0) REVERT: F 497 ASP cc_start: 0.8084 (p0) cc_final: 0.7825 (p0) REVERT: F 499 ASN cc_start: 0.8738 (m-40) cc_final: 0.7850 (m-40) REVERT: F 557 GLN cc_start: 0.8648 (mp10) cc_final: 0.7821 (mp10) REVERT: F 560 GLN cc_start: 0.9151 (tp-100) cc_final: 0.8727 (tp-100) REVERT: F 563 LYS cc_start: 0.9058 (ptpt) cc_final: 0.8763 (ptpt) REVERT: F 565 GLN cc_start: 0.8926 (mp10) cc_final: 0.8560 (mp10) REVERT: F 633 LYS cc_start: 0.9284 (pptt) cc_final: 0.8968 (pptt) REVERT: F 636 ARG cc_start: 0.8486 (ptp90) cc_final: 0.8106 (ptp90) REVERT: G 250 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7419 (tp30) REVERT: G 439 PHE cc_start: 0.9376 (t80) cc_final: 0.9126 (t80) REVERT: G 444 LYS cc_start: 0.9242 (ptpp) cc_final: 0.8973 (pttm) REVERT: G 462 TYR cc_start: 0.9047 (t80) cc_final: 0.8740 (t80) REVERT: G 465 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8221 (mm-30) REVERT: G 515 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8439 (mm-30) REVERT: G 529 ILE cc_start: 0.9227 (tp) cc_final: 0.8792 (tp) REVERT: G 549 GLU cc_start: 0.8848 (mp0) cc_final: 0.8594 (mp0) REVERT: G 551 ASP cc_start: 0.7845 (t0) cc_final: 0.7573 (t0) REVERT: G 560 GLN cc_start: 0.9271 (tp-100) cc_final: 0.8727 (mm-40) REVERT: G 565 GLN cc_start: 0.9132 (mt0) cc_final: 0.8761 (tt0) REVERT: G 589 ILE cc_start: 0.8657 (mt) cc_final: 0.8408 (mm) REVERT: G 593 ASP cc_start: 0.8922 (t70) cc_final: 0.8266 (t0) REVERT: G 595 ARG cc_start: 0.9146 (ttp80) cc_final: 0.8942 (ttp-110) REVERT: G 617 ARG cc_start: 0.9055 (ttp80) cc_final: 0.8828 (ttp80) REVERT: H 74 TYR cc_start: 0.7676 (t80) cc_final: 0.6916 (t80) REVERT: H 118 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.6134 (p90) REVERT: H 158 ASP cc_start: 0.8161 (t70) cc_final: 0.7774 (t70) REVERT: H 184 ASP cc_start: 0.8726 (m-30) cc_final: 0.7960 (p0) REVERT: H 187 ASP cc_start: 0.8369 (m-30) cc_final: 0.8101 (m-30) REVERT: H 201 PHE cc_start: 0.9079 (m-80) cc_final: 0.8695 (m-80) REVERT: H 215 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7829 (pt0) REVERT: H 236 TYR cc_start: 0.8245 (m-80) cc_final: 0.7976 (m-80) REVERT: H 393 GLN cc_start: 0.8547 (pm20) cc_final: 0.8029 (pm20) REVERT: H 398 LEU cc_start: 0.8303 (mm) cc_final: 0.7217 (pp) REVERT: H 415 ASP cc_start: 0.8229 (m-30) cc_final: 0.7938 (m-30) REVERT: H 434 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7271 (ttpp) REVERT: H 441 MET cc_start: 0.8138 (tpp) cc_final: 0.7851 (tpt) REVERT: H 472 LYS cc_start: 0.8930 (pttm) cc_final: 0.8666 (tttp) REVERT: H 510 ARG cc_start: 0.7295 (mmm-85) cc_final: 0.6754 (mmm-85) REVERT: H 548 LYS cc_start: 0.7500 (mmmt) cc_final: 0.7256 (tptp) REVERT: H 589 ASN cc_start: 0.7556 (m110) cc_final: 0.6904 (m110) REVERT: H 607 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.9003 (tmmt) REVERT: H 693 ASP cc_start: 0.8547 (t0) cc_final: 0.8159 (t0) REVERT: H 707 LEU cc_start: 0.8106 (tp) cc_final: 0.7661 (tp) REVERT: H 718 PHE cc_start: 0.7884 (t80) cc_final: 0.7622 (t80) REVERT: H 737 PHE cc_start: 0.8761 (m-80) cc_final: 0.8251 (m-10) REVERT: H 741 PHE cc_start: 0.8671 (t80) cc_final: 0.8358 (t80) REVERT: H 764 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8519 (pm20) REVERT: I 35 HIS cc_start: 0.7480 (m170) cc_final: 0.7030 (m170) REVERT: I 38 GLU cc_start: 0.7998 (mp0) cc_final: 0.7554 (mp0) REVERT: I 61 LYS cc_start: 0.9142 (mmpt) cc_final: 0.8730 (mttm) REVERT: I 72 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: I 184 ASP cc_start: 0.8198 (p0) cc_final: 0.7742 (p0) REVERT: I 190 PHE cc_start: 0.8497 (m-10) cc_final: 0.8277 (m-10) REVERT: I 215 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7877 (mt-10) REVERT: I 277 HIS cc_start: 0.8582 (t-90) cc_final: 0.7941 (t-90) REVERT: I 533 GLN cc_start: 0.7441 (pm20) cc_final: 0.7078 (pm20) REVERT: I 537 GLN cc_start: 0.9096 (tp40) cc_final: 0.8581 (mp10) REVERT: I 544 ARG cc_start: 0.7024 (tpt90) cc_final: 0.6586 (mmm160) REVERT: I 769 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8460 (mm-40) REVERT: J 74 TYR cc_start: 0.8982 (t80) cc_final: 0.8584 (t80) REVERT: J 108 TYR cc_start: 0.7484 (m-80) cc_final: 0.7086 (m-80) REVERT: J 153 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8703 (mtpt) REVERT: J 201 PHE cc_start: 0.8153 (m-80) cc_final: 0.7952 (m-80) REVERT: J 205 PHE cc_start: 0.8396 (t80) cc_final: 0.7820 (t80) REVERT: J 217 PHE cc_start: 0.8071 (t80) cc_final: 0.7627 (t80) REVERT: J 221 PHE cc_start: 0.9018 (t80) cc_final: 0.8509 (t80) REVERT: J 235 LEU cc_start: 0.8629 (tp) cc_final: 0.8302 (mt) REVERT: J 236 TYR cc_start: 0.8658 (m-80) cc_final: 0.8373 (m-80) REVERT: J 277 HIS cc_start: 0.7527 (t-90) cc_final: 0.7317 (t-90) REVERT: J 501 TRP cc_start: 0.5901 (OUTLIER) cc_final: 0.5635 (m-10) REVERT: J 582 LEU cc_start: 0.9091 (tp) cc_final: 0.8520 (tp) REVERT: J 586 ASN cc_start: 0.8049 (m-40) cc_final: 0.7663 (m-40) REVERT: J 590 ARG cc_start: 0.8176 (mmm160) cc_final: 0.7502 (mmm-85) REVERT: J 629 PHE cc_start: 0.8397 (m-10) cc_final: 0.7624 (m-10) outliers start: 134 outliers final: 92 residues processed: 1042 average time/residue: 0.2391 time to fit residues: 408.8025 Evaluate side-chains 984 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 885 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 488 THR Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 200 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 434 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 607 LYS Chi-restraints excluded: chain H residue 708 VAL Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 115 HIS Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 501 TRP Chi-restraints excluded: chain J residue 534 ILE Chi-restraints excluded: chain J residue 543 ILE Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 580 THR Chi-restraints excluded: chain J residue 769 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 351 optimal weight: 3.9990 chunk 494 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 227 optimal weight: 0.8980 chunk 228 optimal weight: 0.4980 chunk 556 optimal weight: 40.0000 chunk 558 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 ASN C 570 ASN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 541 GLN G 326 ASN ** G 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 GLN G 541 GLN ** G 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 424 HIS ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 ASN ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.185496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.106399 restraints weight = 73245.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110491 restraints weight = 37107.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113125 restraints weight = 25041.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114585 restraints weight = 19897.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115547 restraints weight = 17514.155| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 42994 Z= 0.230 Angle : 0.675 14.264 58617 Z= 0.350 Chirality : 0.047 0.206 6906 Planarity : 0.005 0.053 7726 Dihedral : 4.764 48.088 6116 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 4.11 % Allowed : 16.94 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.83 (0.11), residues: 5704 helix: -0.12 (0.13), residues: 1684 sheet: -0.06 (0.15), residues: 1075 loop : -0.94 (0.12), residues: 2945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 544 TYR 0.024 0.002 TYR D 436 PHE 0.049 0.002 PHE H 765 TRP 0.016 0.001 TRP H 570 HIS 0.009 0.001 HIS D 616 Details of bonding type rmsd covalent geometry : bond 0.00529 (42994) covalent geometry : angle 0.67503 (58617) hydrogen bonds : bond 0.04087 ( 1540) hydrogen bonds : angle 5.10162 ( 4500) *********************** REFINEMENT MACRO_CYCLE 4 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 1080 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 912 time to evaluate : 1.178 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 178 ARG cc_start: 0.7339 (ttp-110) cc_final: 0.6821 (ttp-110) REVERT: A 224 GLU cc_start: 0.8494 (tp30) cc_final: 0.7757 (mm-30) REVERT: A 265 ASP cc_start: 0.8199 (t0) cc_final: 0.7391 (p0) REVERT: A 344 ARG cc_start: 0.8431 (mtm-85) cc_final: 0.8157 (ptp90) REVERT: A 446 LYS cc_start: 0.8665 (mttt) cc_final: 0.8389 (mmmt) REVERT: A 447 GLN cc_start: 0.8917 (tt0) cc_final: 0.8077 (tm-30) REVERT: A 551 ASP cc_start: 0.7679 (m-30) cc_final: 0.7291 (m-30) REVERT: A 595 ARG cc_start: 0.8829 (mtm110) cc_final: 0.8505 (mtm110) REVERT: A 602 ASN cc_start: 0.8740 (m-40) cc_final: 0.8221 (m110) REVERT: A 633 LYS cc_start: 0.9600 (tmtt) cc_final: 0.9265 (tppt) REVERT: A 703 LYS cc_start: 0.8254 (mmtm) cc_final: 0.7939 (mmtm) REVERT: B 220 LYS cc_start: 0.9094 (mttt) cc_final: 0.8838 (mttm) REVERT: B 227 SER cc_start: 0.8912 (p) cc_final: 0.8637 (p) REVERT: B 265 ASP cc_start: 0.7802 (t0) cc_final: 0.7350 (t0) REVERT: B 267 GLU cc_start: 0.7421 (mp0) cc_final: 0.7189 (mp0) REVERT: B 326 ASN cc_start: 0.8759 (p0) cc_final: 0.8463 (p0) REVERT: B 403 GLN cc_start: 0.8290 (mp10) cc_final: 0.7968 (mp10) REVERT: B 434 MET cc_start: 0.8012 (tmm) cc_final: 0.7662 (tmm) REVERT: B 450 LEU cc_start: 0.9223 (mt) cc_final: 0.9018 (mt) REVERT: B 453 ASP cc_start: 0.8959 (p0) cc_final: 0.8645 (p0) REVERT: B 486 GLU cc_start: 0.8226 (tp30) cc_final: 0.7901 (tp30) REVERT: B 563 LYS cc_start: 0.9247 (mmmm) cc_final: 0.8904 (mmtm) REVERT: B 577 VAL cc_start: 0.8911 (m) cc_final: 0.8451 (p) REVERT: B 593 ASP cc_start: 0.8112 (t0) cc_final: 0.7776 (t0) REVERT: B 602 ASN cc_start: 0.8979 (m-40) cc_final: 0.8601 (m-40) REVERT: B 633 LYS cc_start: 0.9180 (pptt) cc_final: 0.8677 (pptt) REVERT: B 635 ILE cc_start: 0.9179 (mm) cc_final: 0.8866 (mm) REVERT: B 703 LYS cc_start: 0.8550 (mptt) cc_final: 0.8171 (mmtp) REVERT: B 722 LYS cc_start: 0.9382 (tppt) cc_final: 0.9132 (tppt) REVERT: C 434 MET cc_start: 0.8310 (ppp) cc_final: 0.7568 (ppp) REVERT: C 444 LYS cc_start: 0.9532 (tptp) cc_final: 0.9212 (tppt) REVERT: C 462 TYR cc_start: 0.9038 (t80) cc_final: 0.8773 (t80) REVERT: C 486 GLU cc_start: 0.8348 (tp30) cc_final: 0.8141 (tp30) REVERT: C 509 ASN cc_start: 0.8498 (t0) cc_final: 0.8275 (t0) REVERT: C 525 GLU cc_start: 0.8130 (pt0) cc_final: 0.7930 (pt0) REVERT: C 551 ASP cc_start: 0.8350 (t0) cc_final: 0.7900 (t0) REVERT: C 555 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7505 (t70) REVERT: C 579 ASP cc_start: 0.8661 (t0) cc_final: 0.8441 (t0) REVERT: C 587 MET cc_start: 0.9013 (mtp) cc_final: 0.8402 (mtt) REVERT: C 602 ASN cc_start: 0.8715 (m-40) cc_final: 0.8401 (m110) REVERT: C 616 HIS cc_start: 0.8674 (m90) cc_final: 0.8413 (m-70) REVERT: C 637 LYS cc_start: 0.9257 (mmmt) cc_final: 0.8918 (ttpt) REVERT: D 291 LYS cc_start: 0.8895 (mmtm) cc_final: 0.8472 (mmtt) REVERT: D 346 TRP cc_start: 0.8430 (m-10) cc_final: 0.8101 (m-10) REVERT: D 444 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8731 (mmtt) REVERT: D 472 ASP cc_start: 0.8091 (t0) cc_final: 0.7338 (t0) REVERT: D 486 GLU cc_start: 0.8602 (tp30) cc_final: 0.8262 (tp30) REVERT: D 497 ASP cc_start: 0.8319 (p0) cc_final: 0.7851 (p0) REVERT: D 499 ASN cc_start: 0.8441 (m-40) cc_final: 0.7751 (m-40) REVERT: D 509 ASN cc_start: 0.9231 (t0) cc_final: 0.8963 (t0) REVERT: D 551 ASP cc_start: 0.7808 (m-30) cc_final: 0.6804 (p0) REVERT: D 559 SER cc_start: 0.9091 (t) cc_final: 0.8863 (p) REVERT: D 602 ASN cc_start: 0.8951 (m-40) cc_final: 0.8559 (m110) REVERT: E 195 ASP cc_start: 0.8076 (t70) cc_final: 0.7766 (t0) REVERT: E 220 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8021 (mmtt) REVERT: E 359 ARG cc_start: 0.8046 (pmt170) cc_final: 0.7734 (ptt-90) REVERT: E 385 LEU cc_start: 0.8831 (mm) cc_final: 0.8474 (mm) REVERT: E 391 LEU cc_start: 0.9249 (mm) cc_final: 0.8746 (mm) REVERT: E 444 LYS cc_start: 0.9238 (tppt) cc_final: 0.8913 (tppt) REVERT: E 449 ARG cc_start: 0.9287 (mtm110) cc_final: 0.9069 (mtm110) REVERT: E 470 ARG cc_start: 0.7815 (tmm-80) cc_final: 0.7577 (tmm-80) REVERT: E 472 ASP cc_start: 0.8722 (t0) cc_final: 0.8366 (t0) REVERT: E 475 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8830 (p) REVERT: E 512 ASP cc_start: 0.8114 (t0) cc_final: 0.7052 (t0) REVERT: E 515 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8221 (mm-30) REVERT: E 541 GLN cc_start: 0.7985 (mt0) cc_final: 0.7292 (mm-40) REVERT: E 593 ASP cc_start: 0.7395 (t0) cc_final: 0.6911 (t0) REVERT: E 722 LYS cc_start: 0.8825 (tptt) cc_final: 0.8496 (tptp) REVERT: F 245 LYS cc_start: 0.9314 (mmmm) cc_final: 0.9113 (mmtm) REVERT: F 376 ASN cc_start: 0.9056 (m-40) cc_final: 0.8477 (t0) REVERT: F 389 GLN cc_start: 0.8709 (mp10) cc_final: 0.8412 (mp10) REVERT: F 438 GLN cc_start: 0.9389 (mt0) cc_final: 0.9129 (mt0) REVERT: F 444 LYS cc_start: 0.8952 (ptpp) cc_final: 0.8700 (ptpp) REVERT: F 479 GLU cc_start: 0.8420 (mp0) cc_final: 0.8025 (mp0) REVERT: F 497 ASP cc_start: 0.8024 (p0) cc_final: 0.7696 (p0) REVERT: F 499 ASN cc_start: 0.8716 (m-40) cc_final: 0.7851 (m-40) REVERT: F 521 MET cc_start: 0.8661 (mmm) cc_final: 0.8381 (tpp) REVERT: F 557 GLN cc_start: 0.8495 (mp10) cc_final: 0.7780 (mp10) REVERT: F 560 GLN cc_start: 0.9107 (tp-100) cc_final: 0.8723 (tp-100) REVERT: F 563 LYS cc_start: 0.9047 (ptpt) cc_final: 0.8729 (ptpt) REVERT: F 565 GLN cc_start: 0.8935 (mp10) cc_final: 0.8530 (mp10) REVERT: F 633 LYS cc_start: 0.9299 (pptt) cc_final: 0.8967 (pptt) REVERT: F 636 ARG cc_start: 0.8486 (ptp90) cc_final: 0.8074 (ptp90) REVERT: G 250 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7379 (tp30) REVERT: G 439 PHE cc_start: 0.9336 (t80) cc_final: 0.9098 (t80) REVERT: G 462 TYR cc_start: 0.9050 (t80) cc_final: 0.8744 (t80) REVERT: G 465 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8199 (mm-30) REVERT: G 515 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8387 (mm-30) REVERT: G 529 ILE cc_start: 0.9271 (tp) cc_final: 0.8845 (tp) REVERT: G 551 ASP cc_start: 0.7878 (t0) cc_final: 0.7547 (t0) REVERT: G 587 MET cc_start: 0.8116 (mtm) cc_final: 0.7563 (ptp) REVERT: G 589 ILE cc_start: 0.8747 (mt) cc_final: 0.8495 (mm) REVERT: G 593 ASP cc_start: 0.8866 (t70) cc_final: 0.8326 (t0) REVERT: G 595 ARG cc_start: 0.9142 (ttp80) cc_final: 0.8909 (ttp-110) REVERT: G 617 ARG cc_start: 0.9076 (ttp80) cc_final: 0.8823 (ttp80) REVERT: G 636 ARG cc_start: 0.8208 (mpp-170) cc_final: 0.7882 (ptp-170) REVERT: G 703 LYS cc_start: 0.8610 (ptpp) cc_final: 0.8288 (ptpp) REVERT: H 118 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6238 (p90) REVERT: H 158 ASP cc_start: 0.8131 (t70) cc_final: 0.7718 (t70) REVERT: H 184 ASP cc_start: 0.8749 (m-30) cc_final: 0.8035 (p0) REVERT: H 186 GLN cc_start: 0.7894 (pt0) cc_final: 0.7517 (mt0) REVERT: H 201 PHE cc_start: 0.9069 (m-80) cc_final: 0.8654 (m-80) REVERT: H 215 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7841 (pt0) REVERT: H 236 TYR cc_start: 0.8435 (m-80) cc_final: 0.8110 (m-80) REVERT: H 244 MET cc_start: 0.8787 (tpp) cc_final: 0.7838 (tpp) REVERT: H 384 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7738 (mm-40) REVERT: H 393 GLN cc_start: 0.8540 (pm20) cc_final: 0.8290 (pm20) REVERT: H 398 LEU cc_start: 0.8363 (mm) cc_final: 0.7315 (pp) REVERT: H 415 ASP cc_start: 0.8255 (m-30) cc_final: 0.7948 (m-30) REVERT: H 434 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7766 (tmmt) REVERT: H 472 LYS cc_start: 0.8943 (pttm) cc_final: 0.8722 (tttp) REVERT: H 548 LYS cc_start: 0.7561 (mmmt) cc_final: 0.7321 (tptp) REVERT: H 589 ASN cc_start: 0.7764 (m110) cc_final: 0.7139 (m110) REVERT: H 607 LYS cc_start: 0.9245 (pptt) cc_final: 0.8987 (tmmt) REVERT: H 617 LYS cc_start: 0.9224 (ttpt) cc_final: 0.8992 (mtmt) REVERT: H 718 PHE cc_start: 0.7792 (t80) cc_final: 0.7541 (t80) REVERT: H 737 PHE cc_start: 0.8744 (m-80) cc_final: 0.8085 (m-10) REVERT: I 38 GLU cc_start: 0.8022 (mp0) cc_final: 0.7474 (mp0) REVERT: I 61 LYS cc_start: 0.9210 (mmpt) cc_final: 0.8794 (mttp) REVERT: I 72 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8399 (mp0) REVERT: I 148 TYR cc_start: 0.8554 (m-80) cc_final: 0.8278 (m-80) REVERT: I 175 ASN cc_start: 0.8763 (m-40) cc_final: 0.8507 (m-40) REVERT: I 184 ASP cc_start: 0.8244 (p0) cc_final: 0.7778 (p0) REVERT: I 215 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7876 (mt-10) REVERT: I 277 HIS cc_start: 0.8543 (t-90) cc_final: 0.7977 (t-90) REVERT: I 537 GLN cc_start: 0.9094 (tp40) cc_final: 0.8892 (tm-30) REVERT: I 544 ARG cc_start: 0.6825 (tpt90) cc_final: 0.6548 (tpt90) REVERT: J 74 TYR cc_start: 0.8979 (t80) cc_final: 0.8595 (t80) REVERT: J 91 HIS cc_start: 0.0893 (t70) cc_final: 0.0584 (t70) REVERT: J 108 TYR cc_start: 0.7600 (m-80) cc_final: 0.7210 (m-80) REVERT: J 117 HIS cc_start: 0.7162 (t70) cc_final: 0.6950 (t-90) REVERT: J 153 LYS cc_start: 0.9022 (ttmm) cc_final: 0.8788 (mtmt) REVERT: J 201 PHE cc_start: 0.8188 (m-80) cc_final: 0.7980 (m-10) REVERT: J 205 PHE cc_start: 0.8432 (t80) cc_final: 0.7917 (t80) REVERT: J 217 PHE cc_start: 0.8032 (t80) cc_final: 0.7345 (t80) REVERT: J 221 PHE cc_start: 0.9031 (t80) cc_final: 0.8560 (t80) REVERT: J 235 LEU cc_start: 0.8711 (tp) cc_final: 0.8305 (mt) REVERT: J 236 TYR cc_start: 0.8727 (m-80) cc_final: 0.8402 (m-80) REVERT: J 277 HIS cc_start: 0.7420 (t-90) cc_final: 0.7215 (t-90) REVERT: J 546 ASP cc_start: 0.7255 (m-30) cc_final: 0.5515 (p0) REVERT: J 582 LEU cc_start: 0.9090 (tp) cc_final: 0.8436 (tp) REVERT: J 586 ASN cc_start: 0.8003 (m-40) cc_final: 0.7632 (m-40) REVERT: J 590 ARG cc_start: 0.8121 (mmm160) cc_final: 0.7613 (mmm-85) REVERT: J 629 PHE cc_start: 0.8464 (m-10) cc_final: 0.7617 (m-10) outliers start: 168 outliers final: 117 residues processed: 1002 average time/residue: 0.2362 time to fit residues: 387.6016 Evaluate side-chains 993 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 871 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 475 SER Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain E residue 555 ASP Chi-restraints excluded: chain E residue 723 LYS Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 438 GLN Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 488 THR Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 200 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 434 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 708 VAL Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 115 HIS Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 216 VAL Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 501 TRP Chi-restraints excluded: chain J residue 534 ILE Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 769 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 220 optimal weight: 0.0970 chunk 36 optimal weight: 0.6980 chunk 483 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 396 optimal weight: 0.5980 chunk 526 optimal weight: 20.0000 chunk 558 optimal weight: 40.0000 chunk 315 optimal weight: 0.9980 chunk 360 optimal weight: 9.9990 chunk 368 optimal weight: 4.9990 chunk 17 optimal weight: 0.0040 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 ASN ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 ASN G 246 ASN G 326 ASN G 483 GLN ** G 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 ASN ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 620 ASN J 197 HIS ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.188603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.110453 restraints weight = 73043.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114904 restraints weight = 35911.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117709 restraints weight = 23781.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119339 restraints weight = 18675.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120374 restraints weight = 16280.646| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 42994 Z= 0.116 Angle : 0.636 12.819 58617 Z= 0.325 Chirality : 0.046 0.209 6906 Planarity : 0.004 0.048 7726 Dihedral : 4.453 50.203 6116 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.25 % Rotamer: Outliers : 2.67 % Allowed : 19.69 % Favored : 77.64 % 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: -0.56 (0.11), residues: 5704 helix: 0.04 (0.13), residues: 1686 sheet: 0.16 (0.16), residues: 1063 loop : -0.75 (0.12), residues: 2955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 470 TYR 0.026 0.001 TYR J 243 PHE 0.059 0.001 PHE H 765 TRP 0.013 0.001 TRP I 570 HIS 0.005 0.001 HIS H 645 Details of bonding type rmsd covalent geometry : bond 0.00258 (42994) covalent geometry : angle 0.63609 (58617) hydrogen bonds : bond 0.03463 ( 1540) hydrogen bonds : angle 4.87049 ( 4500) *********************** REFINEMENT MACRO_CYCLE 5 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 1084 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 975 time to evaluate : 1.617 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 178 ARG cc_start: 0.7403 (ttp-110) cc_final: 0.6543 (ttp-170) REVERT: A 188 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7061 (tt0) REVERT: A 224 GLU cc_start: 0.8478 (tp30) cc_final: 0.7320 (mm-30) REVERT: A 238 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8367 (ttmt) REVERT: A 265 ASP cc_start: 0.8143 (t0) cc_final: 0.7571 (p0) REVERT: A 344 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.8244 (ptp90) REVERT: A 447 GLN cc_start: 0.8849 (tt0) cc_final: 0.8065 (tm-30) REVERT: A 487 THR cc_start: 0.9377 (t) cc_final: 0.9172 (t) REVERT: A 551 ASP cc_start: 0.7501 (m-30) cc_final: 0.7073 (m-30) REVERT: A 586 LYS cc_start: 0.9080 (mmmt) cc_final: 0.8819 (mmmt) REVERT: A 589 ILE cc_start: 0.8799 (mt) cc_final: 0.8573 (mm) REVERT: A 595 ARG cc_start: 0.8869 (mtm110) cc_final: 0.8524 (mtm110) REVERT: A 602 ASN cc_start: 0.8662 (m-40) cc_final: 0.8151 (m110) REVERT: A 633 LYS cc_start: 0.9564 (tmtt) cc_final: 0.9220 (tppt) REVERT: A 635 ILE cc_start: 0.9469 (tp) cc_final: 0.9208 (mm) REVERT: A 636 ARG cc_start: 0.8630 (ptt-90) cc_final: 0.7856 (ptt-90) REVERT: A 703 LYS cc_start: 0.8203 (mmtm) cc_final: 0.7870 (mmtm) REVERT: B 190 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7661 (mt-10) REVERT: B 220 LYS cc_start: 0.8998 (mttt) cc_final: 0.8704 (mttm) REVERT: B 227 SER cc_start: 0.8746 (p) cc_final: 0.8466 (p) REVERT: B 265 ASP cc_start: 0.7872 (t0) cc_final: 0.7311 (t0) REVERT: B 267 GLU cc_start: 0.7235 (mp0) cc_final: 0.7003 (mp0) REVERT: B 326 ASN cc_start: 0.8762 (p0) cc_final: 0.8501 (p0) REVERT: B 366 TYR cc_start: 0.9106 (m-80) cc_final: 0.8463 (m-80) REVERT: B 403 GLN cc_start: 0.8205 (mp10) cc_final: 0.7897 (mp10) REVERT: B 434 MET cc_start: 0.8018 (tmm) cc_final: 0.7638 (tmm) REVERT: B 439 PHE cc_start: 0.9322 (t80) cc_final: 0.9054 (t80) REVERT: B 453 ASP cc_start: 0.8979 (p0) cc_final: 0.8746 (p0) REVERT: B 486 GLU cc_start: 0.8182 (tp30) cc_final: 0.7867 (tp30) REVERT: B 515 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8334 (mm-30) REVERT: B 516 THR cc_start: 0.8832 (m) cc_final: 0.8631 (p) REVERT: B 563 LYS cc_start: 0.9277 (mmmm) cc_final: 0.8782 (mmtm) REVERT: B 577 VAL cc_start: 0.8966 (m) cc_final: 0.8495 (p) REVERT: B 593 ASP cc_start: 0.8003 (t0) cc_final: 0.7777 (t0) REVERT: B 602 ASN cc_start: 0.8922 (m-40) cc_final: 0.8627 (m110) REVERT: B 633 LYS cc_start: 0.9163 (pptt) cc_final: 0.8161 (tppt) REVERT: B 635 ILE cc_start: 0.9167 (mm) cc_final: 0.8851 (mm) REVERT: B 703 LYS cc_start: 0.8434 (mptt) cc_final: 0.8027 (mmtp) REVERT: B 722 LYS cc_start: 0.9376 (tppt) cc_final: 0.9131 (tppt) REVERT: C 444 LYS cc_start: 0.9535 (tptp) cc_final: 0.9221 (tppt) REVERT: C 462 TYR cc_start: 0.8987 (t80) cc_final: 0.8759 (t80) REVERT: C 486 GLU cc_start: 0.8264 (tp30) cc_final: 0.8063 (tp30) REVERT: C 496 LYS cc_start: 0.8336 (ttpp) cc_final: 0.7998 (tmmt) REVERT: C 509 ASN cc_start: 0.8344 (t0) cc_final: 0.8089 (t0) REVERT: C 521 MET cc_start: 0.7800 (tmm) cc_final: 0.7206 (tmm) REVERT: C 551 ASP cc_start: 0.8268 (t0) cc_final: 0.7754 (t0) REVERT: C 583 LEU cc_start: 0.9252 (mt) cc_final: 0.8831 (mp) REVERT: C 587 MET cc_start: 0.8900 (mtp) cc_final: 0.8289 (mtt) REVERT: C 616 HIS cc_start: 0.8632 (m90) cc_final: 0.8242 (m90) REVERT: C 629 LEU cc_start: 0.9174 (tp) cc_final: 0.8859 (mm) REVERT: C 637 LYS cc_start: 0.9255 (mmmt) cc_final: 0.8971 (ttpt) REVERT: D 291 LYS cc_start: 0.8801 (mmtm) cc_final: 0.8367 (mmtt) REVERT: D 346 TRP cc_start: 0.8227 (m-10) cc_final: 0.7935 (m-10) REVERT: D 378 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9066 (tt) REVERT: D 437 ASN cc_start: 0.8755 (m-40) cc_final: 0.8238 (p0) REVERT: D 444 LYS cc_start: 0.9118 (mmtt) cc_final: 0.8637 (mmtt) REVERT: D 472 ASP cc_start: 0.7605 (t0) cc_final: 0.6837 (t0) REVERT: D 483 GLN cc_start: 0.8079 (mp10) cc_final: 0.7277 (mt0) REVERT: D 551 ASP cc_start: 0.7693 (m-30) cc_final: 0.6876 (p0) REVERT: D 569 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8629 (mm) REVERT: D 602 ASN cc_start: 0.8929 (m-40) cc_final: 0.8533 (m110) REVERT: D 637 LYS cc_start: 0.8889 (mmtm) cc_final: 0.8641 (mtpt) REVERT: D 703 LYS cc_start: 0.9069 (mppt) cc_final: 0.8715 (mmtm) REVERT: E 178 ARG cc_start: 0.7884 (mtt180) cc_final: 0.7626 (mtm180) REVERT: E 200 ARG cc_start: 0.8170 (mtm-85) cc_final: 0.7749 (mtm110) REVERT: E 359 ARG cc_start: 0.8001 (pmt170) cc_final: 0.7758 (mtm180) REVERT: E 385 LEU cc_start: 0.8781 (mm) cc_final: 0.8073 (mm) REVERT: E 391 LEU cc_start: 0.9122 (mm) cc_final: 0.8892 (mm) REVERT: E 434 MET cc_start: 0.8034 (ppp) cc_final: 0.7482 (tmm) REVERT: E 444 LYS cc_start: 0.9038 (tppt) cc_final: 0.8835 (tppt) REVERT: E 470 ARG cc_start: 0.7738 (tmm-80) cc_final: 0.7475 (tmm-80) REVERT: E 472 ASP cc_start: 0.8567 (t0) cc_final: 0.8237 (t0) REVERT: E 481 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8683 (mp) REVERT: E 512 ASP cc_start: 0.7843 (t0) cc_final: 0.6690 (t0) REVERT: E 515 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8095 (mm-30) REVERT: E 541 GLN cc_start: 0.7981 (mt0) cc_final: 0.7246 (mm-40) REVERT: E 637 LYS cc_start: 0.9027 (mttp) cc_final: 0.8624 (mptt) REVERT: E 709 ASN cc_start: 0.8753 (t0) cc_final: 0.7781 (p0) REVERT: E 722 LYS cc_start: 0.8798 (tptt) cc_final: 0.8524 (tptp) REVERT: F 245 LYS cc_start: 0.9284 (mmmm) cc_final: 0.9072 (mmtm) REVERT: F 326 ASN cc_start: 0.8143 (m-40) cc_final: 0.6651 (t0) REVERT: F 376 ASN cc_start: 0.8992 (m-40) cc_final: 0.8430 (t0) REVERT: F 389 GLN cc_start: 0.8626 (mp10) cc_final: 0.8338 (mp10) REVERT: F 438 GLN cc_start: 0.9401 (mt0) cc_final: 0.9116 (mt0) REVERT: F 444 LYS cc_start: 0.8952 (ptpp) cc_final: 0.8666 (pttm) REVERT: F 449 ARG cc_start: 0.8640 (mtm110) cc_final: 0.7382 (ptp90) REVERT: F 472 ASP cc_start: 0.7760 (t0) cc_final: 0.7254 (t0) REVERT: F 479 GLU cc_start: 0.8467 (mp0) cc_final: 0.8175 (mp0) REVERT: F 497 ASP cc_start: 0.8038 (p0) cc_final: 0.7661 (p0) REVERT: F 499 ASN cc_start: 0.8570 (m110) cc_final: 0.7691 (m-40) REVERT: F 550 PHE cc_start: 0.9442 (m-80) cc_final: 0.9220 (m-80) REVERT: F 556 GLN cc_start: 0.7612 (pm20) cc_final: 0.7245 (pm20) REVERT: F 557 GLN cc_start: 0.8416 (mp10) cc_final: 0.7748 (mp10) REVERT: F 563 LYS cc_start: 0.9071 (ptpt) cc_final: 0.8730 (ptpp) REVERT: F 565 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8491 (mp10) REVERT: F 599 ASP cc_start: 0.8300 (t0) cc_final: 0.7931 (t0) REVERT: F 633 LYS cc_start: 0.9315 (pptt) cc_final: 0.8981 (pptt) REVERT: G 267 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7810 (pp20) REVERT: G 434 MET cc_start: 0.8387 (pmm) cc_final: 0.8121 (pmm) REVERT: G 446 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8050 (mmtt) REVERT: G 462 TYR cc_start: 0.8930 (t80) cc_final: 0.8689 (t80) REVERT: G 465 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8228 (mm-30) REVERT: G 515 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8384 (mm-30) REVERT: G 541 GLN cc_start: 0.8695 (tt0) cc_final: 0.8038 (pp30) REVERT: G 551 ASP cc_start: 0.7868 (t0) cc_final: 0.7537 (t0) REVERT: G 560 GLN cc_start: 0.9272 (tp-100) cc_final: 0.8749 (mm-40) REVERT: G 565 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8718 (tt0) REVERT: G 587 MET cc_start: 0.7719 (mtm) cc_final: 0.7407 (ptp) REVERT: G 589 ILE cc_start: 0.8594 (mt) cc_final: 0.8365 (mm) REVERT: G 593 ASP cc_start: 0.8742 (t70) cc_final: 0.7882 (t0) REVERT: G 595 ARG cc_start: 0.9132 (ttp80) cc_final: 0.8859 (ttp-110) REVERT: G 617 ARG cc_start: 0.9107 (ttp80) cc_final: 0.8861 (ttp80) REVERT: G 703 LYS cc_start: 0.8623 (ptpp) cc_final: 0.8374 (ptpp) REVERT: H 65 LYS cc_start: 0.9217 (mmmt) cc_final: 0.8832 (mmmt) REVERT: H 74 TYR cc_start: 0.7521 (t80) cc_final: 0.6610 (t80) REVERT: H 158 ASP cc_start: 0.8012 (t70) cc_final: 0.7671 (t70) REVERT: H 184 ASP cc_start: 0.8590 (m-30) cc_final: 0.8122 (p0) REVERT: H 201 PHE cc_start: 0.9099 (m-80) cc_final: 0.8614 (m-80) REVERT: H 244 MET cc_start: 0.8690 (tpp) cc_final: 0.7679 (tpp) REVERT: H 393 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8208 (pm20) REVERT: H 398 LEU cc_start: 0.8376 (mm) cc_final: 0.7387 (pp) REVERT: H 415 ASP cc_start: 0.8232 (m-30) cc_final: 0.7915 (m-30) REVERT: H 434 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7789 (tmmt) REVERT: H 472 LYS cc_start: 0.8930 (pttm) cc_final: 0.8588 (tptm) REVERT: H 510 ARG cc_start: 0.7062 (mmm-85) cc_final: 0.6650 (mmm-85) REVERT: H 548 LYS cc_start: 0.7576 (mmmt) cc_final: 0.7337 (tptp) REVERT: H 589 ASN cc_start: 0.7703 (m110) cc_final: 0.7045 (m110) REVERT: H 607 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8979 (tmmt) REVERT: H 617 LYS cc_start: 0.9333 (ttpt) cc_final: 0.9042 (mtmt) REVERT: H 718 PHE cc_start: 0.7756 (t80) cc_final: 0.7385 (t80) REVERT: H 736 PHE cc_start: 0.8002 (t80) cc_final: 0.7515 (t80) REVERT: H 737 PHE cc_start: 0.8714 (m-80) cc_final: 0.8220 (m-10) REVERT: H 741 PHE cc_start: 0.8585 (t80) cc_final: 0.7956 (t80) REVERT: I 38 GLU cc_start: 0.8095 (mp0) cc_final: 0.7684 (mp0) REVERT: I 61 LYS cc_start: 0.9199 (mmpt) cc_final: 0.8773 (mttm) REVERT: I 72 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8372 (mp0) REVERT: I 150 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8704 (mm-30) REVERT: I 175 ASN cc_start: 0.8726 (m-40) cc_final: 0.8449 (m-40) REVERT: I 184 ASP cc_start: 0.8057 (p0) cc_final: 0.7538 (p0) REVERT: I 215 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7980 (mt-10) REVERT: I 239 GLU cc_start: 0.7976 (pm20) cc_final: 0.7432 (pm20) REVERT: I 243 TYR cc_start: 0.9290 (t80) cc_final: 0.8844 (t80) REVERT: I 277 HIS cc_start: 0.8664 (t-90) cc_final: 0.8131 (t-90) REVERT: I 475 PHE cc_start: 0.7946 (t80) cc_final: 0.7654 (t80) REVERT: I 531 ASP cc_start: 0.7757 (t70) cc_final: 0.7185 (t0) REVERT: I 533 GLN cc_start: 0.7566 (pm20) cc_final: 0.7264 (pm20) REVERT: I 566 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7132 (mt) REVERT: I 600 TYR cc_start: 0.8999 (m-80) cc_final: 0.8275 (m-80) REVERT: J 74 TYR cc_start: 0.9006 (t80) cc_final: 0.8647 (t80) REVERT: J 108 TYR cc_start: 0.7658 (m-80) cc_final: 0.7253 (m-80) REVERT: J 117 HIS cc_start: 0.6952 (t70) cc_final: 0.6673 (t-90) REVERT: J 153 LYS cc_start: 0.9023 (ttmm) cc_final: 0.8763 (mtpt) REVERT: J 221 PHE cc_start: 0.9022 (t80) cc_final: 0.8522 (t80) REVERT: J 277 HIS cc_start: 0.7380 (t-90) cc_final: 0.7180 (t-90) REVERT: J 437 LEU cc_start: 0.8161 (mm) cc_final: 0.7902 (tp) REVERT: J 502 ARG cc_start: 0.7477 (ptp-110) cc_final: 0.6628 (ttm110) REVERT: J 546 ASP cc_start: 0.7081 (m-30) cc_final: 0.5052 (p0) REVERT: J 579 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.6548 (m-10) REVERT: J 582 LEU cc_start: 0.9091 (tp) cc_final: 0.8541 (tp) REVERT: J 586 ASN cc_start: 0.8124 (m-40) cc_final: 0.7755 (m-40) REVERT: J 629 PHE cc_start: 0.8531 (m-10) cc_final: 0.7654 (m-10) outliers start: 109 outliers final: 65 residues processed: 1033 average time/residue: 0.2456 time to fit residues: 417.6193 Evaluate side-chains 973 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 895 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 702 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 627 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 565 GLN Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 267 GLU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 565 GLN Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 434 LYS Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 607 LYS Chi-restraints excluded: chain H residue 708 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 566 ILE Chi-restraints excluded: chain I residue 597 GLU Chi-restraints excluded: chain J residue 115 HIS Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 501 TRP Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 769 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 148 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 177 optimal weight: 0.0670 chunk 73 optimal weight: 3.9990 chunk 419 optimal weight: 5.9990 chunk 530 optimal weight: 50.0000 chunk 487 optimal weight: 9.9990 chunk 515 optimal weight: 10.0000 chunk 210 optimal weight: 0.6980 chunk 238 optimal weight: 0.8980 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 ASN D 408 ASN ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 GLN ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 326 ASN G 485 GLN ** G 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.187923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.109621 restraints weight = 73256.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114002 restraints weight = 36311.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.116765 restraints weight = 24121.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118441 restraints weight = 18971.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119428 restraints weight = 16536.443| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 42994 Z= 0.128 Angle : 0.628 13.387 58617 Z= 0.323 Chirality : 0.046 0.256 6906 Planarity : 0.004 0.045 7726 Dihedral : 4.366 51.514 6116 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 3.26 % Allowed : 20.74 % Favored : 76.00 % 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: 5704 helix: 0.11 (0.13), residues: 1689 sheet: 0.29 (0.16), residues: 1063 loop : -0.71 (0.12), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 470 TYR 0.024 0.001 TYR F 462 PHE 0.059 0.001 PHE H 765 TRP 0.012 0.001 TRP H 570 HIS 0.004 0.001 HIS H 645 Details of bonding type rmsd covalent geometry : bond 0.00291 (42994) covalent geometry : angle 0.62821 (58617) hydrogen bonds : bond 0.03427 ( 1540) hydrogen bonds : angle 4.75521 ( 4500) *********************** REFINEMENT MACRO_CYCLE 6 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 1048 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 915 time to evaluate : 1.677 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 178 ARG cc_start: 0.7551 (ttp-110) cc_final: 0.7003 (ttp-170) REVERT: A 188 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7091 (tt0) REVERT: A 224 GLU cc_start: 0.8457 (tp30) cc_final: 0.7603 (mm-30) REVERT: A 238 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8385 (ttmt) REVERT: A 265 ASP cc_start: 0.8215 (t0) cc_final: 0.7596 (p0) REVERT: A 344 ARG cc_start: 0.8520 (mtm-85) cc_final: 0.8271 (ptp90) REVERT: A 447 GLN cc_start: 0.8800 (tt0) cc_final: 0.8032 (tm-30) REVERT: A 479 GLU cc_start: 0.7740 (tt0) cc_final: 0.7027 (tt0) REVERT: A 551 ASP cc_start: 0.7578 (m-30) cc_final: 0.7158 (m-30) REVERT: A 586 LYS cc_start: 0.9098 (mmmt) cc_final: 0.8839 (mmmt) REVERT: A 589 ILE cc_start: 0.8854 (mt) cc_final: 0.8601 (mm) REVERT: A 595 ARG cc_start: 0.8863 (mtm110) cc_final: 0.8518 (mtm110) REVERT: A 602 ASN cc_start: 0.8675 (m-40) cc_final: 0.8175 (m110) REVERT: A 633 LYS cc_start: 0.9572 (tmtt) cc_final: 0.9213 (tppt) REVERT: A 636 ARG cc_start: 0.8594 (ptt-90) cc_final: 0.7932 (ptt-90) REVERT: A 703 LYS cc_start: 0.8252 (mmtm) cc_final: 0.7896 (mmtm) REVERT: B 220 LYS cc_start: 0.9052 (mttt) cc_final: 0.8777 (mttm) REVERT: B 227 SER cc_start: 0.8818 (p) cc_final: 0.8527 (p) REVERT: B 265 ASP cc_start: 0.7935 (t0) cc_final: 0.7206 (t0) REVERT: B 326 ASN cc_start: 0.8785 (p0) cc_final: 0.8501 (p0) REVERT: B 366 TYR cc_start: 0.9099 (m-80) cc_final: 0.8866 (m-80) REVERT: B 403 GLN cc_start: 0.8317 (mp10) cc_final: 0.7978 (mp10) REVERT: B 453 ASP cc_start: 0.9018 (p0) cc_final: 0.8642 (p0) REVERT: B 468 ARG cc_start: 0.8397 (mmm-85) cc_final: 0.8137 (mmm-85) REVERT: B 486 GLU cc_start: 0.8226 (tp30) cc_final: 0.7811 (tm-30) REVERT: B 515 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8537 (mm-30) REVERT: B 563 LYS cc_start: 0.9275 (mmmm) cc_final: 0.8913 (ptpp) REVERT: B 577 VAL cc_start: 0.8970 (m) cc_final: 0.8523 (p) REVERT: B 594 LYS cc_start: 0.8478 (ptpt) cc_final: 0.8251 (ptpt) REVERT: B 602 ASN cc_start: 0.8889 (m-40) cc_final: 0.8565 (m110) REVERT: B 629 LEU cc_start: 0.8895 (tt) cc_final: 0.8001 (mm) REVERT: B 633 LYS cc_start: 0.9099 (pptt) cc_final: 0.7792 (tppt) REVERT: B 635 ILE cc_start: 0.9192 (mm) cc_final: 0.8886 (mm) REVERT: B 636 ARG cc_start: 0.8755 (ptt-90) cc_final: 0.7547 (ptt-90) REVERT: B 703 LYS cc_start: 0.8447 (mptt) cc_final: 0.8053 (mmtp) REVERT: B 722 LYS cc_start: 0.9396 (tppt) cc_final: 0.9160 (tppt) REVERT: C 389 GLN cc_start: 0.7900 (mp10) cc_final: 0.7631 (mp10) REVERT: C 444 LYS cc_start: 0.9543 (tptp) cc_final: 0.9229 (tppt) REVERT: C 454 GLN cc_start: 0.8474 (mp10) cc_final: 0.8165 (mp10) REVERT: C 462 TYR cc_start: 0.9022 (t80) cc_final: 0.8726 (t80) REVERT: C 486 GLU cc_start: 0.8292 (tp30) cc_final: 0.8062 (tp30) REVERT: C 499 ASN cc_start: 0.8725 (m-40) cc_final: 0.8350 (m-40) REVERT: C 509 ASN cc_start: 0.8360 (t0) cc_final: 0.8096 (t0) REVERT: C 521 MET cc_start: 0.7873 (tmm) cc_final: 0.7413 (tmm) REVERT: C 551 ASP cc_start: 0.8334 (t0) cc_final: 0.7842 (t0) REVERT: C 583 LEU cc_start: 0.9255 (mt) cc_final: 0.8893 (mp) REVERT: C 629 LEU cc_start: 0.9195 (tp) cc_final: 0.8886 (mm) REVERT: C 637 LYS cc_start: 0.9230 (mmmt) cc_final: 0.8892 (ttpt) REVERT: D 291 LYS cc_start: 0.8812 (mmtm) cc_final: 0.8549 (mmtm) REVERT: D 346 TRP cc_start: 0.8168 (m-10) cc_final: 0.7893 (m-10) REVERT: D 434 MET cc_start: 0.8128 (tpp) cc_final: 0.7662 (tpp) REVERT: D 437 ASN cc_start: 0.8747 (m-40) cc_final: 0.8251 (p0) REVERT: D 444 LYS cc_start: 0.9164 (mmtt) cc_final: 0.8778 (mmtt) REVERT: D 472 ASP cc_start: 0.7498 (t0) cc_final: 0.6822 (t0) REVERT: D 497 ASP cc_start: 0.8373 (p0) cc_final: 0.7765 (p0) REVERT: D 499 ASN cc_start: 0.8569 (m-40) cc_final: 0.8024 (m-40) REVERT: D 551 ASP cc_start: 0.7697 (m-30) cc_final: 0.6882 (p0) REVERT: D 569 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8617 (mm) REVERT: D 602 ASN cc_start: 0.8937 (m-40) cc_final: 0.8485 (m110) REVERT: D 614 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8234 (pm20) REVERT: D 703 LYS cc_start: 0.9056 (mppt) cc_final: 0.8691 (mmtm) REVERT: E 359 ARG cc_start: 0.7975 (pmt170) cc_final: 0.7460 (ptt-90) REVERT: E 385 LEU cc_start: 0.8770 (mm) cc_final: 0.8306 (mm) REVERT: E 387 LYS cc_start: 0.9308 (ptmm) cc_final: 0.9021 (ptmm) REVERT: E 391 LEU cc_start: 0.9190 (mm) cc_final: 0.8836 (mm) REVERT: E 449 ARG cc_start: 0.9156 (mtm110) cc_final: 0.8923 (mtm110) REVERT: E 470 ARG cc_start: 0.7728 (tmm-80) cc_final: 0.7435 (tmm-80) REVERT: E 472 ASP cc_start: 0.8609 (t0) cc_final: 0.8269 (t0) REVERT: E 481 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8751 (mp) REVERT: E 512 ASP cc_start: 0.8073 (t0) cc_final: 0.7007 (t0) REVERT: E 515 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8267 (mm-30) REVERT: E 541 GLN cc_start: 0.8055 (mt0) cc_final: 0.7394 (mm-40) REVERT: E 722 LYS cc_start: 0.8755 (tptt) cc_final: 0.8491 (tptp) REVERT: F 224 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8027 (mm-30) REVERT: F 326 ASN cc_start: 0.7747 (m-40) cc_final: 0.6902 (t0) REVERT: F 376 ASN cc_start: 0.9025 (m-40) cc_final: 0.8414 (t0) REVERT: F 389 GLN cc_start: 0.8678 (mp10) cc_final: 0.8412 (mp10) REVERT: F 438 GLN cc_start: 0.9350 (mt0) cc_final: 0.9107 (mt0) REVERT: F 449 ARG cc_start: 0.8570 (mtm110) cc_final: 0.7334 (ptp90) REVERT: F 472 ASP cc_start: 0.7757 (t0) cc_final: 0.7249 (t0) REVERT: F 479 GLU cc_start: 0.8522 (mp0) cc_final: 0.8196 (mp0) REVERT: F 485 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8226 (mm-40) REVERT: F 497 ASP cc_start: 0.7974 (p0) cc_final: 0.7524 (p0) REVERT: F 499 ASN cc_start: 0.8580 (m110) cc_final: 0.7669 (m-40) REVERT: F 565 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8497 (mp10) REVERT: F 599 ASP cc_start: 0.8275 (t0) cc_final: 0.7889 (t0) REVERT: F 633 LYS cc_start: 0.9315 (pptt) cc_final: 0.8964 (pptt) REVERT: G 267 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7811 (pp20) REVERT: G 441 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8934 (mt-10) REVERT: G 443 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8946 (mm-30) REVERT: G 462 TYR cc_start: 0.8939 (t80) cc_final: 0.8629 (t80) REVERT: G 465 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8151 (mm-30) REVERT: G 515 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8396 (mm-30) REVERT: G 549 GLU cc_start: 0.8806 (mp0) cc_final: 0.8470 (mp0) REVERT: G 551 ASP cc_start: 0.7833 (t0) cc_final: 0.7451 (t0) REVERT: G 568 GLU cc_start: 0.8481 (pm20) cc_final: 0.8278 (pm20) REVERT: G 569 LEU cc_start: 0.9219 (mt) cc_final: 0.8973 (mt) REVERT: G 587 MET cc_start: 0.7773 (mtm) cc_final: 0.7433 (ptp) REVERT: G 589 ILE cc_start: 0.8602 (mt) cc_final: 0.8363 (mm) REVERT: G 617 ARG cc_start: 0.9113 (ttp80) cc_final: 0.8854 (ttp80) REVERT: G 703 LYS cc_start: 0.8635 (ptpp) cc_final: 0.8344 (ptpp) REVERT: H 65 LYS cc_start: 0.9192 (mmmt) cc_final: 0.8887 (mmmt) REVERT: H 74 TYR cc_start: 0.7658 (t80) cc_final: 0.6706 (t80) REVERT: H 158 ASP cc_start: 0.8006 (t70) cc_final: 0.7674 (t70) REVERT: H 184 ASP cc_start: 0.8621 (m-30) cc_final: 0.8143 (p0) REVERT: H 201 PHE cc_start: 0.9068 (m-80) cc_final: 0.8584 (m-80) REVERT: H 215 GLU cc_start: 0.8144 (pt0) cc_final: 0.7875 (pp20) REVERT: H 235 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8500 (mm) REVERT: H 244 MET cc_start: 0.8711 (tpp) cc_final: 0.7732 (tpp) REVERT: H 281 TRP cc_start: 0.8204 (t-100) cc_final: 0.7946 (t-100) REVERT: H 393 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: H 398 LEU cc_start: 0.8296 (mm) cc_final: 0.7276 (pp) REVERT: H 415 ASP cc_start: 0.8237 (m-30) cc_final: 0.7914 (m-30) REVERT: H 434 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7925 (tmmt) REVERT: H 472 LYS cc_start: 0.8932 (pttm) cc_final: 0.8577 (tptm) REVERT: H 510 ARG cc_start: 0.6942 (mmm-85) cc_final: 0.6429 (mmm-85) REVERT: H 548 LYS cc_start: 0.7576 (mmmt) cc_final: 0.7338 (tptp) REVERT: H 585 PHE cc_start: 0.7302 (p90) cc_final: 0.7003 (p90) REVERT: H 589 ASN cc_start: 0.7682 (m110) cc_final: 0.7026 (m110) REVERT: H 607 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8984 (tmmt) REVERT: H 628 ARG cc_start: 0.7421 (ptp90) cc_final: 0.7137 (ptp90) REVERT: H 718 PHE cc_start: 0.7682 (t80) cc_final: 0.7306 (t80) REVERT: H 736 PHE cc_start: 0.7957 (t80) cc_final: 0.7509 (t80) REVERT: H 737 PHE cc_start: 0.8860 (m-80) cc_final: 0.8200 (m-10) REVERT: I 38 GLU cc_start: 0.8125 (mp0) cc_final: 0.7775 (mp0) REVERT: I 61 LYS cc_start: 0.9209 (mmpt) cc_final: 0.8776 (mttm) REVERT: I 72 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8353 (mp0) REVERT: I 150 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8739 (mm-30) REVERT: I 175 ASN cc_start: 0.8724 (m-40) cc_final: 0.8310 (m-40) REVERT: I 184 ASP cc_start: 0.8127 (p0) cc_final: 0.7605 (p0) REVERT: I 215 GLU cc_start: 0.8220 (mt-10) cc_final: 0.8008 (mt-10) REVERT: I 243 TYR cc_start: 0.9318 (t80) cc_final: 0.8985 (t80) REVERT: I 246 LYS cc_start: 0.9236 (tptp) cc_final: 0.8997 (mmtm) REVERT: I 277 HIS cc_start: 0.8536 (t-90) cc_final: 0.7952 (t-90) REVERT: I 475 PHE cc_start: 0.7944 (t80) cc_final: 0.7634 (t80) REVERT: I 531 ASP cc_start: 0.7616 (t70) cc_final: 0.6574 (p0) REVERT: I 533 GLN cc_start: 0.7434 (pm20) cc_final: 0.6822 (pm20) REVERT: I 566 ILE cc_start: 0.7459 (OUTLIER) cc_final: 0.7214 (mt) REVERT: I 600 TYR cc_start: 0.9035 (m-80) cc_final: 0.8417 (m-80) REVERT: J 91 HIS cc_start: 0.0712 (t70) cc_final: 0.0481 (t70) REVERT: J 108 TYR cc_start: 0.7600 (m-80) cc_final: 0.7238 (m-80) REVERT: J 110 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8295 (mmtm) REVERT: J 117 HIS cc_start: 0.6897 (OUTLIER) cc_final: 0.6591 (t-90) REVERT: J 153 LYS cc_start: 0.9087 (ttmm) cc_final: 0.8803 (mtpt) REVERT: J 221 PHE cc_start: 0.8991 (t80) cc_final: 0.8582 (t80) REVERT: J 277 HIS cc_start: 0.7401 (t-90) cc_final: 0.7196 (t-90) REVERT: J 437 LEU cc_start: 0.8167 (mm) cc_final: 0.7948 (tp) REVERT: J 544 ARG cc_start: 0.6353 (tpp-160) cc_final: 0.5927 (tpt170) REVERT: J 546 ASP cc_start: 0.6962 (m-30) cc_final: 0.5289 (p0) REVERT: J 579 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6378 (m-10) REVERT: J 582 LEU cc_start: 0.9067 (tp) cc_final: 0.8399 (tp) REVERT: J 586 ASN cc_start: 0.8161 (m-40) cc_final: 0.7799 (m-40) REVERT: J 629 PHE cc_start: 0.8590 (m-10) cc_final: 0.7825 (m-80) outliers start: 133 outliers final: 90 residues processed: 988 average time/residue: 0.2439 time to fit residues: 396.5660 Evaluate side-chains 978 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 874 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 702 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 438 GLN Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 627 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 565 GLN Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 638 ILE Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 267 GLU Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 438 GLN Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 376 LEU Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 434 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 607 LYS Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 566 ILE Chi-restraints excluded: chain I residue 586 ASN Chi-restraints excluded: chain I residue 597 GLU Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 170 PHE Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 501 TRP Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 664 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 492 optimal weight: 8.9990 chunk 263 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 341 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 115 optimal weight: 0.4980 chunk 403 optimal weight: 4.9990 chunk 435 optimal weight: 0.5980 chunk 512 optimal weight: 1.9990 chunk 414 optimal weight: 5.9990 chunk 537 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 326 ASN G 483 GLN ** G 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.187460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109301 restraints weight = 72930.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113616 restraints weight = 36271.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.116305 restraints weight = 24147.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.118028 restraints weight = 19012.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.119024 restraints weight = 16526.517| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 42994 Z= 0.140 Angle : 0.642 12.892 58617 Z= 0.327 Chirality : 0.046 0.283 6906 Planarity : 0.004 0.053 7726 Dihedral : 4.301 30.610 6113 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.17 % Favored : 95.79 % Rotamer: Outliers : 3.57 % Allowed : 21.16 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.41 (0.11), residues: 5704 helix: 0.17 (0.13), residues: 1681 sheet: 0.31 (0.16), residues: 1076 loop : -0.69 (0.12), residues: 2947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 470 TYR 0.023 0.001 TYR F 462 PHE 0.018 0.001 PHE I 471 TRP 0.012 0.001 TRP H 570 HIS 0.005 0.001 HIS H 645 Details of bonding type rmsd covalent geometry : bond 0.00324 (42994) covalent geometry : angle 0.64176 (58617) hydrogen bonds : bond 0.03449 ( 1540) hydrogen bonds : angle 4.70309 ( 4500) *********************** REFINEMENT MACRO_CYCLE 7 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 1037 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 891 time to evaluate : 1.334 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 178 ARG cc_start: 0.7561 (ttp-110) cc_final: 0.7085 (ttp-110) REVERT: A 188 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7099 (tt0) REVERT: A 224 GLU cc_start: 0.8490 (tp30) cc_final: 0.7920 (mm-30) REVERT: A 265 ASP cc_start: 0.8217 (t0) cc_final: 0.7534 (p0) REVERT: A 344 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8226 (ptp90) REVERT: A 411 TYR cc_start: 0.8303 (t80) cc_final: 0.8092 (t80) REVERT: A 447 GLN cc_start: 0.8776 (tt0) cc_final: 0.7971 (tm-30) REVERT: A 479 GLU cc_start: 0.7714 (tt0) cc_final: 0.7483 (tt0) REVERT: A 551 ASP cc_start: 0.7638 (m-30) cc_final: 0.7235 (m-30) REVERT: A 563 LYS cc_start: 0.8969 (tmmt) cc_final: 0.8661 (ptmt) REVERT: A 586 LYS cc_start: 0.9016 (mmmt) cc_final: 0.8742 (mmmt) REVERT: A 589 ILE cc_start: 0.8883 (mt) cc_final: 0.8625 (mm) REVERT: A 595 ARG cc_start: 0.8863 (mtm110) cc_final: 0.8518 (mtm110) REVERT: A 602 ASN cc_start: 0.8711 (m-40) cc_final: 0.8210 (m110) REVERT: A 633 LYS cc_start: 0.9579 (tmtt) cc_final: 0.9201 (tppt) REVERT: A 636 ARG cc_start: 0.8561 (ptt-90) cc_final: 0.7878 (ptt-90) REVERT: A 703 LYS cc_start: 0.8292 (mmtm) cc_final: 0.7999 (mmtm) REVERT: B 220 LYS cc_start: 0.9064 (mttt) cc_final: 0.8789 (mttm) REVERT: B 227 SER cc_start: 0.8834 (p) cc_final: 0.8540 (p) REVERT: B 265 ASP cc_start: 0.7926 (t0) cc_final: 0.7434 (t0) REVERT: B 267 GLU cc_start: 0.7533 (mp0) cc_final: 0.7123 (mp0) REVERT: B 326 ASN cc_start: 0.8759 (p0) cc_final: 0.8507 (p0) REVERT: B 366 TYR cc_start: 0.9172 (m-80) cc_final: 0.8900 (m-80) REVERT: B 403 GLN cc_start: 0.8300 (mp10) cc_final: 0.7993 (mp10) REVERT: B 453 ASP cc_start: 0.8987 (p0) cc_final: 0.8765 (p0) REVERT: B 486 GLU cc_start: 0.8193 (tp30) cc_final: 0.7864 (tm-30) REVERT: B 496 LYS cc_start: 0.9224 (tppt) cc_final: 0.8981 (tppt) REVERT: B 515 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8375 (mm-30) REVERT: B 525 GLU cc_start: 0.8230 (pt0) cc_final: 0.7859 (pt0) REVERT: B 563 LYS cc_start: 0.9275 (mmmm) cc_final: 0.8922 (ptpp) REVERT: B 594 LYS cc_start: 0.8528 (ptpt) cc_final: 0.8249 (ptpt) REVERT: B 602 ASN cc_start: 0.8884 (m-40) cc_final: 0.8548 (m110) REVERT: B 629 LEU cc_start: 0.8891 (tt) cc_final: 0.8095 (mm) REVERT: B 635 ILE cc_start: 0.9186 (mm) cc_final: 0.8900 (mm) REVERT: B 636 ARG cc_start: 0.8738 (ptt-90) cc_final: 0.8301 (ptp90) REVERT: B 703 LYS cc_start: 0.8462 (mptt) cc_final: 0.8020 (mmtp) REVERT: B 722 LYS cc_start: 0.9410 (tppt) cc_final: 0.9198 (tppt) REVERT: C 326 ASN cc_start: 0.8700 (p0) cc_final: 0.8358 (p0) REVERT: C 444 LYS cc_start: 0.9545 (tptp) cc_final: 0.9233 (tppt) REVERT: C 454 GLN cc_start: 0.8477 (mp10) cc_final: 0.8181 (mp10) REVERT: C 462 TYR cc_start: 0.9028 (t80) cc_final: 0.8721 (t80) REVERT: C 486 GLU cc_start: 0.8295 (tp30) cc_final: 0.8057 (tp30) REVERT: C 499 ASN cc_start: 0.8847 (m-40) cc_final: 0.8427 (m-40) REVERT: C 509 ASN cc_start: 0.8354 (t0) cc_final: 0.8068 (t0) REVERT: C 521 MET cc_start: 0.7898 (tmm) cc_final: 0.7683 (tmm) REVERT: C 551 ASP cc_start: 0.8315 (t0) cc_final: 0.7857 (t0) REVERT: C 587 MET cc_start: 0.8901 (mtp) cc_final: 0.8214 (mtt) REVERT: C 629 LEU cc_start: 0.9228 (tp) cc_final: 0.8921 (mm) REVERT: D 291 LYS cc_start: 0.8797 (mmtm) cc_final: 0.8424 (mmtm) REVERT: D 346 TRP cc_start: 0.8137 (m-10) cc_final: 0.7852 (m-10) REVERT: D 434 MET cc_start: 0.8228 (tpp) cc_final: 0.7752 (tpp) REVERT: D 437 ASN cc_start: 0.8744 (m-40) cc_final: 0.8254 (p0) REVERT: D 468 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.7692 (tmm-80) REVERT: D 472 ASP cc_start: 0.7526 (t0) cc_final: 0.6807 (t0) REVERT: D 497 ASP cc_start: 0.8338 (p0) cc_final: 0.7801 (p0) REVERT: D 499 ASN cc_start: 0.8490 (m-40) cc_final: 0.7803 (m-40) REVERT: D 551 ASP cc_start: 0.7680 (m-30) cc_final: 0.6806 (p0) REVERT: D 569 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8609 (mm) REVERT: D 602 ASN cc_start: 0.8938 (m-40) cc_final: 0.8475 (m110) REVERT: D 614 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: D 703 LYS cc_start: 0.9030 (mppt) cc_final: 0.8659 (mmtm) REVERT: E 220 LYS cc_start: 0.8272 (mmtt) cc_final: 0.7935 (mmtt) REVERT: E 359 ARG cc_start: 0.7892 (pmt170) cc_final: 0.7360 (ptt-90) REVERT: E 387 LYS cc_start: 0.9400 (ptmm) cc_final: 0.9079 (ptmm) REVERT: E 449 ARG cc_start: 0.9191 (mtm110) cc_final: 0.8873 (mtm110) REVERT: E 470 ARG cc_start: 0.7741 (tmm-80) cc_final: 0.7427 (tmm-80) REVERT: E 472 ASP cc_start: 0.8637 (t0) cc_final: 0.8323 (t0) REVERT: E 481 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8756 (mp) REVERT: E 512 ASP cc_start: 0.8157 (t0) cc_final: 0.7109 (t0) REVERT: E 515 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8385 (mm-30) REVERT: E 541 GLN cc_start: 0.8079 (mt0) cc_final: 0.7373 (mm-40) REVERT: E 637 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8756 (mmtm) REVERT: E 709 ASN cc_start: 0.8758 (t0) cc_final: 0.7777 (p0) REVERT: E 722 LYS cc_start: 0.8749 (tptt) cc_final: 0.8510 (tptp) REVERT: F 224 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7581 (tm-30) REVERT: F 326 ASN cc_start: 0.7652 (m-40) cc_final: 0.6438 (t0) REVERT: F 376 ASN cc_start: 0.9008 (m-40) cc_final: 0.8377 (t0) REVERT: F 389 GLN cc_start: 0.8699 (mp10) cc_final: 0.8446 (mp10) REVERT: F 438 GLN cc_start: 0.9343 (mt0) cc_final: 0.9101 (mt0) REVERT: F 449 ARG cc_start: 0.8576 (mtm110) cc_final: 0.7345 (ptp90) REVERT: F 479 GLU cc_start: 0.8498 (mp0) cc_final: 0.8191 (mp0) REVERT: F 485 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8296 (mm-40) REVERT: F 497 ASP cc_start: 0.7982 (p0) cc_final: 0.7511 (p0) REVERT: F 499 ASN cc_start: 0.8538 (m110) cc_final: 0.7592 (m-40) REVERT: F 557 GLN cc_start: 0.8253 (mp10) cc_final: 0.7885 (mm110) REVERT: F 565 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8498 (mp10) REVERT: F 599 ASP cc_start: 0.8254 (t0) cc_final: 0.7903 (t0) REVERT: F 633 LYS cc_start: 0.9288 (pptt) cc_final: 0.8964 (pptt) REVERT: G 329 SER cc_start: 0.9079 (p) cc_final: 0.8711 (t) REVERT: G 446 LYS cc_start: 0.8450 (mmtt) cc_final: 0.8236 (mmtt) REVERT: G 462 TYR cc_start: 0.8934 (t80) cc_final: 0.8651 (t80) REVERT: G 465 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8180 (mm-30) REVERT: G 541 GLN cc_start: 0.8617 (tt0) cc_final: 0.8184 (tt0) REVERT: G 551 ASP cc_start: 0.7810 (t0) cc_final: 0.7466 (t0) REVERT: G 560 GLN cc_start: 0.9261 (tp-100) cc_final: 0.8756 (mm-40) REVERT: G 565 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8732 (tt0) REVERT: G 587 MET cc_start: 0.7799 (mtm) cc_final: 0.7463 (ptp) REVERT: G 589 ILE cc_start: 0.8638 (mt) cc_final: 0.8401 (mm) REVERT: G 617 ARG cc_start: 0.9108 (ttp80) cc_final: 0.8684 (ttp80) REVERT: G 703 LYS cc_start: 0.8641 (ptpp) cc_final: 0.8399 (ptpp) REVERT: H 65 LYS cc_start: 0.9182 (mmmt) cc_final: 0.8881 (mmmt) REVERT: H 74 TYR cc_start: 0.7656 (t80) cc_final: 0.6682 (t80) REVERT: H 118 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.6146 (p90) REVERT: H 158 ASP cc_start: 0.8007 (t70) cc_final: 0.7701 (t70) REVERT: H 170 PHE cc_start: 0.8515 (t80) cc_final: 0.8302 (t80) REVERT: H 184 ASP cc_start: 0.8683 (m-30) cc_final: 0.8163 (p0) REVERT: H 186 GLN cc_start: 0.7661 (pt0) cc_final: 0.7324 (mt0) REVERT: H 201 PHE cc_start: 0.9075 (m-80) cc_final: 0.8594 (m-80) REVERT: H 215 GLU cc_start: 0.8106 (pt0) cc_final: 0.7857 (pp20) REVERT: H 244 MET cc_start: 0.8694 (tpp) cc_final: 0.7690 (tpp) REVERT: H 281 TRP cc_start: 0.8192 (t-100) cc_final: 0.7948 (t-100) REVERT: H 393 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8218 (pm20) REVERT: H 398 LEU cc_start: 0.8263 (mm) cc_final: 0.7234 (pp) REVERT: H 415 ASP cc_start: 0.8211 (m-30) cc_final: 0.7867 (m-30) REVERT: H 434 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8126 (tmmt) REVERT: H 436 TYR cc_start: 0.6822 (m-80) cc_final: 0.6556 (m-80) REVERT: H 472 LYS cc_start: 0.8919 (pttm) cc_final: 0.8687 (tttp) REVERT: H 510 ARG cc_start: 0.6912 (mmm-85) cc_final: 0.6403 (mmm-85) REVERT: H 548 LYS cc_start: 0.7632 (mmmt) cc_final: 0.7401 (tptp) REVERT: H 585 PHE cc_start: 0.7376 (p90) cc_final: 0.7106 (p90) REVERT: H 589 ASN cc_start: 0.7684 (m110) cc_final: 0.7011 (m110) REVERT: H 607 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8981 (tmmt) REVERT: H 628 ARG cc_start: 0.7407 (ptp90) cc_final: 0.7158 (ptp90) REVERT: H 718 PHE cc_start: 0.7808 (t80) cc_final: 0.7425 (t80) REVERT: H 736 PHE cc_start: 0.7965 (t80) cc_final: 0.7495 (t80) REVERT: H 737 PHE cc_start: 0.8862 (m-80) cc_final: 0.8257 (m-10) REVERT: I 38 GLU cc_start: 0.8176 (mp0) cc_final: 0.7813 (mp0) REVERT: I 61 LYS cc_start: 0.9251 (mmpt) cc_final: 0.8827 (mttm) REVERT: I 72 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8360 (mp0) REVERT: I 150 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8776 (mm-30) REVERT: I 175 ASN cc_start: 0.8725 (m-40) cc_final: 0.8329 (m-40) REVERT: I 184 ASP cc_start: 0.8112 (p0) cc_final: 0.7597 (p0) REVERT: I 215 GLU cc_start: 0.8211 (mt-10) cc_final: 0.8001 (mt-10) REVERT: I 245 ASP cc_start: 0.8364 (t0) cc_final: 0.8014 (t0) REVERT: I 246 LYS cc_start: 0.9242 (tptp) cc_final: 0.8955 (mmtm) REVERT: I 277 HIS cc_start: 0.8476 (t-90) cc_final: 0.8016 (t-90) REVERT: I 468 PHE cc_start: 0.9277 (t80) cc_final: 0.8742 (t80) REVERT: I 475 PHE cc_start: 0.7880 (t80) cc_final: 0.7564 (t80) REVERT: I 537 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8064 (pm20) REVERT: I 544 ARG cc_start: 0.6532 (tpp-160) cc_final: 0.6239 (tpt170) REVERT: I 566 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.7111 (mt) REVERT: I 600 TYR cc_start: 0.9040 (m-80) cc_final: 0.8436 (m-80) REVERT: J 91 HIS cc_start: 0.0629 (t70) cc_final: 0.0410 (t70) REVERT: J 108 TYR cc_start: 0.7605 (m-80) cc_final: 0.7236 (m-80) REVERT: J 117 HIS cc_start: 0.6886 (OUTLIER) cc_final: 0.6597 (t-90) REVERT: J 153 LYS cc_start: 0.9132 (ttmm) cc_final: 0.8851 (mtmt) REVERT: J 221 PHE cc_start: 0.9007 (t80) cc_final: 0.8584 (t80) REVERT: J 277 HIS cc_start: 0.7450 (t-90) cc_final: 0.7245 (t-90) REVERT: J 546 ASP cc_start: 0.6664 (m-30) cc_final: 0.6313 (m-30) REVERT: J 579 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.6465 (m-10) REVERT: J 582 LEU cc_start: 0.9041 (tp) cc_final: 0.8285 (tp) REVERT: J 586 ASN cc_start: 0.8171 (m-40) cc_final: 0.7788 (m-40) REVERT: J 629 PHE cc_start: 0.8591 (m-10) cc_final: 0.7796 (m-80) REVERT: J 664 ARG cc_start: 0.6101 (OUTLIER) cc_final: 0.5412 (ttp80) outliers start: 146 outliers final: 102 residues processed: 975 average time/residue: 0.2413 time to fit residues: 385.5328 Evaluate side-chains 986 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 870 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 702 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 627 LEU Chi-restraints excluded: chain E residue 723 LYS Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 565 GLN Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 701 VAL Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 438 GLN Chi-restraints excluded: chain G residue 565 GLN Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 376 LEU Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 434 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 583 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 607 LYS Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 566 ILE Chi-restraints excluded: chain I residue 597 GLU Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 170 PHE Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 501 TRP Chi-restraints excluded: chain J residue 543 ILE Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 664 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 546 optimal weight: 10.0000 chunk 278 optimal weight: 1.9990 chunk 331 optimal weight: 0.2980 chunk 193 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 541 optimal weight: 30.0000 chunk 202 optimal weight: 20.0000 chunk 6 optimal weight: 0.5980 chunk 387 optimal weight: 0.0170 chunk 362 optimal weight: 2.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 HIS A 630 ASN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 GLN E 601 ASN G 326 ASN G 541 GLN ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 HIS ** J 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.189117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.110905 restraints weight = 73085.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.115329 restraints weight = 36128.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.118134 restraints weight = 23955.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119797 restraints weight = 18795.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120841 restraints weight = 16354.145| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 42994 Z= 0.116 Angle : 0.646 13.441 58617 Z= 0.326 Chirality : 0.046 0.295 6906 Planarity : 0.004 0.042 7726 Dihedral : 4.183 27.425 6113 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.82 % Favored : 96.14 % Rotamer: Outliers : 2.82 % Allowed : 22.43 % Favored : 74.76 % 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: -0.27 (0.11), residues: 5704 helix: 0.28 (0.13), residues: 1673 sheet: 0.43 (0.16), residues: 1088 loop : -0.63 (0.12), residues: 2943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 470 TYR 0.032 0.001 TYR I 82 PHE 0.019 0.001 PHE J 765 TRP 0.010 0.001 TRP H 570 HIS 0.005 0.001 HIS H 645 Details of bonding type rmsd covalent geometry : bond 0.00265 (42994) covalent geometry : angle 0.64556 (58617) hydrogen bonds : bond 0.03251 ( 1540) hydrogen bonds : angle 4.62624 ( 4500) *********************** REFINEMENT MACRO_CYCLE 8 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 1033 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 918 time to evaluate : 1.654 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 178 ARG cc_start: 0.7557 (ttp-110) cc_final: 0.6777 (ttp-170) REVERT: A 188 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6751 (tt0) REVERT: A 224 GLU cc_start: 0.8464 (tp30) cc_final: 0.7214 (mm-30) REVERT: A 235 ASP cc_start: 0.8377 (m-30) cc_final: 0.8042 (m-30) REVERT: A 265 ASP cc_start: 0.8221 (t0) cc_final: 0.7572 (p0) REVERT: A 344 ARG cc_start: 0.8491 (mtm-85) cc_final: 0.8246 (ptp90) REVERT: A 447 GLN cc_start: 0.8761 (tt0) cc_final: 0.7969 (tm-30) REVERT: A 551 ASP cc_start: 0.7647 (m-30) cc_final: 0.7232 (m-30) REVERT: A 563 LYS cc_start: 0.8968 (tmmt) cc_final: 0.8658 (ptmt) REVERT: A 586 LYS cc_start: 0.9094 (mmmt) cc_final: 0.8797 (mmmt) REVERT: A 589 ILE cc_start: 0.8825 (mt) cc_final: 0.8558 (mm) REVERT: A 595 ARG cc_start: 0.8868 (mtm110) cc_final: 0.8525 (mtm110) REVERT: A 600 ARG cc_start: 0.8156 (mmp80) cc_final: 0.7764 (mmp80) REVERT: A 602 ASN cc_start: 0.8660 (m-40) cc_final: 0.7827 (m110) REVERT: A 633 LYS cc_start: 0.9575 (tmtt) cc_final: 0.9177 (tppt) REVERT: A 636 ARG cc_start: 0.8536 (ptt-90) cc_final: 0.7838 (ptt-90) REVERT: A 703 LYS cc_start: 0.8287 (mmtm) cc_final: 0.7948 (mmtm) REVERT: B 220 LYS cc_start: 0.9031 (mttt) cc_final: 0.8763 (mttm) REVERT: B 227 SER cc_start: 0.8782 (p) cc_final: 0.8490 (p) REVERT: B 265 ASP cc_start: 0.7910 (t0) cc_final: 0.7377 (t0) REVERT: B 267 GLU cc_start: 0.7612 (mp0) cc_final: 0.7135 (mp0) REVERT: B 326 ASN cc_start: 0.8796 (p0) cc_final: 0.8528 (p0) REVERT: B 366 TYR cc_start: 0.9119 (m-80) cc_final: 0.8861 (m-80) REVERT: B 381 THR cc_start: 0.9157 (t) cc_final: 0.8911 (t) REVERT: B 403 GLN cc_start: 0.8317 (mp10) cc_final: 0.8018 (mp10) REVERT: B 434 MET cc_start: 0.7888 (tmm) cc_final: 0.7643 (tmm) REVERT: B 453 ASP cc_start: 0.9010 (p0) cc_final: 0.8778 (p0) REVERT: B 486 GLU cc_start: 0.8253 (tp30) cc_final: 0.7934 (tm-30) REVERT: B 496 LYS cc_start: 0.9215 (tppt) cc_final: 0.8983 (tppt) REVERT: B 515 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8351 (mm-30) REVERT: B 524 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8749 (tptm) REVERT: B 563 LYS cc_start: 0.9262 (mmmm) cc_final: 0.8772 (mtmm) REVERT: B 594 LYS cc_start: 0.8524 (ptpt) cc_final: 0.8203 (ptpt) REVERT: B 602 ASN cc_start: 0.8868 (m-40) cc_final: 0.8562 (m110) REVERT: B 635 ILE cc_start: 0.9146 (mm) cc_final: 0.8860 (mm) REVERT: B 703 LYS cc_start: 0.8398 (mptt) cc_final: 0.7963 (mmtp) REVERT: B 722 LYS cc_start: 0.9414 (tppt) cc_final: 0.9208 (tppt) REVERT: C 444 LYS cc_start: 0.9546 (tptp) cc_final: 0.9237 (tppt) REVERT: C 454 GLN cc_start: 0.8462 (mp10) cc_final: 0.8144 (mp10) REVERT: C 462 TYR cc_start: 0.8990 (t80) cc_final: 0.8669 (t80) REVERT: C 486 GLU cc_start: 0.8258 (tp30) cc_final: 0.7963 (tp30) REVERT: C 499 ASN cc_start: 0.8765 (m-40) cc_final: 0.8330 (m-40) REVERT: C 509 ASN cc_start: 0.8325 (t0) cc_final: 0.8088 (t0) REVERT: C 521 MET cc_start: 0.8055 (tmm) cc_final: 0.7639 (tmm) REVERT: C 551 ASP cc_start: 0.8310 (t0) cc_final: 0.7880 (t0) REVERT: C 582 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8136 (mmtt) REVERT: C 586 LYS cc_start: 0.9241 (mmmm) cc_final: 0.8777 (mmmt) REVERT: C 587 MET cc_start: 0.8851 (mtp) cc_final: 0.8368 (mtp) REVERT: C 629 LEU cc_start: 0.9226 (tp) cc_final: 0.8897 (mm) REVERT: C 637 LYS cc_start: 0.9166 (mmmt) cc_final: 0.8951 (ttpt) REVERT: D 434 MET cc_start: 0.8190 (tpp) cc_final: 0.7758 (tpp) REVERT: D 437 ASN cc_start: 0.8731 (m-40) cc_final: 0.8247 (p0) REVERT: D 454 GLN cc_start: 0.8791 (mp10) cc_final: 0.8400 (mp10) REVERT: D 497 ASP cc_start: 0.8364 (p0) cc_final: 0.7830 (p0) REVERT: D 499 ASN cc_start: 0.8413 (m-40) cc_final: 0.7692 (m-40) REVERT: D 551 ASP cc_start: 0.7654 (m-30) cc_final: 0.6805 (p0) REVERT: D 569 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8597 (mm) REVERT: D 600 ARG cc_start: 0.8600 (ptm-80) cc_final: 0.8255 (ptm-80) REVERT: D 602 ASN cc_start: 0.8900 (m-40) cc_final: 0.8437 (m110) REVERT: D 614 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: D 703 LYS cc_start: 0.9009 (mppt) cc_final: 0.8628 (mmtm) REVERT: E 220 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7902 (mmtt) REVERT: E 359 ARG cc_start: 0.7995 (pmt170) cc_final: 0.7779 (mtm180) REVERT: E 387 LYS cc_start: 0.9384 (ptmm) cc_final: 0.9113 (ptmm) REVERT: E 402 SER cc_start: 0.8860 (m) cc_final: 0.8540 (p) REVERT: E 449 ARG cc_start: 0.9169 (mtm110) cc_final: 0.8848 (mtm110) REVERT: E 470 ARG cc_start: 0.7693 (tmm-80) cc_final: 0.7396 (tmm-80) REVERT: E 472 ASP cc_start: 0.8412 (t0) cc_final: 0.8202 (t0) REVERT: E 481 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8739 (mp) REVERT: E 512 ASP cc_start: 0.8003 (t0) cc_final: 0.7578 (t0) REVERT: E 541 GLN cc_start: 0.8098 (mt0) cc_final: 0.7353 (mm-40) REVERT: E 582 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8875 (mmtt) REVERT: E 709 ASN cc_start: 0.8795 (t0) cc_final: 0.7645 (p0) REVERT: E 722 LYS cc_start: 0.8743 (tptt) cc_final: 0.8479 (tptp) REVERT: F 224 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7580 (tm-30) REVERT: F 326 ASN cc_start: 0.7755 (m-40) cc_final: 0.6331 (t0) REVERT: F 376 ASN cc_start: 0.8987 (m-40) cc_final: 0.8363 (t0) REVERT: F 389 GLN cc_start: 0.8717 (mp10) cc_final: 0.8501 (mp10) REVERT: F 438 GLN cc_start: 0.9339 (mt0) cc_final: 0.9124 (mt0) REVERT: F 449 ARG cc_start: 0.8553 (mtm110) cc_final: 0.7288 (ptp90) REVERT: F 479 GLU cc_start: 0.8506 (mp0) cc_final: 0.8254 (mp0) REVERT: F 485 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8216 (mm-40) REVERT: F 497 ASP cc_start: 0.7910 (p0) cc_final: 0.7497 (p0) REVERT: F 499 ASN cc_start: 0.8516 (m110) cc_final: 0.7586 (m-40) REVERT: F 565 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8375 (mp10) REVERT: F 587 MET cc_start: 0.8568 (ptp) cc_final: 0.7948 (ptp) REVERT: F 599 ASP cc_start: 0.8273 (t0) cc_final: 0.7957 (t0) REVERT: F 633 LYS cc_start: 0.9296 (pptt) cc_final: 0.8607 (pptt) REVERT: F 637 LYS cc_start: 0.8957 (mptt) cc_final: 0.8375 (mmtt) REVERT: G 250 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7089 (tp30) REVERT: G 329 SER cc_start: 0.9046 (p) cc_final: 0.8672 (t) REVERT: G 434 MET cc_start: 0.8278 (pmm) cc_final: 0.8076 (pmm) REVERT: G 441 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8905 (mt-10) REVERT: G 443 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8885 (mm-30) REVERT: G 462 TYR cc_start: 0.8921 (t80) cc_final: 0.8554 (t80) REVERT: G 465 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8148 (mm-30) REVERT: G 549 GLU cc_start: 0.8791 (mp0) cc_final: 0.8442 (mp0) REVERT: G 551 ASP cc_start: 0.7799 (t0) cc_final: 0.7454 (t0) REVERT: G 560 GLN cc_start: 0.9248 (tp-100) cc_final: 0.8744 (mm-40) REVERT: G 565 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: G 587 MET cc_start: 0.7651 (mtm) cc_final: 0.7367 (ptp) REVERT: G 589 ILE cc_start: 0.8609 (mt) cc_final: 0.8375 (mm) REVERT: G 595 ARG cc_start: 0.8994 (ttp-110) cc_final: 0.8587 (ttp-110) REVERT: G 617 ARG cc_start: 0.9128 (ttp80) cc_final: 0.8693 (ttp80) REVERT: G 703 LYS cc_start: 0.8635 (ptpp) cc_final: 0.8350 (ptpp) REVERT: H 65 LYS cc_start: 0.9170 (mmmt) cc_final: 0.8856 (mmmt) REVERT: H 74 TYR cc_start: 0.7519 (t80) cc_final: 0.6510 (t80) REVERT: H 118 TYR cc_start: 0.7363 (OUTLIER) cc_final: 0.6023 (p90) REVERT: H 158 ASP cc_start: 0.7984 (t70) cc_final: 0.7679 (t70) REVERT: H 184 ASP cc_start: 0.8662 (m-30) cc_final: 0.8123 (p0) REVERT: H 186 GLN cc_start: 0.7609 (pt0) cc_final: 0.7285 (mt0) REVERT: H 201 PHE cc_start: 0.9036 (m-80) cc_final: 0.8564 (m-80) REVERT: H 215 GLU cc_start: 0.8176 (pt0) cc_final: 0.7827 (pp20) REVERT: H 244 MET cc_start: 0.8645 (tpp) cc_final: 0.7611 (tpp) REVERT: H 268 TYR cc_start: 0.8080 (m-80) cc_final: 0.7808 (m-80) REVERT: H 393 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8204 (pm20) REVERT: H 398 LEU cc_start: 0.8252 (mm) cc_final: 0.7246 (pp) REVERT: H 415 ASP cc_start: 0.8212 (m-30) cc_final: 0.7868 (m-30) REVERT: H 434 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8038 (tmmt) REVERT: H 436 TYR cc_start: 0.6625 (m-80) cc_final: 0.6249 (m-80) REVERT: H 472 LYS cc_start: 0.8900 (pttm) cc_final: 0.8551 (tptm) REVERT: H 510 ARG cc_start: 0.6878 (mmm-85) cc_final: 0.6363 (mmm-85) REVERT: H 548 LYS cc_start: 0.7611 (mmmt) cc_final: 0.7386 (tptp) REVERT: H 585 PHE cc_start: 0.7379 (p90) cc_final: 0.7110 (p90) REVERT: H 586 ASN cc_start: 0.8734 (t0) cc_final: 0.8521 (t0) REVERT: H 589 ASN cc_start: 0.7619 (m110) cc_final: 0.6947 (m110) REVERT: H 607 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8955 (tmmt) REVERT: H 628 ARG cc_start: 0.7340 (ptp90) cc_final: 0.7130 (ptp90) REVERT: H 658 LEU cc_start: 0.7795 (tt) cc_final: 0.7372 (mt) REVERT: H 718 PHE cc_start: 0.7784 (t80) cc_final: 0.7386 (t80) REVERT: H 736 PHE cc_start: 0.8002 (t80) cc_final: 0.7536 (t80) REVERT: H 737 PHE cc_start: 0.8806 (m-80) cc_final: 0.8239 (m-10) REVERT: I 38 GLU cc_start: 0.8136 (mp0) cc_final: 0.7793 (mp0) REVERT: I 61 LYS cc_start: 0.9221 (mmpt) cc_final: 0.8751 (mtmm) REVERT: I 72 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8315 (mp0) REVERT: I 175 ASN cc_start: 0.8670 (m-40) cc_final: 0.8365 (m-40) REVERT: I 184 ASP cc_start: 0.8081 (p0) cc_final: 0.7551 (p0) REVERT: I 215 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7999 (mt-10) REVERT: I 245 ASP cc_start: 0.8358 (t0) cc_final: 0.8115 (t0) REVERT: I 246 LYS cc_start: 0.9246 (tptp) cc_final: 0.8961 (mmtm) REVERT: I 277 HIS cc_start: 0.8507 (t-90) cc_final: 0.8035 (t-90) REVERT: I 475 PHE cc_start: 0.7958 (t80) cc_final: 0.7710 (t80) REVERT: I 546 ASP cc_start: 0.6058 (OUTLIER) cc_final: 0.5592 (t70) REVERT: I 600 TYR cc_start: 0.9064 (m-80) cc_final: 0.8492 (m-80) REVERT: J 91 HIS cc_start: 0.0659 (t70) cc_final: 0.0458 (t70) REVERT: J 108 TYR cc_start: 0.7559 (m-80) cc_final: 0.7329 (m-80) REVERT: J 117 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.6456 (t-90) REVERT: J 153 LYS cc_start: 0.9184 (ttmm) cc_final: 0.8894 (mtmt) REVERT: J 221 PHE cc_start: 0.9024 (t80) cc_final: 0.8599 (t80) REVERT: J 235 LEU cc_start: 0.9013 (tp) cc_final: 0.8577 (mt) REVERT: J 277 HIS cc_start: 0.7440 (t-90) cc_final: 0.7234 (t-90) REVERT: J 546 ASP cc_start: 0.6515 (m-30) cc_final: 0.6088 (m-30) REVERT: J 579 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.6316 (m-10) REVERT: J 582 LEU cc_start: 0.9038 (tp) cc_final: 0.8361 (tp) REVERT: J 586 ASN cc_start: 0.8142 (m-40) cc_final: 0.7756 (m-40) REVERT: J 590 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.6786 (mmm-85) REVERT: J 629 PHE cc_start: 0.8588 (m-10) cc_final: 0.7848 (m-80) outliers start: 115 outliers final: 89 residues processed: 984 average time/residue: 0.2477 time to fit residues: 398.5968 Evaluate side-chains 986 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 883 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 702 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 627 LEU Chi-restraints excluded: chain E residue 723 LYS Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 565 GLN Chi-restraints excluded: chain F residue 701 VAL Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 438 GLN Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 565 GLN Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 376 LEU Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 434 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 583 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 607 LYS Chi-restraints excluded: chain H residue 614 LEU Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 546 ASP Chi-restraints excluded: chain I residue 597 GLU Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 170 PHE Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 543 ILE Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 664 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 166 optimal weight: 3.9990 chunk 156 optimal weight: 0.0050 chunk 113 optimal weight: 1.9990 chunk 265 optimal weight: 0.9980 chunk 458 optimal weight: 30.0000 chunk 335 optimal weight: 6.9990 chunk 523 optimal weight: 10.0000 chunk 267 optimal weight: 0.2980 chunk 167 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 312 optimal weight: 5.9990 overall best weight: 1.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 HIS B 246 ASN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 326 ASN ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 563 GLN ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 GLN J 690 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.187703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108849 restraints weight = 72497.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113096 restraints weight = 36575.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.115750 restraints weight = 24593.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117339 restraints weight = 19477.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.118339 restraints weight = 17014.625| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 42994 Z= 0.157 Angle : 0.665 13.273 58617 Z= 0.338 Chirality : 0.046 0.309 6906 Planarity : 0.004 0.059 7726 Dihedral : 4.238 26.355 6113 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 3.01 % Allowed : 22.72 % Favored : 74.27 % 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: -0.26 (0.11), residues: 5704 helix: 0.31 (0.13), residues: 1669 sheet: 0.48 (0.16), residues: 1056 loop : -0.64 (0.12), residues: 2979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 470 TYR 0.025 0.001 TYR F 462 PHE 0.021 0.001 PHE I 468 TRP 0.012 0.001 TRP H 570 HIS 0.005 0.001 HIS H 645 Details of bonding type rmsd covalent geometry : bond 0.00365 (42994) covalent geometry : angle 0.66472 (58617) hydrogen bonds : bond 0.03416 ( 1540) hydrogen bonds : angle 4.62795 ( 4500) *********************** REFINEMENT MACRO_CYCLE 9 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 1019 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 896 time to evaluate : 1.631 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 178 ARG cc_start: 0.7588 (ttp-110) cc_final: 0.6853 (ttp-170) REVERT: A 188 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7175 (tt0) REVERT: A 224 GLU cc_start: 0.8511 (tp30) cc_final: 0.7269 (mm-30) REVERT: A 265 ASP cc_start: 0.8220 (t0) cc_final: 0.7535 (p0) REVERT: A 344 ARG cc_start: 0.8517 (mtm-85) cc_final: 0.8270 (ptp90) REVERT: A 447 GLN cc_start: 0.8758 (tt0) cc_final: 0.7941 (tm-30) REVERT: A 551 ASP cc_start: 0.7696 (m-30) cc_final: 0.7295 (m-30) REVERT: A 563 LYS cc_start: 0.8973 (tmmt) cc_final: 0.8666 (ptmt) REVERT: A 586 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8745 (mmmt) REVERT: A 589 ILE cc_start: 0.8900 (mt) cc_final: 0.8620 (mm) REVERT: A 602 ASN cc_start: 0.8742 (m-40) cc_final: 0.8240 (m110) REVERT: A 633 LYS cc_start: 0.9565 (tmtt) cc_final: 0.9207 (tptt) REVERT: A 636 ARG cc_start: 0.8512 (ptt-90) cc_final: 0.7979 (ptt-90) REVERT: A 703 LYS cc_start: 0.8363 (mmtm) cc_final: 0.8004 (mmtm) REVERT: B 220 LYS cc_start: 0.9028 (mttt) cc_final: 0.8746 (mttm) REVERT: B 227 SER cc_start: 0.8863 (p) cc_final: 0.8589 (p) REVERT: B 265 ASP cc_start: 0.8001 (t0) cc_final: 0.7428 (t0) REVERT: B 267 GLU cc_start: 0.7616 (mp0) cc_final: 0.7108 (mp0) REVERT: B 326 ASN cc_start: 0.8780 (p0) cc_final: 0.8472 (p0) REVERT: B 366 TYR cc_start: 0.9195 (m-80) cc_final: 0.8891 (m-80) REVERT: B 381 THR cc_start: 0.9180 (t) cc_final: 0.8937 (t) REVERT: B 403 GLN cc_start: 0.8366 (mp10) cc_final: 0.8046 (mp10) REVERT: B 485 GLN cc_start: 0.8870 (mt0) cc_final: 0.8552 (mt0) REVERT: B 486 GLU cc_start: 0.8272 (tp30) cc_final: 0.7984 (tm-30) REVERT: B 496 LYS cc_start: 0.9272 (tppt) cc_final: 0.9019 (tppt) REVERT: B 515 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8426 (mm-30) REVERT: B 524 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8498 (tptp) REVERT: B 563 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8894 (mmtm) REVERT: B 580 LYS cc_start: 0.9402 (mmmm) cc_final: 0.9056 (mmmt) REVERT: B 594 LYS cc_start: 0.8545 (ptpt) cc_final: 0.8229 (ptpt) REVERT: B 602 ASN cc_start: 0.8900 (m-40) cc_final: 0.8492 (m110) REVERT: B 635 ILE cc_start: 0.9147 (mm) cc_final: 0.8856 (mm) REVERT: B 636 ARG cc_start: 0.8648 (ptt-90) cc_final: 0.8302 (ptp90) REVERT: B 703 LYS cc_start: 0.8464 (mptt) cc_final: 0.8015 (mmtp) REVERT: C 389 GLN cc_start: 0.7913 (mp10) cc_final: 0.7512 (mp10) REVERT: C 444 LYS cc_start: 0.9549 (tptp) cc_final: 0.9243 (tppt) REVERT: C 454 GLN cc_start: 0.8425 (mp10) cc_final: 0.8066 (mp10) REVERT: C 462 TYR cc_start: 0.9032 (t80) cc_final: 0.8708 (t80) REVERT: C 486 GLU cc_start: 0.8300 (tp30) cc_final: 0.7956 (tp30) REVERT: C 499 ASN cc_start: 0.8786 (m-40) cc_final: 0.8359 (m-40) REVERT: C 509 ASN cc_start: 0.8436 (t0) cc_final: 0.8191 (t0) REVERT: C 521 MET cc_start: 0.7935 (tmm) cc_final: 0.7680 (tmm) REVERT: C 551 ASP cc_start: 0.8360 (t0) cc_final: 0.7991 (t0) REVERT: C 582 LYS cc_start: 0.8506 (mmtt) cc_final: 0.8246 (mmtt) REVERT: C 586 LYS cc_start: 0.9233 (mmmm) cc_final: 0.8741 (mmmt) REVERT: C 587 MET cc_start: 0.8885 (mtp) cc_final: 0.8363 (mtp) REVERT: C 629 LEU cc_start: 0.9214 (tp) cc_final: 0.8849 (mm) REVERT: D 291 LYS cc_start: 0.8809 (mmtm) cc_final: 0.8484 (mmtt) REVERT: D 359 ARG cc_start: 0.7191 (mpt-90) cc_final: 0.5859 (mtt90) REVERT: D 434 MET cc_start: 0.8171 (tpp) cc_final: 0.7719 (tpp) REVERT: D 437 ASN cc_start: 0.8750 (m-40) cc_final: 0.8260 (p0) REVERT: D 472 ASP cc_start: 0.7654 (t0) cc_final: 0.6770 (t0) REVERT: D 497 ASP cc_start: 0.8347 (p0) cc_final: 0.7196 (p0) REVERT: D 499 ASN cc_start: 0.8432 (m-40) cc_final: 0.7372 (p0) REVERT: D 551 ASP cc_start: 0.7683 (m-30) cc_final: 0.6823 (p0) REVERT: D 569 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8611 (mm) REVERT: D 600 ARG cc_start: 0.8643 (ptm-80) cc_final: 0.8309 (ptm-80) REVERT: D 602 ASN cc_start: 0.8893 (m-40) cc_final: 0.8406 (m110) REVERT: D 614 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8070 (pm20) REVERT: D 703 LYS cc_start: 0.9037 (mppt) cc_final: 0.8701 (mmtm) REVERT: E 178 ARG cc_start: 0.7844 (ptp-170) cc_final: 0.7543 (ptp-170) REVERT: E 220 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7989 (mmtt) REVERT: E 387 LYS cc_start: 0.9372 (ptmm) cc_final: 0.9122 (ptmm) REVERT: E 470 ARG cc_start: 0.7764 (tmm-80) cc_final: 0.7450 (tmm-80) REVERT: E 472 ASP cc_start: 0.8531 (t0) cc_final: 0.8038 (t0) REVERT: E 481 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8822 (mp) REVERT: E 497 ASP cc_start: 0.7899 (p0) cc_final: 0.7585 (p0) REVERT: E 499 ASN cc_start: 0.8629 (m110) cc_final: 0.8185 (m-40) REVERT: E 512 ASP cc_start: 0.8174 (t0) cc_final: 0.7764 (t0) REVERT: E 541 GLN cc_start: 0.8107 (mt0) cc_final: 0.7369 (mm-40) REVERT: E 582 LYS cc_start: 0.9094 (mmmt) cc_final: 0.8847 (mmtt) REVERT: E 709 ASN cc_start: 0.8759 (t0) cc_final: 0.7597 (p0) REVERT: E 722 LYS cc_start: 0.8773 (tptt) cc_final: 0.8503 (tptp) REVERT: F 224 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7610 (tm-30) REVERT: F 326 ASN cc_start: 0.7837 (m-40) cc_final: 0.6171 (t0) REVERT: F 376 ASN cc_start: 0.9024 (m-40) cc_final: 0.8354 (t0) REVERT: F 389 GLN cc_start: 0.8709 (mp10) cc_final: 0.8466 (mp10) REVERT: F 438 GLN cc_start: 0.9336 (mt0) cc_final: 0.9126 (mt0) REVERT: F 449 ARG cc_start: 0.8576 (mtm110) cc_final: 0.7334 (ptp90) REVERT: F 479 GLU cc_start: 0.8503 (mp0) cc_final: 0.8192 (mp0) REVERT: F 485 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8241 (mm-40) REVERT: F 497 ASP cc_start: 0.7956 (p0) cc_final: 0.7552 (p0) REVERT: F 499 ASN cc_start: 0.8516 (m110) cc_final: 0.7636 (m-40) REVERT: F 557 GLN cc_start: 0.8189 (mp10) cc_final: 0.7985 (mm110) REVERT: F 565 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8330 (mp10) REVERT: F 569 LEU cc_start: 0.9270 (mm) cc_final: 0.9059 (mm) REVERT: F 599 ASP cc_start: 0.8388 (t0) cc_final: 0.8061 (t0) REVERT: F 633 LYS cc_start: 0.9295 (pptt) cc_final: 0.8634 (pptt) REVERT: F 637 LYS cc_start: 0.8969 (mptt) cc_final: 0.8407 (mmtt) REVERT: G 190 GLU cc_start: 0.8698 (tp30) cc_final: 0.7957 (mp0) REVERT: G 329 SER cc_start: 0.9034 (p) cc_final: 0.8649 (t) REVERT: G 446 LYS cc_start: 0.8404 (mmtt) cc_final: 0.8063 (mmtt) REVERT: G 462 TYR cc_start: 0.8985 (t80) cc_final: 0.8645 (t80) REVERT: G 465 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8189 (mm-30) REVERT: G 549 GLU cc_start: 0.8794 (mp0) cc_final: 0.8540 (mp0) REVERT: G 551 ASP cc_start: 0.7801 (t0) cc_final: 0.7446 (t0) REVERT: G 560 GLN cc_start: 0.9248 (tp-100) cc_final: 0.8772 (mm-40) REVERT: G 587 MET cc_start: 0.7750 (mtm) cc_final: 0.7478 (ptp) REVERT: G 589 ILE cc_start: 0.8662 (mt) cc_final: 0.8410 (mm) REVERT: G 595 ARG cc_start: 0.9021 (ttp-110) cc_final: 0.8623 (ttp-110) REVERT: G 617 ARG cc_start: 0.9126 (ttp80) cc_final: 0.8683 (ttp80) REVERT: G 723 LYS cc_start: 0.9136 (mttt) cc_final: 0.8905 (mttm) REVERT: H 65 LYS cc_start: 0.9166 (mmmt) cc_final: 0.8850 (mmmt) REVERT: H 74 TYR cc_start: 0.7684 (t80) cc_final: 0.6559 (t80) REVERT: H 118 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.6060 (p90) REVERT: H 145 LEU cc_start: 0.8301 (tp) cc_final: 0.7983 (tp) REVERT: H 158 ASP cc_start: 0.7939 (t70) cc_final: 0.7650 (t70) REVERT: H 170 PHE cc_start: 0.8495 (t80) cc_final: 0.8277 (t80) REVERT: H 184 ASP cc_start: 0.8705 (m-30) cc_final: 0.8364 (p0) REVERT: H 186 GLN cc_start: 0.7694 (pt0) cc_final: 0.7313 (mt0) REVERT: H 201 PHE cc_start: 0.8999 (m-80) cc_final: 0.8518 (m-80) REVERT: H 215 GLU cc_start: 0.8116 (pt0) cc_final: 0.7849 (pp20) REVERT: H 235 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8532 (mm) REVERT: H 244 MET cc_start: 0.8679 (tpp) cc_final: 0.7669 (tpp) REVERT: H 268 TYR cc_start: 0.8170 (m-80) cc_final: 0.7901 (m-80) REVERT: H 393 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8197 (pm20) REVERT: H 398 LEU cc_start: 0.8259 (mm) cc_final: 0.7259 (pp) REVERT: H 415 ASP cc_start: 0.8219 (m-30) cc_final: 0.7855 (m-30) REVERT: H 434 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7902 (tmmt) REVERT: H 436 TYR cc_start: 0.6756 (m-80) cc_final: 0.6414 (m-80) REVERT: H 472 LYS cc_start: 0.8895 (pttm) cc_final: 0.8646 (tttp) REVERT: H 510 ARG cc_start: 0.6900 (mmm-85) cc_final: 0.6394 (mmm-85) REVERT: H 548 LYS cc_start: 0.7631 (mmmt) cc_final: 0.7400 (tptp) REVERT: H 556 ASP cc_start: 0.8947 (m-30) cc_final: 0.8462 (p0) REVERT: H 585 PHE cc_start: 0.7513 (p90) cc_final: 0.7176 (p90) REVERT: H 586 ASN cc_start: 0.8739 (t0) cc_final: 0.8519 (t0) REVERT: H 589 ASN cc_start: 0.7667 (m110) cc_final: 0.7164 (m110) REVERT: H 607 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8974 (tmmt) REVERT: H 658 LEU cc_start: 0.7900 (tt) cc_final: 0.7459 (mt) REVERT: H 718 PHE cc_start: 0.7800 (t80) cc_final: 0.7382 (t80) REVERT: H 736 PHE cc_start: 0.8027 (t80) cc_final: 0.7534 (t80) REVERT: H 737 PHE cc_start: 0.8818 (m-80) cc_final: 0.8247 (m-10) REVERT: I 38 GLU cc_start: 0.8173 (mp0) cc_final: 0.7791 (mp0) REVERT: I 61 LYS cc_start: 0.9268 (mmpt) cc_final: 0.8873 (mmtm) REVERT: I 82 TYR cc_start: 0.6740 (p90) cc_final: 0.6429 (p90) REVERT: I 175 ASN cc_start: 0.8706 (m-40) cc_final: 0.8382 (m-40) REVERT: I 184 ASP cc_start: 0.8187 (p0) cc_final: 0.7674 (p0) REVERT: I 215 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7999 (mt-10) REVERT: I 245 ASP cc_start: 0.8384 (t0) cc_final: 0.7981 (t0) REVERT: I 246 LYS cc_start: 0.9267 (tptp) cc_final: 0.8973 (mmtm) REVERT: I 277 HIS cc_start: 0.8517 (t-90) cc_final: 0.8010 (t-90) REVERT: I 474 ASN cc_start: 0.6911 (m-40) cc_final: 0.5861 (p0) REVERT: I 475 PHE cc_start: 0.7965 (t80) cc_final: 0.7476 (t80) REVERT: I 531 ASP cc_start: 0.7655 (t70) cc_final: 0.7386 (t70) REVERT: I 546 ASP cc_start: 0.6138 (OUTLIER) cc_final: 0.5515 (t70) REVERT: I 637 PRO cc_start: 0.8660 (Cg_endo) cc_final: 0.8460 (Cg_exo) REVERT: J 91 HIS cc_start: 0.1005 (t70) cc_final: 0.0800 (t70) REVERT: J 108 TYR cc_start: 0.7585 (m-80) cc_final: 0.7375 (m-80) REVERT: J 117 HIS cc_start: 0.6755 (OUTLIER) cc_final: 0.6477 (t-90) REVERT: J 153 LYS cc_start: 0.9212 (ttmm) cc_final: 0.8890 (mtmm) REVERT: J 217 PHE cc_start: 0.7494 (t80) cc_final: 0.7022 (t80) REVERT: J 221 PHE cc_start: 0.9003 (t80) cc_final: 0.8565 (t80) REVERT: J 235 LEU cc_start: 0.9061 (tp) cc_final: 0.8679 (mt) REVERT: J 250 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8064 (mm-40) REVERT: J 579 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.6414 (m-10) REVERT: J 582 LEU cc_start: 0.9037 (tp) cc_final: 0.8278 (tp) REVERT: J 586 ASN cc_start: 0.8162 (m-40) cc_final: 0.7764 (m-40) REVERT: J 629 PHE cc_start: 0.8505 (m-10) cc_final: 0.7714 (m-80) REVERT: J 664 ARG cc_start: 0.6270 (OUTLIER) cc_final: 0.5283 (ttp80) outliers start: 123 outliers final: 99 residues processed: 962 average time/residue: 0.2534 time to fit residues: 397.9010 Evaluate side-chains 983 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 870 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 627 LEU Chi-restraints excluded: chain E residue 723 LYS Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 565 GLN Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 701 VAL Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 438 GLN Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 488 THR Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 376 LEU Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 434 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 583 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 607 LYS Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 546 ASP Chi-restraints excluded: chain I residue 597 GLU Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 170 PHE Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 664 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 409 optimal weight: 1.9990 chunk 417 optimal weight: 8.9990 chunk 318 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 327 optimal weight: 6.9990 chunk 314 optimal weight: 3.9990 chunk 460 optimal weight: 7.9990 chunk 444 optimal weight: 0.8980 chunk 214 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 316 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 541 GLN G 326 ASN G 485 GLN ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 690 HIS ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.189108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110400 restraints weight = 72648.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.114741 restraints weight = 36311.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117516 restraints weight = 24285.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119082 restraints weight = 19111.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120129 restraints weight = 16722.959| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 42994 Z= 0.128 Angle : 0.668 13.922 58617 Z= 0.337 Chirality : 0.046 0.307 6906 Planarity : 0.004 0.042 7726 Dihedral : 4.177 27.790 6113 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.20 % Rotamer: Outliers : 2.69 % Allowed : 23.41 % Favored : 73.90 % 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: -0.18 (0.11), residues: 5704 helix: 0.37 (0.13), residues: 1668 sheet: 0.52 (0.16), residues: 1092 loop : -0.59 (0.12), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 628 TYR 0.036 0.001 TYR H 621 PHE 0.037 0.001 PHE I 468 TRP 0.011 0.001 TRP H 570 HIS 0.006 0.001 HIS H 645 Details of bonding type rmsd covalent geometry : bond 0.00297 (42994) covalent geometry : angle 0.66766 (58617) hydrogen bonds : bond 0.03231 ( 1540) hydrogen bonds : angle 4.62834 ( 4500) ********************** REFINEMENT MACRO_CYCLE 10 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 1018 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 908 time to evaluate : 1.581 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 178 ARG cc_start: 0.7594 (ttp-110) cc_final: 0.6686 (ttp-170) REVERT: A 188 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7062 (tt0) REVERT: A 224 GLU cc_start: 0.8460 (tp30) cc_final: 0.7124 (mm-30) REVERT: A 265 ASP cc_start: 0.8232 (t0) cc_final: 0.7523 (p0) REVERT: A 344 ARG cc_start: 0.8528 (mtm-85) cc_final: 0.8279 (ptp90) REVERT: A 447 GLN cc_start: 0.8765 (tt0) cc_final: 0.7939 (tm-30) REVERT: A 551 ASP cc_start: 0.7670 (m-30) cc_final: 0.7275 (m-30) REVERT: A 559 SER cc_start: 0.8981 (t) cc_final: 0.8712 (p) REVERT: A 563 LYS cc_start: 0.8978 (tmmt) cc_final: 0.8674 (ptmt) REVERT: A 586 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8791 (mmmt) REVERT: A 589 ILE cc_start: 0.8874 (mt) cc_final: 0.8612 (mm) REVERT: A 595 ARG cc_start: 0.8854 (mtm110) cc_final: 0.8494 (mtm110) REVERT: A 602 ASN cc_start: 0.8713 (m-40) cc_final: 0.8208 (m110) REVERT: A 633 LYS cc_start: 0.9551 (tmtt) cc_final: 0.9145 (tptt) REVERT: A 636 ARG cc_start: 0.8493 (ptt-90) cc_final: 0.7982 (ptt-90) REVERT: A 703 LYS cc_start: 0.8346 (mmtm) cc_final: 0.8008 (mmtm) REVERT: B 220 LYS cc_start: 0.8995 (mttt) cc_final: 0.8721 (mttm) REVERT: B 227 SER cc_start: 0.8812 (p) cc_final: 0.8529 (p) REVERT: B 265 ASP cc_start: 0.7929 (t0) cc_final: 0.7311 (t0) REVERT: B 267 GLU cc_start: 0.7625 (mp0) cc_final: 0.7086 (mp0) REVERT: B 326 ASN cc_start: 0.8778 (p0) cc_final: 0.8484 (p0) REVERT: B 366 TYR cc_start: 0.9155 (m-80) cc_final: 0.8868 (m-80) REVERT: B 381 THR cc_start: 0.9152 (t) cc_final: 0.8935 (t) REVERT: B 403 GLN cc_start: 0.8391 (mp10) cc_final: 0.8143 (mp10) REVERT: B 485 GLN cc_start: 0.8860 (mt0) cc_final: 0.8545 (mt0) REVERT: B 486 GLU cc_start: 0.8255 (tp30) cc_final: 0.8004 (tm-30) REVERT: B 496 LYS cc_start: 0.9272 (tppt) cc_final: 0.9009 (tppt) REVERT: B 515 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8492 (mm-30) REVERT: B 524 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8506 (tptp) REVERT: B 541 GLN cc_start: 0.8451 (pt0) cc_final: 0.8195 (pt0) REVERT: B 563 LYS cc_start: 0.9265 (mmmm) cc_final: 0.8814 (mtmm) REVERT: B 580 LYS cc_start: 0.9343 (mmmm) cc_final: 0.8974 (mmmt) REVERT: B 594 LYS cc_start: 0.8538 (ptpt) cc_final: 0.8239 (ptpt) REVERT: B 602 ASN cc_start: 0.8904 (m-40) cc_final: 0.8481 (m110) REVERT: B 635 ILE cc_start: 0.9142 (mm) cc_final: 0.8850 (mm) REVERT: B 636 ARG cc_start: 0.8636 (ptt-90) cc_final: 0.8258 (ptp90) REVERT: B 703 LYS cc_start: 0.8466 (mptt) cc_final: 0.7997 (mmtp) REVERT: C 389 GLN cc_start: 0.7961 (mp10) cc_final: 0.7241 (mp10) REVERT: C 444 LYS cc_start: 0.9540 (tptp) cc_final: 0.9232 (tppt) REVERT: C 454 GLN cc_start: 0.8316 (mp10) cc_final: 0.7972 (mp10) REVERT: C 462 TYR cc_start: 0.9025 (t80) cc_final: 0.8714 (t80) REVERT: C 498 LEU cc_start: 0.9369 (mt) cc_final: 0.9139 (mt) REVERT: C 499 ASN cc_start: 0.8698 (m-40) cc_final: 0.8195 (m-40) REVERT: C 509 ASN cc_start: 0.8384 (t0) cc_final: 0.8155 (t0) REVERT: C 521 MET cc_start: 0.8011 (tmm) cc_final: 0.7653 (tmm) REVERT: C 551 ASP cc_start: 0.8322 (t0) cc_final: 0.7934 (t0) REVERT: C 582 LYS cc_start: 0.8506 (mmtt) cc_final: 0.8159 (mmtt) REVERT: C 586 LYS cc_start: 0.9257 (mmmm) cc_final: 0.8889 (mmmt) REVERT: C 587 MET cc_start: 0.8941 (mtp) cc_final: 0.8459 (mtp) REVERT: C 629 LEU cc_start: 0.9227 (tp) cc_final: 0.8688 (mm) REVERT: D 434 MET cc_start: 0.8275 (tpp) cc_final: 0.7898 (tpp) REVERT: D 437 ASN cc_start: 0.8732 (m-40) cc_final: 0.8247 (p0) REVERT: D 470 ARG cc_start: 0.8023 (mmm-85) cc_final: 0.7804 (mmm160) REVERT: D 472 ASP cc_start: 0.7711 (t0) cc_final: 0.7058 (t0) REVERT: D 497 ASP cc_start: 0.8320 (p0) cc_final: 0.7129 (p0) REVERT: D 499 ASN cc_start: 0.8399 (m-40) cc_final: 0.7326 (p0) REVERT: D 551 ASP cc_start: 0.7664 (m-30) cc_final: 0.6809 (p0) REVERT: D 569 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8588 (mm) REVERT: D 600 ARG cc_start: 0.8625 (ptm-80) cc_final: 0.8296 (ptm-80) REVERT: D 602 ASN cc_start: 0.8838 (m-40) cc_final: 0.8401 (m110) REVERT: D 614 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: D 703 LYS cc_start: 0.9032 (mppt) cc_final: 0.8527 (mmtp) REVERT: E 178 ARG cc_start: 0.7869 (ptp-170) cc_final: 0.7552 (ptp-170) REVERT: E 220 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7989 (mmtt) REVERT: E 359 ARG cc_start: 0.8075 (pmt170) cc_final: 0.7556 (ptt-90) REVERT: E 387 LYS cc_start: 0.9365 (ptmm) cc_final: 0.9140 (ptmm) REVERT: E 402 SER cc_start: 0.8857 (m) cc_final: 0.8511 (p) REVERT: E 470 ARG cc_start: 0.7741 (tmm-80) cc_final: 0.7423 (tmm-80) REVERT: E 472 ASP cc_start: 0.8461 (t0) cc_final: 0.8184 (t0) REVERT: E 481 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8794 (mp) REVERT: E 512 ASP cc_start: 0.8118 (t0) cc_final: 0.7729 (t0) REVERT: E 541 GLN cc_start: 0.8122 (mt0) cc_final: 0.7338 (mm-40) REVERT: E 582 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8826 (mmtt) REVERT: E 587 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7471 (mpp) REVERT: E 616 HIS cc_start: 0.8846 (m-70) cc_final: 0.8584 (m-70) REVERT: E 709 ASN cc_start: 0.8699 (t0) cc_final: 0.7578 (p0) REVERT: E 722 LYS cc_start: 0.8778 (tptt) cc_final: 0.8505 (tptp) REVERT: F 224 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7609 (tm-30) REVERT: F 326 ASN cc_start: 0.7777 (m-40) cc_final: 0.6094 (t0) REVERT: F 353 ASN cc_start: 0.8629 (t0) cc_final: 0.8425 (t0) REVERT: F 376 ASN cc_start: 0.9014 (m-40) cc_final: 0.8337 (t0) REVERT: F 389 GLN cc_start: 0.8676 (mp10) cc_final: 0.8452 (mp10) REVERT: F 449 ARG cc_start: 0.8524 (mtm110) cc_final: 0.7284 (ptp90) REVERT: F 479 GLU cc_start: 0.8507 (mp0) cc_final: 0.8232 (mp0) REVERT: F 485 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8180 (mm-40) REVERT: F 497 ASP cc_start: 0.7959 (p0) cc_final: 0.7534 (p0) REVERT: F 499 ASN cc_start: 0.8534 (m110) cc_final: 0.7564 (m-40) REVERT: F 525 GLU cc_start: 0.8181 (pt0) cc_final: 0.7872 (pp20) REVERT: F 541 GLN cc_start: 0.8884 (tt0) cc_final: 0.8645 (tp40) REVERT: F 565 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8351 (mp10) REVERT: F 569 LEU cc_start: 0.9261 (mm) cc_final: 0.9047 (mm) REVERT: F 599 ASP cc_start: 0.8284 (t0) cc_final: 0.7972 (t0) REVERT: F 633 LYS cc_start: 0.9302 (pptt) cc_final: 0.8623 (pptt) REVERT: F 637 LYS cc_start: 0.8996 (mptt) cc_final: 0.8400 (mmtt) REVERT: G 190 GLU cc_start: 0.8651 (tp30) cc_final: 0.7925 (mp0) REVERT: G 329 SER cc_start: 0.9039 (p) cc_final: 0.8671 (t) REVERT: G 446 LYS cc_start: 0.8388 (mmtt) cc_final: 0.7979 (mmtt) REVERT: G 462 TYR cc_start: 0.8961 (t80) cc_final: 0.8581 (t80) REVERT: G 465 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8187 (mm-30) REVERT: G 551 ASP cc_start: 0.7797 (t0) cc_final: 0.7433 (t0) REVERT: G 560 GLN cc_start: 0.9216 (tp-100) cc_final: 0.8733 (mm-40) REVERT: G 565 GLN cc_start: 0.8865 (tt0) cc_final: 0.8639 (tt0) REVERT: G 587 MET cc_start: 0.7639 (mtm) cc_final: 0.7376 (ptp) REVERT: G 589 ILE cc_start: 0.8634 (mt) cc_final: 0.8382 (mm) REVERT: G 595 ARG cc_start: 0.9031 (ttp-110) cc_final: 0.8751 (ttp-110) REVERT: G 617 ARG cc_start: 0.9120 (ttp80) cc_final: 0.8678 (ttp80) REVERT: G 723 LYS cc_start: 0.9164 (mttt) cc_final: 0.8937 (mttm) REVERT: H 65 LYS cc_start: 0.9147 (mmmt) cc_final: 0.8821 (mmmt) REVERT: H 74 TYR cc_start: 0.7602 (t80) cc_final: 0.6470 (t80) REVERT: H 118 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.5996 (p90) REVERT: H 158 ASP cc_start: 0.7906 (t70) cc_final: 0.7597 (t70) REVERT: H 184 ASP cc_start: 0.8607 (m-30) cc_final: 0.8151 (p0) REVERT: H 186 GLN cc_start: 0.7605 (pt0) cc_final: 0.7188 (mt0) REVERT: H 201 PHE cc_start: 0.9021 (m-80) cc_final: 0.8575 (m-80) REVERT: H 215 GLU cc_start: 0.8131 (pt0) cc_final: 0.7833 (pp20) REVERT: H 244 MET cc_start: 0.8661 (tpp) cc_final: 0.7649 (tpp) REVERT: H 268 TYR cc_start: 0.8185 (m-80) cc_final: 0.7900 (m-80) REVERT: H 393 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8164 (pm20) REVERT: H 398 LEU cc_start: 0.8227 (mm) cc_final: 0.7229 (pp) REVERT: H 415 ASP cc_start: 0.8203 (m-30) cc_final: 0.7862 (m-30) REVERT: H 434 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7780 (tmmt) REVERT: H 436 TYR cc_start: 0.6741 (m-80) cc_final: 0.6539 (m-80) REVERT: H 472 LYS cc_start: 0.8887 (pttm) cc_final: 0.8628 (tttp) REVERT: H 510 ARG cc_start: 0.6862 (mmm-85) cc_final: 0.6342 (mmm-85) REVERT: H 548 LYS cc_start: 0.7649 (mmmt) cc_final: 0.7417 (tptp) REVERT: H 556 ASP cc_start: 0.8934 (m-30) cc_final: 0.8457 (p0) REVERT: H 585 PHE cc_start: 0.7435 (p90) cc_final: 0.6887 (p90) REVERT: H 586 ASN cc_start: 0.8727 (t0) cc_final: 0.8491 (t0) REVERT: H 589 ASN cc_start: 0.7624 (m110) cc_final: 0.6943 (m110) REVERT: H 607 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8959 (tmmt) REVERT: H 658 LEU cc_start: 0.7864 (tt) cc_final: 0.7445 (mt) REVERT: H 718 PHE cc_start: 0.7763 (t80) cc_final: 0.7349 (t80) REVERT: H 736 PHE cc_start: 0.8023 (t80) cc_final: 0.7579 (t80) REVERT: H 737 PHE cc_start: 0.8822 (m-80) cc_final: 0.8299 (m-10) REVERT: I 38 GLU cc_start: 0.8142 (mp0) cc_final: 0.7791 (mp0) REVERT: I 61 LYS cc_start: 0.9248 (mmpt) cc_final: 0.8809 (mtmm) REVERT: I 72 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: I 175 ASN cc_start: 0.8643 (m-40) cc_final: 0.8334 (m-40) REVERT: I 184 ASP cc_start: 0.8103 (p0) cc_final: 0.7574 (p0) REVERT: I 215 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7995 (mt-10) REVERT: I 245 ASP cc_start: 0.8410 (t0) cc_final: 0.8072 (t0) REVERT: I 246 LYS cc_start: 0.9259 (tptp) cc_final: 0.8959 (mmtm) REVERT: I 277 HIS cc_start: 0.8527 (t-90) cc_final: 0.8023 (t-90) REVERT: I 474 ASN cc_start: 0.6890 (m-40) cc_final: 0.6055 (p0) REVERT: I 475 PHE cc_start: 0.8065 (t80) cc_final: 0.7656 (t80) REVERT: I 544 ARG cc_start: 0.6332 (tpm170) cc_final: 0.6119 (tpm170) REVERT: I 637 PRO cc_start: 0.8674 (Cg_endo) cc_final: 0.8463 (Cg_exo) REVERT: J 91 HIS cc_start: 0.0977 (t70) cc_final: 0.0765 (t70) REVERT: J 117 HIS cc_start: 0.6719 (OUTLIER) cc_final: 0.6428 (t-90) REVERT: J 153 LYS cc_start: 0.9247 (ttmm) cc_final: 0.8960 (mtmt) REVERT: J 217 PHE cc_start: 0.7500 (t80) cc_final: 0.7005 (t80) REVERT: J 221 PHE cc_start: 0.9016 (t80) cc_final: 0.8571 (t80) REVERT: J 235 LEU cc_start: 0.9064 (tp) cc_final: 0.8637 (mt) REVERT: J 250 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7979 (mm-40) REVERT: J 579 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.6246 (m-10) REVERT: J 582 LEU cc_start: 0.9041 (tp) cc_final: 0.8342 (tp) REVERT: J 586 ASN cc_start: 0.8157 (m-40) cc_final: 0.7751 (m-40) REVERT: J 629 PHE cc_start: 0.8513 (m-10) cc_final: 0.7810 (m-80) outliers start: 110 outliers final: 88 residues processed: 973 average time/residue: 0.2454 time to fit residues: 391.0127 Evaluate side-chains 979 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 878 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 587 MET Chi-restraints excluded: chain E residue 723 LYS Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 565 GLN Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 638 ILE Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 438 GLN Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 434 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 583 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 607 LYS Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 597 GLU Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 170 PHE Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 543 ILE Chi-restraints excluded: chain J residue 579 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 223 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 564 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 419 optimal weight: 8.9990 chunk 72 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 343 optimal weight: 3.9990 chunk 58 optimal weight: 0.0670 chunk 477 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 HIS ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 326 ASN G 485 GLN ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 690 HIS ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.188660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109785 restraints weight = 73224.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114149 restraints weight = 36543.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.116841 restraints weight = 24393.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118460 restraints weight = 19261.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.119540 restraints weight = 16820.733| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 42994 Z= 0.136 Angle : 0.674 13.803 58617 Z= 0.339 Chirality : 0.046 0.292 6906 Planarity : 0.004 0.071 7726 Dihedral : 4.163 27.247 6113 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.31 % Favored : 95.67 % Rotamer: Outliers : 2.79 % Allowed : 23.33 % Favored : 73.87 % 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: -0.15 (0.11), residues: 5704 helix: 0.41 (0.13), residues: 1664 sheet: 0.49 (0.16), residues: 1111 loop : -0.57 (0.12), residues: 2929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 502 TYR 0.026 0.001 TYR I 82 PHE 0.033 0.001 PHE I 468 TRP 0.011 0.001 TRP H 570 HIS 0.006 0.001 HIS H 645 Details of bonding type rmsd covalent geometry : bond 0.00316 (42994) covalent geometry : angle 0.67441 (58617) hydrogen bonds : bond 0.03255 ( 1540) hydrogen bonds : angle 4.60278 ( 4500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11079.95 seconds wall clock time: 190 minutes 13.30 seconds (11413.30 seconds total)