Starting phenix.real_space_refine on Mon Jul 6 11:31:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rla_24523/07_2026/7rla_24523.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rla_24523/07_2026/7rla_24523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rla_24523/07_2026/7rla_24523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rla_24523/07_2026/7rla_24523.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rla_24523/07_2026/7rla_24523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rla_24523/07_2026/7rla_24523.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rla_24523/07_2026/7rla_24523.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rla_24523/07_2026/7rla_24523.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 192 5.16 5 C 21876 2.51 5 N 6132 2.21 5 O 6696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34944 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5760 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5760 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5760 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5760 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5760 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5760 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.67, per 1000 atoms: 0.22 Number of scatterers: 34944 At special positions: 0 Unit cell: (180.728, 184.034, 123.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 36 15.00 Mg 12 11.99 O 6696 8.00 N 6132 7.00 C 21876 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: 3.24 Conformation dependent library (CDL) restraints added in 1.6 seconds 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8244 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 12 sheets defined 42.7% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 removed outlier: 4.043A pdb=" N GLU A 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.853A pdb=" N TYR A 138 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE A 139 " --> pdb=" O LYS A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 191 through 199 removed outlier: 3.549A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 removed outlier: 3.966A pdb=" N ALA A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.771A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.664A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.656A pdb=" N ILE A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 removed outlier: 3.932A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.899A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.984A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.746A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 removed outlier: 3.985A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.604A pdb=" N SER A 457 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN A 458 " --> pdb=" O TRP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 494 removed outlier: 3.808A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.707A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 507 " --> pdb=" O PHE A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 4.078A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 removed outlier: 3.610A pdb=" N LEU A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 569 removed outlier: 3.648A pdb=" N ASP A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 585 removed outlier: 4.048A pdb=" N ILE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 610 removed outlier: 3.519A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 removed outlier: 4.326A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 683 through 705 Processing helix chain 'A' and resid 732 through 742 removed outlier: 3.706A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 739 " --> pdb=" O HIS A 735 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 removed outlier: 3.559A pdb=" N THR A 761 " --> pdb=" O MET A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 766 Processing helix chain 'B' and resid 45 through 49 removed outlier: 4.043A pdb=" N GLU B 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.852A pdb=" N TYR B 138 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE B 139 " --> pdb=" O LYS B 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 139' Processing helix chain 'B' and resid 191 through 199 removed outlier: 3.549A pdb=" N SER B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 3.966A pdb=" N ALA B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 removed outlier: 3.771A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.664A pdb=" N ALA B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 276 removed outlier: 3.657A pdb=" N ILE B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 295 removed outlier: 3.933A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.899A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.982A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.746A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.985A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.604A pdb=" N SER B 457 " --> pdb=" O ARG B 453 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN B 458 " --> pdb=" O TRP B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 494 removed outlier: 3.806A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.708A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 507 " --> pdb=" O PHE B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 4.078A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 550 removed outlier: 3.611A pdb=" N LEU B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 569 removed outlier: 3.648A pdb=" N ASP B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS B 565 " --> pdb=" O GLU B 561 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 566 " --> pdb=" O ILE B 562 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 585 removed outlier: 4.048A pdb=" N ILE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 610 removed outlier: 3.518A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 removed outlier: 4.326A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 676 Processing helix chain 'B' and resid 683 through 705 Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.705A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 739 " --> pdb=" O HIS B 735 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 761 removed outlier: 3.559A pdb=" N THR B 761 " --> pdb=" O MET B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 766 Processing helix chain 'C' and resid 45 through 49 removed outlier: 4.043A pdb=" N GLU C 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.852A pdb=" N TYR C 138 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE C 139 " --> pdb=" O LYS C 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 135 through 139' Processing helix chain 'C' and resid 191 through 199 removed outlier: 3.549A pdb=" N SER C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 226 removed outlier: 3.966A pdb=" N ALA C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 3.771A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.664A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 276 removed outlier: 3.656A pdb=" N ILE C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.932A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.899A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.983A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.746A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 426 removed outlier: 3.985A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.604A pdb=" N SER C 457 " --> pdb=" O ARG C 453 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN C 458 " --> pdb=" O TRP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 494 removed outlier: 3.807A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.707A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 507 " --> pdb=" O PHE C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 4.078A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.610A pdb=" N LEU C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 569 removed outlier: 3.649A pdb=" N ASP C 564 " --> pdb=" O ARG C 560 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS C 565 " --> pdb=" O GLU C 561 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 566 " --> pdb=" O ILE C 562 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 567 " --> pdb=" O PHE C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 585 removed outlier: 4.049A pdb=" N ILE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 610 removed outlier: 3.518A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY C 610 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 removed outlier: 4.327A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 676 Processing helix chain 'C' and resid 683 through 705 Processing helix chain 'C' and resid 732 through 742 removed outlier: 3.706A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 739 " --> pdb=" O HIS C 735 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 761 removed outlier: 3.559A pdb=" N THR C 761 " --> pdb=" O MET C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 766 Processing helix chain 'D' and resid 45 through 49 removed outlier: 4.044A pdb=" N GLU D 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.852A pdb=" N TYR D 138 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE D 139 " --> pdb=" O LYS D 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 135 through 139' Processing helix chain 'D' and resid 191 through 199 removed outlier: 3.550A pdb=" N SER D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 3.968A pdb=" N ALA D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 3.770A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.665A pdb=" N ALA D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 276 removed outlier: 3.656A pdb=" N ILE D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 295 removed outlier: 3.932A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.899A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 removed outlier: 3.983A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.746A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 426 removed outlier: 3.986A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.604A pdb=" N SER D 457 " --> pdb=" O ARG D 453 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN D 458 " --> pdb=" O TRP D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 494 removed outlier: 3.808A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.708A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY D 507 " --> pdb=" O PHE D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 4.078A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 550 removed outlier: 3.611A pdb=" N LEU D 548 " --> pdb=" O GLY D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 569 removed outlier: 3.648A pdb=" N ASP D 564 " --> pdb=" O ARG D 560 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS D 565 " --> pdb=" O GLU D 561 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 566 " --> pdb=" O ILE D 562 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 567 " --> pdb=" O PHE D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 585 removed outlier: 4.048A pdb=" N ILE D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 585 " --> pdb=" O SER D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 610 removed outlier: 3.520A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY D 610 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 removed outlier: 4.326A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 676 Processing helix chain 'D' and resid 683 through 705 Processing helix chain 'D' and resid 732 through 742 removed outlier: 3.706A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA D 739 " --> pdb=" O HIS D 735 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 761 removed outlier: 3.559A pdb=" N THR D 761 " --> pdb=" O MET D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 766 Processing helix chain 'E' and resid 45 through 49 removed outlier: 4.043A pdb=" N GLU E 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 139 removed outlier: 3.853A pdb=" N TYR E 138 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE E 139 " --> pdb=" O LYS E 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 135 through 139' Processing helix chain 'E' and resid 191 through 199 removed outlier: 3.550A pdb=" N SER E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 3.967A pdb=" N ALA E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.771A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 removed outlier: 3.666A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 276 removed outlier: 3.656A pdb=" N ILE E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 295 removed outlier: 3.932A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.899A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 334 removed outlier: 3.983A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.745A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 426 removed outlier: 3.985A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.604A pdb=" N SER E 457 " --> pdb=" O ARG E 453 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN E 458 " --> pdb=" O TRP E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 494 removed outlier: 3.808A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.708A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY E 507 " --> pdb=" O PHE E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 4.079A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 550 removed outlier: 3.610A pdb=" N LEU E 548 " --> pdb=" O GLY E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 569 removed outlier: 3.648A pdb=" N ASP E 564 " --> pdb=" O ARG E 560 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS E 565 " --> pdb=" O GLU E 561 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA E 566 " --> pdb=" O ILE E 562 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG E 567 " --> pdb=" O PHE E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 585 removed outlier: 4.048A pdb=" N ILE E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA E 585 " --> pdb=" O SER E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 610 removed outlier: 3.519A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY E 610 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 removed outlier: 4.326A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 676 Processing helix chain 'E' and resid 683 through 705 Processing helix chain 'E' and resid 732 through 742 removed outlier: 3.706A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 739 " --> pdb=" O HIS E 735 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 761 removed outlier: 3.558A pdb=" N THR E 761 " --> pdb=" O MET E 757 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 766 Processing helix chain 'F' and resid 45 through 49 removed outlier: 4.043A pdb=" N GLU F 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 139 removed outlier: 3.853A pdb=" N TYR F 138 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE F 139 " --> pdb=" O LYS F 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 135 through 139' Processing helix chain 'F' and resid 191 through 199 removed outlier: 3.550A pdb=" N SER F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 226 removed outlier: 3.966A pdb=" N ALA F 214 " --> pdb=" O ARG F 210 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 removed outlier: 3.770A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.664A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA F 259 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 276 removed outlier: 3.656A pdb=" N ILE F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 295 removed outlier: 3.932A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN F 285 " --> pdb=" O GLU F 281 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.899A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 334 removed outlier: 3.983A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.745A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 426 removed outlier: 3.985A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.604A pdb=" N SER F 457 " --> pdb=" O ARG F 453 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN F 458 " --> pdb=" O TRP F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 494 removed outlier: 3.808A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.707A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY F 507 " --> pdb=" O PHE F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 4.079A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 550 removed outlier: 3.610A pdb=" N LEU F 548 " --> pdb=" O GLY F 544 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 569 removed outlier: 3.648A pdb=" N ASP F 564 " --> pdb=" O ARG F 560 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS F 565 " --> pdb=" O GLU F 561 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA F 566 " --> pdb=" O ILE F 562 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG F 567 " --> pdb=" O PHE F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 585 removed outlier: 4.048A pdb=" N ILE F 582 " --> pdb=" O GLU F 578 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 585 " --> pdb=" O SER F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 610 removed outlier: 3.518A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY F 610 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 removed outlier: 4.327A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 676 Processing helix chain 'F' and resid 683 through 705 Processing helix chain 'F' and resid 732 through 742 removed outlier: 3.706A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA F 739 " --> pdb=" O HIS F 735 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 761 removed outlier: 3.559A pdb=" N THR F 761 " --> pdb=" O MET F 757 " (cutoff:3.500A) Processing helix chain 'F' and resid 762 through 766 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 269 removed outlier: 6.201A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.454A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 517 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 269 removed outlier: 6.201A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.454A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR B 517 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 269 removed outlier: 6.202A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.453A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR C 517 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 269 removed outlier: 6.201A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.454A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR D 517 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 265 through 269 removed outlier: 6.200A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.454A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR E 517 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 265 through 269 removed outlier: 6.202A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.453A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR F 517 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2844 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.70 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 12083 1.37 - 1.52: 9425 1.52 - 1.66: 13706 1.66 - 1.80: 198 1.80 - 1.95: 102 Bond restraints: 35514 Sorted by residual: bond pdb=" C ASP F 169 " pdb=" N PRO F 170 " ideal model delta sigma weight residual 1.330 1.368 -0.038 1.23e-02 6.61e+03 9.31e+00 bond pdb=" C ASP E 169 " pdb=" N PRO E 170 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.23e-02 6.61e+03 9.15e+00 bond pdb=" C ASP C 169 " pdb=" N PRO C 170 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.23e-02 6.61e+03 9.07e+00 bond pdb=" C ASP D 169 " pdb=" N PRO D 170 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.23e-02 6.61e+03 8.90e+00 bond pdb=" C ASP A 169 " pdb=" N PRO A 170 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.23e-02 6.61e+03 8.83e+00 ... (remaining 35509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 47606 2.95 - 5.90: 364 5.90 - 8.85: 48 8.85 - 11.81: 18 11.81 - 14.76: 6 Bond angle restraints: 48042 Sorted by residual: angle pdb=" N GLU E 470 " pdb=" CA GLU E 470 " pdb=" C GLU E 470 " ideal model delta sigma weight residual 109.81 121.06 -11.25 1.53e+00 4.27e-01 5.40e+01 angle pdb=" N GLU B 470 " pdb=" CA GLU B 470 " pdb=" C GLU B 470 " ideal model delta sigma weight residual 109.81 121.05 -11.24 1.53e+00 4.27e-01 5.40e+01 angle pdb=" N GLU A 470 " pdb=" CA GLU A 470 " pdb=" C GLU A 470 " ideal model delta sigma weight residual 109.81 121.04 -11.23 1.53e+00 4.27e-01 5.39e+01 angle pdb=" N GLU D 470 " pdb=" CA GLU D 470 " pdb=" C GLU D 470 " ideal model delta sigma weight residual 109.81 121.02 -11.21 1.53e+00 4.27e-01 5.37e+01 angle pdb=" N GLU F 470 " pdb=" CA GLU F 470 " pdb=" C GLU F 470 " ideal model delta sigma weight residual 109.81 121.01 -11.20 1.53e+00 4.27e-01 5.36e+01 ... (remaining 48037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 19330 15.59 - 31.19: 1964 31.19 - 46.78: 504 46.78 - 62.38: 84 62.38 - 77.97: 42 Dihedral angle restraints: 21924 sinusoidal: 9204 harmonic: 12720 Sorted by residual: dihedral pdb=" CA GLU A 470 " pdb=" C GLU A 470 " pdb=" N VAL A 471 " pdb=" CA VAL A 471 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLU B 470 " pdb=" C GLU B 470 " pdb=" N VAL B 471 " pdb=" CA VAL B 471 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLU E 470 " pdb=" C GLU E 470 " pdb=" N VAL E 471 " pdb=" CA VAL E 471 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 21921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 4170 0.050 - 0.100: 1018 0.100 - 0.150: 218 0.150 - 0.200: 12 0.200 - 0.250: 18 Chirality restraints: 5436 Sorted by residual: chirality pdb=" CA GLU D 470 " pdb=" N GLU D 470 " pdb=" C GLU D 470 " pdb=" CB GLU D 470 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA GLU A 470 " pdb=" N GLU A 470 " pdb=" C GLU A 470 " pdb=" CB GLU A 470 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA GLU E 470 " pdb=" N GLU E 470 " pdb=" C GLU E 470 " pdb=" CB GLU E 470 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 5433 not shown) Planarity restraints: 6288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 517 " 0.021 2.00e-02 2.50e+03 2.50e-02 1.25e+01 pdb=" CG TYR D 517 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR D 517 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR D 517 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR D 517 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR D 517 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 517 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR D 517 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 517 " -0.021 2.00e-02 2.50e+03 2.50e-02 1.25e+01 pdb=" CG TYR F 517 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR F 517 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR F 517 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR F 517 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR F 517 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR F 517 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR F 517 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 517 " -0.021 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" CG TYR A 517 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR A 517 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 517 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 517 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 517 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 517 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 517 " 0.003 2.00e-02 2.50e+03 ... (remaining 6285 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 372 2.61 - 3.18: 29206 3.18 - 3.75: 51643 3.75 - 4.33: 66945 4.33 - 4.90: 108585 Nonbonded interactions: 256751 Sorted by model distance: nonbonded pdb=" O ARG A 745 " pdb=" NE2 GLN F 763 " model vdw 2.035 3.120 nonbonded pdb=" O1A AGS F 902 " pdb="MG MG F 903 " model vdw 2.088 2.170 nonbonded pdb=" O1A AGS E 902 " pdb="MG MG E 903 " model vdw 2.088 2.170 nonbonded pdb=" O1A AGS D 902 " pdb="MG MG D 903 " model vdw 2.088 2.170 nonbonded pdb=" O1A AGS C 902 " pdb="MG MG C 903 " model vdw 2.088 2.170 ... (remaining 256746 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 33.620 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 : 0.003 0.046 35514 Z= 0.163 Angle : 0.778 14.758 48042 Z= 0.435 Chirality : 0.047 0.250 5436 Planarity : 0.004 0.046 6288 Dihedral : 13.592 77.971 13680 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.12), residues: 4398 helix: 0.22 (0.14), residues: 1458 sheet: 0.27 (0.26), residues: 402 loop : -2.35 (0.11), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 93 TYR 0.059 0.004 TYR F 517 PHE 0.026 0.002 PHE C 758 TRP 0.040 0.004 TRP D 454 HIS 0.001 0.000 HIS D 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (35514) covalent geometry : angle 0.77819 / 0.43 (48042) hydrogen bonds : bond 0.23606 / 15.92 ( 984) hydrogen bonds : angle 5.93136 / 4.10 ( 2844) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.8825 (m-80) cc_final: 0.8568 (m-80) REVERT: A 338 ARG cc_start: 0.7973 (pmt-80) cc_final: 0.6880 (pmt-80) REVERT: A 562 ILE cc_start: 0.6636 (mt) cc_final: 0.6178 (mt) REVERT: A 678 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7879 (pmm) REVERT: B 203 TYR cc_start: 0.8835 (m-80) cc_final: 0.8140 (m-80) REVERT: C 203 TYR cc_start: 0.8449 (m-80) cc_final: 0.7275 (m-80) REVERT: C 217 LYS cc_start: 0.9429 (mttt) cc_final: 0.9142 (mmtm) REVERT: C 276 SER cc_start: 0.8673 (p) cc_final: 0.8322 (p) REVERT: C 509 THR cc_start: 0.9324 (m) cc_final: 0.9117 (m) REVERT: E 205 ASP cc_start: 0.8642 (m-30) cc_final: 0.8231 (m-30) REVERT: E 217 LYS cc_start: 0.9504 (mttt) cc_final: 0.9230 (mttp) REVERT: F 562 ILE cc_start: 0.6917 (mt) cc_final: 0.6437 (mt) outliers start: 1 outliers final: 0 residues processed: 372 average time/residue: 0.2196 time to fit residues: 133.5516 Evaluate side-chains 259 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.5980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.160362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.112011 restraints weight = 73695.857| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 4.14 r_work: 0.3108 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 35514 Z= 0.162 Angle : 0.611 8.835 48042 Z= 0.308 Chirality : 0.046 0.185 5436 Planarity : 0.004 0.051 6288 Dihedral : 5.454 51.977 4893 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.61 % Allowed : 7.93 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.13), residues: 4398 helix: 0.68 (0.14), residues: 1590 sheet: 1.24 (0.28), residues: 390 loop : -2.23 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 365 TYR 0.012 0.002 TYR D 495 PHE 0.016 0.001 PHE C 552 TRP 0.022 0.003 TRP E 454 HIS 0.003 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (35514) covalent geometry : angle 0.61118 / 0.31 (48042) hydrogen bonds : bond 0.04029 / 2.73 ( 984) hydrogen bonds : angle 4.26535 / 2.89 ( 2844) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 271 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: A 203 TYR cc_start: 0.9127 (m-80) cc_final: 0.8616 (m-80) REVERT: A 454 TRP cc_start: 0.9162 (t-100) cc_final: 0.8912 (t-100) REVERT: A 551 TRP cc_start: 0.8586 (t-100) cc_final: 0.8303 (t-100) REVERT: A 678 MET cc_start: 0.8387 (pmm) cc_final: 0.8095 (pmm) REVERT: A 758 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8370 (t80) REVERT: B 203 TYR cc_start: 0.9294 (m-80) cc_final: 0.9060 (m-80) REVERT: B 454 TRP cc_start: 0.9348 (t-100) cc_final: 0.8878 (t-100) REVERT: B 470 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: B 563 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8009 (t80) REVERT: C 203 TYR cc_start: 0.8789 (m-80) cc_final: 0.8179 (m-80) REVERT: C 217 LYS cc_start: 0.9588 (mttt) cc_final: 0.9372 (mmmm) REVERT: C 315 LYS cc_start: 0.9077 (ptpp) cc_final: 0.8711 (pttp) REVERT: C 563 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.7828 (t80) REVERT: C 618 PHE cc_start: 0.8263 (t80) cc_final: 0.8037 (t80) REVERT: C 678 MET cc_start: 0.8322 (pmm) cc_final: 0.8043 (pmm) REVERT: C 758 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8381 (t80) REVERT: D 203 TYR cc_start: 0.8941 (m-10) cc_final: 0.8282 (m-80) REVERT: D 551 TRP cc_start: 0.8486 (t-100) cc_final: 0.8147 (t-100) REVERT: D 604 ILE cc_start: 0.9402 (mm) cc_final: 0.9181 (mm) REVERT: D 608 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8782 (ptm) REVERT: D 678 MET cc_start: 0.8409 (pmm) cc_final: 0.8153 (pmm) REVERT: D 758 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8369 (t80) REVERT: E 217 LYS cc_start: 0.9617 (mttt) cc_final: 0.9382 (mtmm) REVERT: E 563 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8203 (t80) REVERT: E 678 MET cc_start: 0.8407 (pmm) cc_final: 0.8162 (pmm) REVERT: F 203 TYR cc_start: 0.8934 (m-80) cc_final: 0.8719 (m-80) REVERT: F 454 TRP cc_start: 0.9317 (t-100) cc_final: 0.8913 (t-100) REVERT: F 551 TRP cc_start: 0.8412 (t-100) cc_final: 0.8172 (t-100) REVERT: F 563 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8165 (t80) outliers start: 23 outliers final: 10 residues processed: 285 average time/residue: 0.1955 time to fit residues: 96.2142 Evaluate side-chains 255 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 236 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 758 PHE Chi-restraints excluded: chain E residue 563 PHE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 563 PHE Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 169 optimal weight: 0.9990 chunk 278 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 364 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 326 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 202 optimal weight: 0.2980 chunk 137 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN A 296 ASN B 21 ASN ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN E 21 ASN F 21 ASN F 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.148931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098864 restraints weight = 76243.970| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.97 r_work: 0.2991 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35514 Z= 0.163 Angle : 0.551 10.946 48042 Z= 0.272 Chirality : 0.044 0.229 5436 Planarity : 0.004 0.053 6288 Dihedral : 5.366 51.233 4890 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.65 % Allowed : 9.48 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.91 (0.13), residues: 4398 helix: 0.91 (0.13), residues: 1650 sheet: 1.07 (0.27), residues: 396 loop : -2.16 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 22 TYR 0.013 0.001 TYR C 495 PHE 0.011 0.001 PHE C 682 TRP 0.023 0.002 TRP E 551 HIS 0.004 0.001 HIS E 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (35514) covalent geometry : angle 0.55129 / 0.27 (48042) hydrogen bonds : bond 0.03864 / 2.59 ( 984) hydrogen bonds : angle 3.90072 / 2.64 ( 2844) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 242 time to evaluate : 1.338 Fit side-chains REVERT: A 315 LYS cc_start: 0.9044 (ptpp) cc_final: 0.8713 (pttp) REVERT: A 332 MET cc_start: 0.9410 (mtp) cc_final: 0.9115 (mtp) REVERT: A 454 TRP cc_start: 0.9265 (t-100) cc_final: 0.8944 (t-100) REVERT: A 551 TRP cc_start: 0.8630 (t-100) cc_final: 0.8279 (t-100) REVERT: A 678 MET cc_start: 0.8468 (pmm) cc_final: 0.8247 (pmm) REVERT: A 758 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8447 (t80) REVERT: B 454 TRP cc_start: 0.9422 (t-100) cc_final: 0.8763 (t-100) REVERT: B 563 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8063 (t80) REVERT: C 203 TYR cc_start: 0.8982 (m-80) cc_final: 0.8380 (m-80) REVERT: C 315 LYS cc_start: 0.9080 (ptpp) cc_final: 0.8726 (pttp) REVERT: C 551 TRP cc_start: 0.7979 (t-100) cc_final: 0.7656 (t-100) REVERT: C 563 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8066 (t80) REVERT: C 618 PHE cc_start: 0.8430 (t80) cc_final: 0.8078 (t80) REVERT: C 678 MET cc_start: 0.8245 (pmm) cc_final: 0.8037 (pmm) REVERT: D 203 TYR cc_start: 0.9066 (m-10) cc_final: 0.8804 (m-80) REVERT: D 315 LYS cc_start: 0.9141 (ptpp) cc_final: 0.8850 (pttp) REVERT: D 442 MET cc_start: 0.9225 (mpp) cc_final: 0.8967 (pmm) REVERT: D 551 TRP cc_start: 0.8424 (t-100) cc_final: 0.8078 (t-100) REVERT: D 604 ILE cc_start: 0.9350 (mm) cc_final: 0.9138 (mt) REVERT: D 608 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8864 (ptm) REVERT: D 678 MET cc_start: 0.8402 (pmm) cc_final: 0.8114 (pmm) REVERT: D 757 MET cc_start: 0.9206 (tmm) cc_final: 0.8986 (tmm) REVERT: E 203 TYR cc_start: 0.9178 (m-10) cc_final: 0.8502 (m-80) REVERT: E 315 LYS cc_start: 0.9124 (ptpp) cc_final: 0.8868 (pttp) REVERT: E 563 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8347 (t80) REVERT: E 611 MET cc_start: 0.8147 (mmm) cc_final: 0.7900 (mtp) REVERT: E 678 MET cc_start: 0.8260 (pmm) cc_final: 0.7945 (pmm) REVERT: F 454 TRP cc_start: 0.9411 (t-100) cc_final: 0.8926 (t-100) REVERT: F 551 TRP cc_start: 0.8319 (t-100) cc_final: 0.7642 (t-100) REVERT: F 563 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.7981 (t80) REVERT: F 757 MET cc_start: 0.9237 (tmm) cc_final: 0.9029 (tmm) outliers start: 62 outliers final: 27 residues processed: 296 average time/residue: 0.1883 time to fit residues: 96.6014 Evaluate side-chains 262 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 563 PHE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 563 PHE Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 248 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 chunk 358 optimal weight: 6.9990 chunk 309 optimal weight: 0.0870 chunk 132 optimal weight: 0.9980 chunk 428 optimal weight: 0.9990 chunk 391 optimal weight: 0.0040 chunk 108 optimal weight: 0.4980 chunk 112 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 overall best weight: 0.4570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.158123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107786 restraints weight = 72711.144| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 4.08 r_work: 0.2962 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35514 Z= 0.098 Angle : 0.508 9.078 48042 Z= 0.248 Chirality : 0.043 0.141 5436 Planarity : 0.003 0.054 6288 Dihedral : 5.288 51.390 4890 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.14 % Allowed : 11.00 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.76 (0.13), residues: 4398 helix: 1.15 (0.13), residues: 1638 sheet: 1.08 (0.27), residues: 390 loop : -2.12 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 210 TYR 0.011 0.001 TYR C 517 PHE 0.010 0.001 PHE C 563 TRP 0.021 0.001 TRP E 551 HIS 0.002 0.000 HIS D 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (35514) covalent geometry : angle 0.50777 / 0.25 (48042) hydrogen bonds : bond 0.03086 / 2.07 ( 984) hydrogen bonds : angle 3.67178 / 2.48 ( 2844) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 1.529 Fit side-chains REVERT: A 315 LYS cc_start: 0.9023 (ptpp) cc_final: 0.8559 (pttp) REVERT: A 332 MET cc_start: 0.9361 (mtp) cc_final: 0.9027 (mtp) REVERT: A 454 TRP cc_start: 0.9286 (t-100) cc_final: 0.9054 (t-100) REVERT: A 758 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8414 (t80) REVERT: B 158 MET cc_start: 0.1852 (pmm) cc_final: 0.1642 (pmm) REVERT: B 454 TRP cc_start: 0.9418 (t-100) cc_final: 0.8755 (t-100) REVERT: B 550 MET cc_start: 0.6959 (ppp) cc_final: 0.6736 (ppp) REVERT: B 563 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8220 (t80) REVERT: C 203 TYR cc_start: 0.8847 (m-80) cc_final: 0.8581 (m-80) REVERT: C 315 LYS cc_start: 0.9099 (ptpp) cc_final: 0.8692 (pttp) REVERT: C 563 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8048 (t80) REVERT: C 618 PHE cc_start: 0.8315 (t80) cc_final: 0.7908 (t80) REVERT: C 678 MET cc_start: 0.8193 (pmm) cc_final: 0.7813 (pmm) REVERT: D 203 TYR cc_start: 0.9062 (m-10) cc_final: 0.8801 (m-80) REVERT: D 315 LYS cc_start: 0.9112 (ptpp) cc_final: 0.8661 (pttp) REVERT: D 551 TRP cc_start: 0.7915 (t-100) cc_final: 0.7710 (t-100) REVERT: D 608 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8897 (ptm) REVERT: D 678 MET cc_start: 0.8312 (pmm) cc_final: 0.8054 (pmm) REVERT: D 758 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8506 (t80) REVERT: E 203 TYR cc_start: 0.9356 (m-10) cc_final: 0.8945 (m-80) REVERT: E 315 LYS cc_start: 0.9090 (ptpp) cc_final: 0.8724 (pttp) REVERT: E 470 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: E 563 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8365 (t80) REVERT: F 315 LYS cc_start: 0.9034 (ptpp) cc_final: 0.8587 (pttp) REVERT: F 454 TRP cc_start: 0.9440 (t-100) cc_final: 0.8835 (t-100) REVERT: F 551 TRP cc_start: 0.7905 (t-100) cc_final: 0.7316 (t-100) REVERT: F 563 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.7866 (t80) REVERT: F 757 MET cc_start: 0.9226 (tmm) cc_final: 0.9009 (tmm) outliers start: 43 outliers final: 22 residues processed: 269 average time/residue: 0.1929 time to fit residues: 90.8285 Evaluate side-chains 250 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 758 PHE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 563 PHE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 563 PHE Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 10.0000 chunk 229 optimal weight: 20.0000 chunk 353 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 300 optimal weight: 0.0870 chunk 210 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 97 optimal weight: 0.0030 chunk 386 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 overall best weight: 2.2172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN B 21 ASN B 296 ASN B 337 GLN C 337 GLN D 21 ASN D 296 ASN E 21 ASN F 21 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.146195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.094995 restraints weight = 76403.439| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.86 r_work: 0.2904 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 35514 Z= 0.165 Angle : 0.571 8.448 48042 Z= 0.275 Chirality : 0.044 0.141 5436 Planarity : 0.003 0.052 6288 Dihedral : 5.357 50.181 4890 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.65 % Allowed : 11.61 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.53 (0.13), residues: 4398 helix: 1.28 (0.13), residues: 1674 sheet: 1.05 (0.27), residues: 390 loop : -1.95 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 599 TYR 0.010 0.001 TYR A 244 PHE 0.010 0.001 PHE C 563 TRP 0.025 0.002 TRP A 551 HIS 0.004 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (35514) covalent geometry : angle 0.57109 / 0.27 (48042) hydrogen bonds : bond 0.03366 / 2.25 ( 984) hydrogen bonds : angle 3.66267 / 2.48 ( 2844) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 228 time to evaluate : 1.361 Fit side-chains REVERT: A 84 MET cc_start: -0.2948 (tpp) cc_final: -0.3235 (tpp) REVERT: A 315 LYS cc_start: 0.9150 (ptpp) cc_final: 0.8788 (pttp) REVERT: A 332 MET cc_start: 0.9388 (mtp) cc_final: 0.9021 (mtp) REVERT: A 454 TRP cc_start: 0.9364 (t-100) cc_final: 0.9102 (t-100) REVERT: A 551 TRP cc_start: 0.8464 (t-100) cc_final: 0.7970 (t-100) REVERT: B 315 LYS cc_start: 0.9097 (pttm) cc_final: 0.8866 (pttp) REVERT: B 392 ASP cc_start: 0.9139 (p0) cc_final: 0.8937 (p0) REVERT: B 449 MET cc_start: 0.9090 (mmm) cc_final: 0.8854 (tpp) REVERT: B 454 TRP cc_start: 0.9461 (t-100) cc_final: 0.8775 (t-100) REVERT: B 563 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8261 (t80) REVERT: B 678 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8164 (pmm) REVERT: B 689 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8645 (tm-30) REVERT: C 315 LYS cc_start: 0.9123 (ptpp) cc_final: 0.8728 (pttp) REVERT: C 551 TRP cc_start: 0.8106 (t-100) cc_final: 0.7251 (t-100) REVERT: C 563 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8327 (t80) REVERT: C 618 PHE cc_start: 0.8488 (t80) cc_final: 0.8068 (t80) REVERT: C 678 MET cc_start: 0.8204 (pmm) cc_final: 0.7910 (pmm) REVERT: D 203 TYR cc_start: 0.9151 (m-10) cc_final: 0.8877 (m-80) REVERT: D 315 LYS cc_start: 0.9203 (ptpp) cc_final: 0.8839 (pttp) REVERT: D 608 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8861 (ptm) REVERT: D 678 MET cc_start: 0.8147 (pmm) cc_final: 0.7904 (pmm) REVERT: E 203 TYR cc_start: 0.9358 (m-10) cc_final: 0.9001 (m-80) REVERT: E 315 LYS cc_start: 0.9144 (ptpp) cc_final: 0.8842 (pttp) REVERT: E 392 ASP cc_start: 0.9115 (p0) cc_final: 0.8909 (p0) REVERT: E 563 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8523 (t80) REVERT: F 203 TYR cc_start: 0.9339 (m-80) cc_final: 0.9131 (m-80) REVERT: F 315 LYS cc_start: 0.9144 (ptpp) cc_final: 0.8645 (pttp) REVERT: F 551 TRP cc_start: 0.8319 (t-100) cc_final: 0.8089 (t-100) REVERT: F 563 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.7935 (t80) outliers start: 62 outliers final: 39 residues processed: 279 average time/residue: 0.1908 time to fit residues: 92.0656 Evaluate side-chains 255 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 210 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 563 PHE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 563 PHE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 678 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 203 optimal weight: 8.9990 chunk 60 optimal weight: 0.1980 chunk 279 optimal weight: 0.6980 chunk 347 optimal weight: 0.7980 chunk 277 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 408 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 234 optimal weight: 30.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.147095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.096085 restraints weight = 76137.520| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.91 r_work: 0.2917 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35514 Z= 0.107 Angle : 0.526 10.177 48042 Z= 0.248 Chirality : 0.043 0.177 5436 Planarity : 0.003 0.054 6288 Dihedral : 5.315 50.858 4890 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.41 % Allowed : 12.46 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.42 (0.13), residues: 4398 helix: 1.40 (0.13), residues: 1668 sheet: 1.02 (0.27), residues: 390 loop : -1.89 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 766 TYR 0.014 0.001 TYR A 203 PHE 0.011 0.001 PHE C 563 TRP 0.027 0.002 TRP E 551 HIS 0.002 0.000 HIS D 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (35514) covalent geometry : angle 0.52606 / 0.25 (48042) hydrogen bonds : bond 0.02815 / 1.89 ( 984) hydrogen bonds : angle 3.53168 / 2.39 ( 2844) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 1.311 Fit side-chains revert: symmetry clash REVERT: A 315 LYS cc_start: 0.9110 (ptpp) cc_final: 0.8752 (pttp) REVERT: A 332 MET cc_start: 0.9383 (mtp) cc_final: 0.9003 (mtp) REVERT: A 454 TRP cc_start: 0.9373 (t-100) cc_final: 0.9092 (t-100) REVERT: A 551 TRP cc_start: 0.8241 (t-100) cc_final: 0.7552 (t-100) REVERT: A 678 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8067 (pmm) REVERT: B 449 MET cc_start: 0.9107 (mmm) cc_final: 0.8857 (tpp) REVERT: B 454 TRP cc_start: 0.9451 (t-100) cc_final: 0.8746 (t-100) REVERT: B 550 MET cc_start: 0.6863 (ppp) cc_final: 0.6651 (ppp) REVERT: B 563 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8366 (t80) REVERT: B 689 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8648 (tm-30) REVERT: C 315 LYS cc_start: 0.9114 (ptpp) cc_final: 0.8732 (pttp) REVERT: C 550 MET cc_start: 0.7125 (ppp) cc_final: 0.6774 (ppp) REVERT: C 551 TRP cc_start: 0.7967 (t-100) cc_final: 0.7306 (t-100) REVERT: C 563 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.8219 (t80) REVERT: C 618 PHE cc_start: 0.8388 (t80) cc_final: 0.7978 (t80) REVERT: C 678 MET cc_start: 0.8209 (pmm) cc_final: 0.7963 (pmm) REVERT: D 203 TYR cc_start: 0.9140 (m-10) cc_final: 0.8829 (m-80) REVERT: D 315 LYS cc_start: 0.9173 (ptpp) cc_final: 0.8837 (pttp) REVERT: D 466 GLU cc_start: 0.8854 (mp0) cc_final: 0.8621 (mp0) REVERT: D 551 TRP cc_start: 0.8127 (t-100) cc_final: 0.7251 (t-100) REVERT: D 608 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8863 (ptm) REVERT: E 203 TYR cc_start: 0.9339 (m-10) cc_final: 0.8879 (m-80) REVERT: E 315 LYS cc_start: 0.9137 (ptpp) cc_final: 0.8834 (pttp) REVERT: E 442 MET cc_start: 0.9321 (mpp) cc_final: 0.9107 (pmm) REVERT: E 563 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.8484 (t80) REVERT: E 678 MET cc_start: 0.8187 (pmm) cc_final: 0.7923 (pmm) REVERT: F 203 TYR cc_start: 0.9316 (m-80) cc_final: 0.9098 (m-80) REVERT: F 315 LYS cc_start: 0.9148 (ptpp) cc_final: 0.8693 (pttp) REVERT: F 546 GLU cc_start: 0.9246 (tt0) cc_final: 0.8885 (mt-10) REVERT: F 563 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.7850 (t80) outliers start: 53 outliers final: 39 residues processed: 261 average time/residue: 0.1907 time to fit residues: 86.3317 Evaluate side-chains 256 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 563 PHE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 563 PHE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 678 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 305 optimal weight: 30.0000 chunk 322 optimal weight: 10.0000 chunk 385 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 226 optimal weight: 8.9990 chunk 422 optimal weight: 10.0000 chunk 359 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 349 optimal weight: 8.9990 chunk 230 optimal weight: 0.9980 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 327 GLN B 337 GLN C 296 ASN D 337 GLN E 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.141761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.088273 restraints weight = 76806.286| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.66 r_work: 0.2710 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 35514 Z= 0.304 Angle : 0.707 12.900 48042 Z= 0.338 Chirality : 0.048 0.201 5436 Planarity : 0.004 0.050 6288 Dihedral : 5.730 52.356 4890 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.62 % Allowed : 12.73 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.41 (0.13), residues: 4398 helix: 1.21 (0.13), residues: 1704 sheet: 0.96 (0.27), residues: 390 loop : -1.73 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 465 TYR 0.012 0.002 TYR E 203 PHE 0.016 0.002 PHE A 506 TRP 0.028 0.003 TRP B 551 HIS 0.004 0.001 HIS D 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00707 / 0.30 (35514) covalent geometry : angle 0.70746 / 0.34 (48042) hydrogen bonds : bond 0.04310 / 2.87 ( 984) hydrogen bonds : angle 3.99677 / 2.73 ( 2844) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 211 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.2242 (pmm) cc_final: 0.1983 (pmm) REVERT: A 449 MET cc_start: 0.9026 (mmm) cc_final: 0.8672 (tpp) REVERT: A 454 TRP cc_start: 0.9426 (t-100) cc_final: 0.9154 (t-100) REVERT: A 464 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9440 (mm) REVERT: A 551 TRP cc_start: 0.8234 (t-100) cc_final: 0.7583 (t-100) REVERT: A 678 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8094 (pmm) REVERT: A 689 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8723 (tm-30) REVERT: B 449 MET cc_start: 0.9010 (mmm) cc_final: 0.8331 (tpp) REVERT: B 464 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9470 (mm) REVERT: B 689 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8631 (tm-30) REVERT: C 315 LYS cc_start: 0.9072 (ptpp) cc_final: 0.8798 (pttm) REVERT: C 449 MET cc_start: 0.9154 (tpp) cc_final: 0.8939 (tpp) REVERT: C 466 GLU cc_start: 0.9005 (mp0) cc_final: 0.8559 (mp0) REVERT: C 550 MET cc_start: 0.7082 (ppp) cc_final: 0.6780 (ppp) REVERT: C 551 TRP cc_start: 0.8220 (t-100) cc_final: 0.7690 (t-100) REVERT: C 561 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8047 (pm20) REVERT: C 689 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8719 (tm-30) REVERT: D 466 GLU cc_start: 0.9042 (mp0) cc_final: 0.8776 (mp0) REVERT: D 551 TRP cc_start: 0.8173 (t-100) cc_final: 0.7384 (t-100) REVERT: D 618 PHE cc_start: 0.8735 (t80) cc_final: 0.8473 (t80) REVERT: E 158 MET cc_start: 0.2591 (pmm) cc_final: 0.2306 (pmm) REVERT: E 203 TYR cc_start: 0.9271 (m-10) cc_final: 0.8694 (m-80) REVERT: E 449 MET cc_start: 0.9061 (mmm) cc_final: 0.8554 (tpp) REVERT: E 464 LEU cc_start: 0.9690 (OUTLIER) cc_final: 0.9482 (mm) REVERT: E 678 MET cc_start: 0.8321 (pmm) cc_final: 0.8069 (pmm) REVERT: E 689 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8583 (tm-30) REVERT: F 203 TYR cc_start: 0.9308 (m-80) cc_final: 0.8950 (m-80) REVERT: F 315 LYS cc_start: 0.9209 (ptpp) cc_final: 0.8789 (pttp) REVERT: F 546 GLU cc_start: 0.9265 (tt0) cc_final: 0.8934 (mt-10) REVERT: F 551 TRP cc_start: 0.7968 (t-100) cc_final: 0.7718 (t-100) outliers start: 61 outliers final: 39 residues processed: 259 average time/residue: 0.2035 time to fit residues: 89.3077 Evaluate side-chains 246 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 563 PHE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 426 optimal weight: 2.9990 chunk 302 optimal weight: 4.9990 chunk 323 optimal weight: 5.9990 chunk 328 optimal weight: 0.8980 chunk 263 optimal weight: 6.9990 chunk 160 optimal weight: 0.1980 chunk 8 optimal weight: 9.9990 chunk 353 optimal weight: 0.6980 chunk 273 optimal weight: 0.2980 chunk 45 optimal weight: 7.9990 chunk 410 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN D 327 GLN E 327 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.144377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.092701 restraints weight = 75714.078| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.76 r_work: 0.2859 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35514 Z= 0.112 Angle : 0.556 10.019 48042 Z= 0.264 Chirality : 0.044 0.182 5436 Planarity : 0.003 0.058 6288 Dihedral : 5.581 50.809 4890 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.49 % Allowed : 13.34 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.21 (0.13), residues: 4398 helix: 1.48 (0.13), residues: 1686 sheet: 1.04 (0.27), residues: 372 loop : -1.66 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 465 TYR 0.013 0.001 TYR C 244 PHE 0.018 0.001 PHE A 363 TRP 0.034 0.002 TRP E 551 HIS 0.002 0.000 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (35514) covalent geometry : angle 0.55590 / 0.26 (48042) hydrogen bonds : bond 0.03139 / 2.09 ( 984) hydrogen bonds : angle 3.59494 / 2.44 ( 2844) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 217 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.2213 (pmm) cc_final: 0.1979 (pmm) REVERT: A 315 LYS cc_start: 0.9173 (ptpp) cc_final: 0.8816 (pttp) REVERT: A 327 GLN cc_start: 0.9487 (OUTLIER) cc_final: 0.9143 (tp-100) REVERT: A 449 MET cc_start: 0.9045 (mmm) cc_final: 0.8653 (tpp) REVERT: A 454 TRP cc_start: 0.9421 (t-100) cc_final: 0.9115 (t-100) REVERT: A 464 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9391 (mm) REVERT: A 551 TRP cc_start: 0.8155 (t-100) cc_final: 0.7865 (t-100) REVERT: A 678 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8184 (pmm) REVERT: A 689 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8707 (tm-30) REVERT: B 454 TRP cc_start: 0.9432 (t-100) cc_final: 0.8714 (t-100) REVERT: B 464 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9340 (mm) REVERT: B 560 ARG cc_start: 0.7799 (mmm-85) cc_final: 0.7464 (mmm-85) REVERT: B 563 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.8418 (t80) REVERT: B 678 MET cc_start: 0.8527 (mpp) cc_final: 0.8315 (mpp) REVERT: B 689 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8601 (tm-30) REVERT: B 740 MET cc_start: 0.9479 (tpp) cc_final: 0.9178 (mmm) REVERT: C 315 LYS cc_start: 0.9144 (ptpp) cc_final: 0.8718 (pttp) REVERT: C 466 GLU cc_start: 0.8860 (mp0) cc_final: 0.8653 (mp0) REVERT: C 561 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: D 315 LYS cc_start: 0.9204 (ptpp) cc_final: 0.8853 (pttp) REVERT: D 327 GLN cc_start: 0.9467 (OUTLIER) cc_final: 0.9115 (tp-100) REVERT: D 464 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9446 (mm) REVERT: D 466 GLU cc_start: 0.8979 (mp0) cc_final: 0.8742 (mp0) REVERT: D 551 TRP cc_start: 0.8084 (t-100) cc_final: 0.7422 (t-100) REVERT: E 158 MET cc_start: 0.2696 (pmm) cc_final: 0.2403 (pmm) REVERT: E 203 TYR cc_start: 0.9262 (m-10) cc_final: 0.8695 (m-80) REVERT: E 315 LYS cc_start: 0.9253 (ptpp) cc_final: 0.8938 (pttp) REVERT: E 449 MET cc_start: 0.9109 (mmm) cc_final: 0.8736 (tpp) REVERT: E 464 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9349 (mm) REVERT: E 678 MET cc_start: 0.8345 (pmm) cc_final: 0.8001 (pmm) REVERT: E 689 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8522 (tm-30) REVERT: E 740 MET cc_start: 0.9446 (tpp) cc_final: 0.9210 (mmm) REVERT: F 203 TYR cc_start: 0.9287 (m-80) cc_final: 0.8962 (m-80) REVERT: F 315 LYS cc_start: 0.9235 (ptpp) cc_final: 0.8804 (pttp) REVERT: F 464 LEU cc_start: 0.9681 (OUTLIER) cc_final: 0.9456 (mm) REVERT: F 551 TRP cc_start: 0.7955 (t-100) cc_final: 0.7744 (t-100) REVERT: F 561 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: F 563 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.8188 (t80) REVERT: F 678 MET cc_start: 0.8537 (mpp) cc_final: 0.8337 (mpp) outliers start: 56 outliers final: 36 residues processed: 266 average time/residue: 0.1979 time to fit residues: 89.0482 Evaluate side-chains 254 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 563 PHE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 563 PHE Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 116 optimal weight: 10.0000 chunk 423 optimal weight: 10.0000 chunk 342 optimal weight: 0.9980 chunk 422 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 118 optimal weight: 0.0170 chunk 94 optimal weight: 7.9990 chunk 391 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 226 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 overall best weight: 1.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN D 327 GLN D 337 GLN F 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.144128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.092501 restraints weight = 75649.336| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.74 r_work: 0.2839 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35514 Z= 0.140 Angle : 0.564 9.534 48042 Z= 0.267 Chirality : 0.044 0.188 5436 Planarity : 0.003 0.055 6288 Dihedral : 5.532 50.677 4890 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.44 % Allowed : 13.47 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.16 (0.13), residues: 4398 helix: 1.51 (0.13), residues: 1692 sheet: 0.92 (0.26), residues: 390 loop : -1.63 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 560 TYR 0.016 0.001 TYR B 203 PHE 0.016 0.001 PHE A 363 TRP 0.037 0.002 TRP E 551 HIS 0.002 0.000 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (35514) covalent geometry : angle 0.56364 / 0.27 (48042) hydrogen bonds : bond 0.03166 / 2.11 ( 984) hydrogen bonds : angle 3.54062 / 2.40 ( 2844) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 213 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.2157 (pmm) cc_final: 0.1893 (pmm) REVERT: A 327 GLN cc_start: 0.9430 (OUTLIER) cc_final: 0.8984 (tp40) REVERT: A 449 MET cc_start: 0.9063 (mmm) cc_final: 0.8709 (tpp) REVERT: A 454 TRP cc_start: 0.9426 (t-100) cc_final: 0.9131 (t-100) REVERT: A 464 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9409 (mm) REVERT: A 551 TRP cc_start: 0.8145 (t-100) cc_final: 0.7870 (t-100) REVERT: A 678 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8200 (pmm) REVERT: A 689 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8696 (tm-30) REVERT: B 454 TRP cc_start: 0.9437 (t-100) cc_final: 0.8727 (t-100) REVERT: B 563 PHE cc_start: 0.9413 (OUTLIER) cc_final: 0.8402 (t80) REVERT: B 678 MET cc_start: 0.8537 (mpp) cc_final: 0.8256 (mmm) REVERT: B 689 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8602 (tm-30) REVERT: B 740 MET cc_start: 0.9488 (tpp) cc_final: 0.9185 (mmm) REVERT: C 466 GLU cc_start: 0.8922 (mp0) cc_final: 0.8527 (mp0) REVERT: C 561 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: C 563 PHE cc_start: 0.9447 (OUTLIER) cc_final: 0.8287 (t80) REVERT: C 678 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8500 (mpp) REVERT: D 315 LYS cc_start: 0.9184 (ptpp) cc_final: 0.8931 (pttp) REVERT: D 464 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9483 (mm) REVERT: D 466 GLU cc_start: 0.9015 (mp0) cc_final: 0.8765 (mp0) REVERT: D 551 TRP cc_start: 0.8110 (t-100) cc_final: 0.7442 (t-100) REVERT: E 158 MET cc_start: 0.2653 (pmm) cc_final: 0.2340 (pmm) REVERT: E 203 TYR cc_start: 0.9244 (m-10) cc_final: 0.8711 (m-80) REVERT: E 315 LYS cc_start: 0.9233 (ptpp) cc_final: 0.8997 (pttp) REVERT: E 449 MET cc_start: 0.9125 (mmm) cc_final: 0.8660 (tpp) REVERT: E 464 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9348 (mm) REVERT: E 678 MET cc_start: 0.8305 (pmm) cc_final: 0.7965 (pmm) REVERT: E 689 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8533 (tm-30) REVERT: E 740 MET cc_start: 0.9454 (tpp) cc_final: 0.9213 (mmm) REVERT: F 203 TYR cc_start: 0.9274 (m-80) cc_final: 0.8939 (m-80) REVERT: F 315 LYS cc_start: 0.9237 (ptpp) cc_final: 0.8803 (pttp) REVERT: F 464 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9452 (mm) REVERT: F 551 TRP cc_start: 0.7995 (t-100) cc_final: 0.7712 (t-100) REVERT: F 561 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8097 (pm20) REVERT: F 563 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8225 (t80) REVERT: F 611 MET cc_start: 0.8388 (mmm) cc_final: 0.7834 (mmm) outliers start: 54 outliers final: 36 residues processed: 260 average time/residue: 0.1852 time to fit residues: 82.2478 Evaluate side-chains 255 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 563 PHE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 563 PHE Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 218 optimal weight: 3.9990 chunk 283 optimal weight: 6.9990 chunk 234 optimal weight: 40.0000 chunk 399 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 202 optimal weight: 6.9990 chunk 405 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 413 optimal weight: 0.3980 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.143807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.092129 restraints weight = 76170.565| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.75 r_work: 0.2817 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35514 Z= 0.160 Angle : 0.576 9.753 48042 Z= 0.271 Chirality : 0.045 0.188 5436 Planarity : 0.003 0.058 6288 Dihedral : 5.549 50.591 4890 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.38 % Allowed : 13.60 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.13), residues: 4398 helix: 1.51 (0.13), residues: 1698 sheet: 0.93 (0.27), residues: 390 loop : -1.62 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 560 TYR 0.011 0.001 TYR C 244 PHE 0.014 0.001 PHE C 563 TRP 0.043 0.002 TRP E 551 HIS 0.002 0.000 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (35514) covalent geometry : angle 0.57577 / 0.27 (48042) hydrogen bonds : bond 0.03205 / 2.12 ( 984) hydrogen bonds : angle 3.54540 / 2.41 ( 2844) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 212 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.2232 (pmm) cc_final: 0.2000 (pmm) REVERT: A 327 GLN cc_start: 0.9428 (OUTLIER) cc_final: 0.9000 (tp-100) REVERT: A 449 MET cc_start: 0.9040 (mmm) cc_final: 0.8664 (tpp) REVERT: A 454 TRP cc_start: 0.9426 (t-100) cc_final: 0.9115 (t-100) REVERT: A 464 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9452 (mm) REVERT: A 551 TRP cc_start: 0.8139 (t-100) cc_final: 0.7826 (t-100) REVERT: A 689 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8721 (tm-30) REVERT: B 454 TRP cc_start: 0.9415 (t-100) cc_final: 0.8732 (t-100) REVERT: B 560 ARG cc_start: 0.7730 (mmm-85) cc_final: 0.7048 (mmm-85) REVERT: B 563 PHE cc_start: 0.9482 (OUTLIER) cc_final: 0.8503 (t80) REVERT: B 689 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8626 (tm-30) REVERT: C 315 LYS cc_start: 0.9264 (ptpp) cc_final: 0.8735 (pttp) REVERT: C 449 MET cc_start: 0.9309 (mmm) cc_final: 0.8984 (tpp) REVERT: C 561 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8022 (pm20) REVERT: C 563 PHE cc_start: 0.9499 (OUTLIER) cc_final: 0.8298 (t80) REVERT: C 678 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8461 (mpp) REVERT: D 449 MET cc_start: 0.9195 (mmm) cc_final: 0.8899 (tpp) REVERT: D 551 TRP cc_start: 0.8104 (t-100) cc_final: 0.7484 (t-100) REVERT: E 158 MET cc_start: 0.2680 (pmm) cc_final: 0.2402 (pmm) REVERT: E 203 TYR cc_start: 0.9230 (m-10) cc_final: 0.8690 (m-80) REVERT: E 449 MET cc_start: 0.9084 (mmm) cc_final: 0.8574 (tpp) REVERT: E 464 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9424 (mm) REVERT: E 678 MET cc_start: 0.8323 (pmm) cc_final: 0.7974 (pmm) REVERT: E 689 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8608 (tm-30) REVERT: F 203 TYR cc_start: 0.9276 (m-80) cc_final: 0.8918 (m-80) REVERT: F 315 LYS cc_start: 0.9229 (ptpp) cc_final: 0.8791 (pttp) REVERT: F 464 LEU cc_start: 0.9703 (OUTLIER) cc_final: 0.9472 (mm) REVERT: F 551 TRP cc_start: 0.7973 (t-100) cc_final: 0.7738 (t-100) REVERT: F 561 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8127 (pm20) outliers start: 52 outliers final: 35 residues processed: 257 average time/residue: 0.1979 time to fit residues: 86.6704 Evaluate side-chains 252 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 563 PHE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 309 optimal weight: 30.0000 chunk 436 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 426 optimal weight: 0.2980 chunk 205 optimal weight: 5.9990 chunk 2 optimal weight: 30.0000 chunk 430 optimal weight: 7.9990 chunk 314 optimal weight: 0.0670 chunk 252 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.144892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.093238 restraints weight = 75510.397| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.75 r_work: 0.2868 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35514 Z= 0.105 Angle : 0.552 9.053 48042 Z= 0.261 Chirality : 0.043 0.183 5436 Planarity : 0.003 0.056 6288 Dihedral : 5.502 50.890 4890 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.12 % Allowed : 13.82 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.11 (0.13), residues: 4398 helix: 1.58 (0.13), residues: 1680 sheet: 1.02 (0.27), residues: 372 loop : -1.59 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 560 TYR 0.011 0.001 TYR C 244 PHE 0.013 0.001 PHE C 563 TRP 0.042 0.002 TRP E 551 HIS 0.002 0.000 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (35514) covalent geometry : angle 0.55215 / 0.26 (48042) hydrogen bonds : bond 0.02913 / 1.94 ( 984) hydrogen bonds : angle 3.43303 / 2.33 ( 2844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9973.43 seconds wall clock time: 171 minutes 5.29 seconds (10265.29 seconds total)