Starting phenix.real_space_refine on Sat Feb 7 16:47:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rla_24523/02_2026/7rla_24523.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rla_24523/02_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_24523/02_2026/7rla_24523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rla_24523/02_2026/7rla_24523.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rla_24523/02_2026/7rla_24523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rla_24523/02_2026/7rla_24523.map" } 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-2.0-5952/lib/python3.9/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: 6.60, per 1000 atoms: 0.19 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: 2.44 Conformation dependent library (CDL) restraints added in 1.3 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: 1.17 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: 5.74 Time building geometry restraints manager: 3.07 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: 19354 15.59 - 31.19: 1982 31.19 - 46.78: 576 46.78 - 62.38: 102 62.38 - 77.97: 42 Dihedral angle restraints: 22056 sinusoidal: 9336 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 22053 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: 0.12 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 26.680 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 13.994 77.971 13812 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 covalent geometry : bond 0.00311 (35514) covalent geometry : angle 0.77819 (48042) hydrogen bonds : bond 0.23606 ( 984) hydrogen bonds : angle 5.93136 ( 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 : 1.497 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: 0.2207 time to fit residues: 133.6706 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 : 1.706 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.160570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.112178 restraints weight = 73720.476| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 4.14 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35514 Z= 0.158 Angle : 0.600 8.086 48042 Z= 0.302 Chirality : 0.046 0.190 5436 Planarity : 0.004 0.050 6288 Dihedral : 7.475 54.941 5025 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.64 % Allowed : 7.72 % Favored : 91.64 % 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: -1.19 (0.13), residues: 4398 helix: 0.61 (0.14), residues: 1584 sheet: 1.24 (0.28), residues: 390 loop : -2.23 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 560 TYR 0.014 0.002 TYR B 203 PHE 0.017 0.002 PHE C 618 TRP 0.034 0.004 TRP F 551 HIS 0.003 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00373 (35514) covalent geometry : angle 0.60025 (48042) hydrogen bonds : bond 0.04924 ( 984) hydrogen bonds : angle 4.30340 ( 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: 24 poor density : 270 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: -0.0553 (tpp) cc_final: -0.0778 (tpp) REVERT: A 203 TYR cc_start: 0.8929 (m-80) cc_final: 0.8554 (m-80) REVERT: A 332 MET cc_start: 0.9343 (mtp) cc_final: 0.9111 (mtp) REVERT: A 454 TRP cc_start: 0.9158 (t-100) cc_final: 0.8885 (t-100) REVERT: A 758 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8265 (t80) REVERT: B 84 MET cc_start: -0.0834 (tpp) cc_final: -0.1034 (tpp) REVERT: B 203 TYR cc_start: 0.9184 (m-80) cc_final: 0.8982 (m-80) REVERT: B 315 LYS cc_start: 0.8987 (ptpp) cc_final: 0.8683 (pttp) REVERT: B 454 TRP cc_start: 0.9352 (t-100) cc_final: 0.8881 (t-100) REVERT: B 470 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: B 563 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8204 (t80) REVERT: C 84 MET cc_start: -0.1359 (tpp) cc_final: -0.1576 (tpp) REVERT: C 203 TYR cc_start: 0.8658 (m-80) cc_final: 0.8047 (m-80) REVERT: C 217 LYS cc_start: 0.9528 (mttt) cc_final: 0.9290 (mmmm) REVERT: C 315 LYS cc_start: 0.9046 (ptpp) cc_final: 0.8728 (pttp) REVERT: C 563 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8098 (t80) REVERT: C 678 MET cc_start: 0.8221 (pmm) cc_final: 0.7928 (pmm) REVERT: C 758 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8292 (t80) REVERT: D 203 TYR cc_start: 0.8752 (m-10) cc_final: 0.8203 (m-80) REVERT: D 604 ILE cc_start: 0.9499 (mm) cc_final: 0.9291 (mm) REVERT: D 608 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8769 (ptm) REVERT: D 758 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8211 (t80) REVERT: E 217 LYS cc_start: 0.9543 (mttt) cc_final: 0.9263 (mtmm) REVERT: E 550 MET cc_start: 0.6904 (ppp) cc_final: 0.6660 (ppp) REVERT: E 563 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8568 (t80) REVERT: F 315 LYS cc_start: 0.8864 (ptpp) cc_final: 0.8524 (pttp) REVERT: F 454 TRP cc_start: 0.9323 (t-100) cc_final: 0.8937 (t-100) REVERT: F 563 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8365 (t80) outliers start: 24 outliers final: 9 residues processed: 284 average time/residue: 0.1972 time to fit residues: 97.1344 Evaluate side-chains 254 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 236 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 278 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 364 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 326 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 76 optimal weight: 0.3980 chunk 41 optimal weight: 9.9990 chunk 202 optimal weight: 0.0070 chunk 137 optimal weight: 6.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 296 ASN B 21 ASN C 21 ASN D 21 ASN E 21 ASN F 21 ASN F 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.160302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110908 restraints weight = 73261.598| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 4.09 r_work: 0.3003 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 35514 Z= 0.127 Angle : 0.532 11.908 48042 Z= 0.263 Chirality : 0.044 0.153 5436 Planarity : 0.003 0.052 6288 Dihedral : 7.247 53.959 5022 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.46 % Allowed : 9.37 % Favored : 89.16 % 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: 0.95 (0.14), residues: 1608 sheet: 1.21 (0.27), residues: 390 loop : -2.15 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 210 TYR 0.014 0.001 TYR C 517 PHE 0.016 0.001 PHE C 618 TRP 0.018 0.002 TRP E 551 HIS 0.004 0.000 HIS E 404 Details of bonding type rmsd covalent geometry : bond 0.00300 (35514) covalent geometry : angle 0.53178 (48042) hydrogen bonds : bond 0.03776 ( 984) hydrogen bonds : angle 3.91424 ( 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 301 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 246 time to evaluate : 1.422 Fit side-chains REVERT: A 203 TYR cc_start: 0.9153 (m-80) cc_final: 0.8731 (m-80) REVERT: A 402 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8871 (mp0) REVERT: A 454 TRP cc_start: 0.9218 (t-100) cc_final: 0.8953 (t-100) REVERT: A 678 MET cc_start: 0.8332 (pmm) cc_final: 0.8072 (pmm) REVERT: A 758 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8373 (t80) REVERT: B 158 MET cc_start: 0.1378 (pmm) cc_final: 0.1104 (pmm) REVERT: B 402 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8827 (mp0) REVERT: B 454 TRP cc_start: 0.9376 (t-100) cc_final: 0.8759 (t-100) REVERT: B 470 GLU cc_start: 0.8434 (mp0) cc_final: 0.8218 (mp0) REVERT: B 563 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8148 (t80) REVERT: C 203 TYR cc_start: 0.8851 (m-80) cc_final: 0.8215 (m-80) REVERT: C 315 LYS cc_start: 0.9056 (ptpp) cc_final: 0.8708 (pttp) REVERT: C 563 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8017 (t80) REVERT: D 203 TYR cc_start: 0.8989 (m-10) cc_final: 0.8343 (m-80) REVERT: D 315 LYS cc_start: 0.9045 (ptpp) cc_final: 0.8784 (pttp) REVERT: D 442 MET cc_start: 0.9404 (mpp) cc_final: 0.9121 (pmm) REVERT: D 551 TRP cc_start: 0.7789 (t-100) cc_final: 0.7049 (t-100) REVERT: D 608 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.9016 (ptm) REVERT: D 678 MET cc_start: 0.8500 (pmm) cc_final: 0.8193 (pmm) REVERT: D 758 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8471 (t80) REVERT: E 217 LYS cc_start: 0.9630 (mttt) cc_final: 0.9378 (mtmm) REVERT: E 315 LYS cc_start: 0.9065 (ptpp) cc_final: 0.8838 (pttp) REVERT: E 402 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8746 (mp0) REVERT: E 550 MET cc_start: 0.7069 (ppp) cc_final: 0.6816 (ppp) REVERT: E 563 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8381 (t80) REVERT: E 678 MET cc_start: 0.8281 (pmm) cc_final: 0.8057 (pmm) REVERT: F 402 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8903 (mp0) REVERT: F 454 TRP cc_start: 0.9382 (t-100) cc_final: 0.8934 (t-100) REVERT: F 551 TRP cc_start: 0.7793 (t-100) cc_final: 0.7564 (t-100) REVERT: F 563 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.7995 (t80) REVERT: F 757 MET cc_start: 0.9207 (tmm) cc_final: 0.8931 (tmm) outliers start: 55 outliers final: 27 residues processed: 295 average time/residue: 0.1789 time to fit residues: 92.2654 Evaluate side-chains 267 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 402 GLU 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 402 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain C residue 21 ASN 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 600 VAL 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 D residue 758 PHE Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 402 GLU 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 402 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 248 optimal weight: 6.9990 chunk 254 optimal weight: 6.9990 chunk 358 optimal weight: 0.9990 chunk 309 optimal weight: 30.0000 chunk 132 optimal weight: 6.9990 chunk 428 optimal weight: 4.9990 chunk 391 optimal weight: 0.3980 chunk 108 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 133 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.149575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099677 restraints weight = 76032.768| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.96 r_work: 0.2997 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2352 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= 0.133 Angle : 0.526 7.524 48042 Z= 0.259 Chirality : 0.044 0.145 5436 Planarity : 0.003 0.053 6288 Dihedral : 7.074 52.640 5022 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.20 % Allowed : 10.78 % Favored : 88.02 % 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: -0.77 (0.13), residues: 4398 helix: 1.12 (0.13), residues: 1632 sheet: 1.08 (0.27), residues: 396 loop : -2.11 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 22 TYR 0.011 0.001 TYR C 517 PHE 0.010 0.001 PHE C 618 TRP 0.020 0.002 TRP B 551 HIS 0.003 0.000 HIS E 404 Details of bonding type rmsd covalent geometry : bond 0.00317 (35514) covalent geometry : angle 0.52642 (48042) hydrogen bonds : bond 0.03279 ( 984) hydrogen bonds : angle 3.74744 ( 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 278 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 1.280 Fit side-chains REVERT: A 203 TYR cc_start: 0.9137 (m-80) cc_final: 0.8770 (m-80) REVERT: A 315 LYS cc_start: 0.9061 (pttm) cc_final: 0.8697 (pttp) REVERT: A 454 TRP cc_start: 0.9283 (t-100) cc_final: 0.8925 (t-100) REVERT: A 678 MET cc_start: 0.8293 (pmm) cc_final: 0.8075 (pmm) REVERT: A 758 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8429 (t80) REVERT: B 158 MET cc_start: 0.1904 (pmm) cc_final: 0.1688 (pmm) REVERT: B 454 TRP cc_start: 0.9421 (t-100) cc_final: 0.8764 (t-100) REVERT: B 550 MET cc_start: 0.6634 (ppp) cc_final: 0.6410 (ppp) REVERT: B 563 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8070 (t80) REVERT: C 203 TYR cc_start: 0.9167 (m-80) cc_final: 0.8896 (m-80) REVERT: C 315 LYS cc_start: 0.9081 (ptpp) cc_final: 0.8737 (pttp) REVERT: C 563 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8036 (t80) REVERT: C 608 MET cc_start: 0.9064 (ptp) cc_final: 0.8772 (ptp) REVERT: C 678 MET cc_start: 0.8390 (pmm) cc_final: 0.8089 (pmm) REVERT: D 203 TYR cc_start: 0.9051 (m-10) cc_final: 0.8784 (m-80) REVERT: D 315 LYS cc_start: 0.9124 (ptpp) cc_final: 0.8737 (pttp) REVERT: D 551 TRP cc_start: 0.8278 (t-100) cc_final: 0.7354 (t-100) REVERT: D 608 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8844 (ptm) REVERT: E 203 TYR cc_start: 0.9171 (m-10) cc_final: 0.8366 (m-80) REVERT: E 217 LYS cc_start: 0.9637 (mttt) cc_final: 0.9418 (mmmm) REVERT: E 315 LYS cc_start: 0.9088 (ptpp) cc_final: 0.8779 (pttp) REVERT: E 470 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: E 550 MET cc_start: 0.7118 (ppp) cc_final: 0.6871 (ppp) REVERT: E 563 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8318 (t80) REVERT: E 678 MET cc_start: 0.8138 (pmm) cc_final: 0.7813 (pmm) REVERT: F 454 TRP cc_start: 0.9413 (t-100) cc_final: 0.8941 (t-100) REVERT: F 551 TRP cc_start: 0.8240 (t-100) cc_final: 0.7946 (t-100) REVERT: F 563 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.7876 (t80) REVERT: F 757 MET cc_start: 0.9239 (tmm) cc_final: 0.9021 (tmm) outliers start: 45 outliers final: 24 residues processed: 269 average time/residue: 0.1828 time to fit residues: 85.8811 Evaluate side-chains 253 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 675 LEU 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 562 ILE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain B residue 678 MET 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 600 VAL Chi-restraints excluded: chain C residue 675 LEU 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 140 LEU Chi-restraints excluded: chain E residue 470 GLU 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 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 Chi-restraints excluded: chain F residue 678 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 8.9990 chunk 229 optimal weight: 0.7980 chunk 353 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 300 optimal weight: 0.5980 chunk 210 optimal weight: 7.9990 chunk 254 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 386 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN B 21 ASN C 337 GLN E 21 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.148607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.098293 restraints weight = 76026.089| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.89 r_work: 0.2927 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2744 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= 0.117 Angle : 0.512 8.549 48042 Z= 0.249 Chirality : 0.043 0.143 5436 Planarity : 0.003 0.052 6288 Dihedral : 6.785 50.190 5022 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.60 % Allowed : 11.42 % Favored : 86.98 % 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: -0.58 (0.13), residues: 4398 helix: 1.30 (0.13), residues: 1656 sheet: 1.18 (0.27), residues: 390 loop : -2.04 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 338 TYR 0.010 0.001 TYR C 517 PHE 0.011 0.001 PHE C 563 TRP 0.023 0.002 TRP B 551 HIS 0.002 0.000 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00280 (35514) covalent geometry : angle 0.51236 (48042) hydrogen bonds : bond 0.02897 ( 984) hydrogen bonds : angle 3.52801 ( 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 301 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 241 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 LYS cc_start: 0.9065 (pttm) cc_final: 0.8784 (pttp) REVERT: A 454 TRP cc_start: 0.9335 (t-100) cc_final: 0.9089 (t-100) REVERT: A 689 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8773 (tm-30) REVERT: A 758 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8394 (t80) REVERT: B 158 MET cc_start: 0.2178 (pmm) cc_final: 0.1977 (pmm) REVERT: B 454 TRP cc_start: 0.9430 (t-100) cc_final: 0.8742 (t-100) REVERT: B 563 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8324 (t80) REVERT: C 563 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8025 (t80) REVERT: C 678 MET cc_start: 0.8368 (pmm) cc_final: 0.8019 (pmm) REVERT: D 203 TYR cc_start: 0.9120 (m-10) cc_final: 0.8843 (m-80) REVERT: D 315 LYS cc_start: 0.9113 (ptpp) cc_final: 0.8712 (pttp) REVERT: D 442 MET cc_start: 0.9385 (mpp) cc_final: 0.9149 (pmm) REVERT: D 551 TRP cc_start: 0.7880 (t-100) cc_final: 0.7169 (t-100) REVERT: D 604 ILE cc_start: 0.9442 (mm) cc_final: 0.9238 (mt) REVERT: D 608 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8915 (ptm) REVERT: E 203 TYR cc_start: 0.9244 (m-10) cc_final: 0.8971 (m-80) REVERT: E 315 LYS cc_start: 0.9072 (ptpp) cc_final: 0.8787 (pttp) REVERT: E 550 MET cc_start: 0.7374 (ppp) cc_final: 0.7087 (ppp) REVERT: E 563 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8473 (t80) REVERT: F 454 TRP cc_start: 0.9453 (t-100) cc_final: 0.8779 (t-100) REVERT: F 563 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.7904 (t80) outliers start: 60 outliers final: 30 residues processed: 288 average time/residue: 0.1865 time to fit residues: 92.3077 Evaluate side-chains 264 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 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 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 B residue 678 MET 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 675 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 332 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 203 optimal weight: 0.8980 chunk 60 optimal weight: 0.0770 chunk 279 optimal weight: 3.9990 chunk 347 optimal weight: 0.8980 chunk 277 optimal weight: 0.0980 chunk 36 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 408 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 234 optimal weight: 30.0000 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN D 21 ASN F 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.148780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.098552 restraints weight = 75987.717| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.91 r_work: 0.2932 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2899 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= 0.099 Angle : 0.522 10.012 48042 Z= 0.246 Chirality : 0.043 0.137 5436 Planarity : 0.003 0.088 6288 Dihedral : 6.595 47.956 5022 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.22 % Allowed : 12.51 % Favored : 86.26 % 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: -0.47 (0.13), residues: 4398 helix: 1.37 (0.13), residues: 1656 sheet: 1.20 (0.27), residues: 390 loop : -1.95 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 599 TYR 0.010 0.001 TYR F 203 PHE 0.010 0.001 PHE C 563 TRP 0.024 0.002 TRP B 551 HIS 0.002 0.000 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00239 (35514) covalent geometry : angle 0.52172 (48042) hydrogen bonds : bond 0.02679 ( 984) hydrogen bonds : angle 3.48246 ( 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 281 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: -0.2005 (tpp) cc_final: -0.2214 (tpp) REVERT: A 315 LYS cc_start: 0.9080 (pttm) cc_final: 0.8663 (pttp) REVERT: A 454 TRP cc_start: 0.9338 (t-100) cc_final: 0.9097 (t-100) REVERT: A 758 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8321 (t80) REVERT: B 158 MET cc_start: 0.2270 (pmm) cc_final: 0.2062 (pmm) REVERT: B 454 TRP cc_start: 0.9411 (t-100) cc_final: 0.8691 (t-100) REVERT: B 550 MET cc_start: 0.7018 (ppp) cc_final: 0.6776 (ppp) REVERT: B 563 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8324 (t80) REVERT: B 689 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8648 (tm-30) REVERT: C 315 LYS cc_start: 0.9216 (ptpp) cc_final: 0.8746 (pttp) REVERT: C 563 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.7936 (t80) REVERT: C 678 MET cc_start: 0.8352 (pmm) cc_final: 0.8018 (pmm) REVERT: D 203 TYR cc_start: 0.9143 (m-10) cc_final: 0.8865 (m-80) REVERT: D 315 LYS cc_start: 0.9122 (ptpp) cc_final: 0.8776 (pttp) REVERT: D 551 TRP cc_start: 0.7764 (t-100) cc_final: 0.7086 (t-100) REVERT: D 608 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8905 (ptm) REVERT: D 678 MET cc_start: 0.8240 (pmm) cc_final: 0.7917 (pmm) REVERT: E 203 TYR cc_start: 0.9272 (m-10) cc_final: 0.8957 (m-80) REVERT: E 315 LYS cc_start: 0.9091 (ptpp) cc_final: 0.8798 (pttp) REVERT: E 563 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.8558 (t80) REVERT: E 611 MET cc_start: 0.8591 (mmm) cc_final: 0.8347 (mmm) REVERT: F 454 TRP cc_start: 0.9458 (t-100) cc_final: 0.8777 (t-100) REVERT: F 563 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7886 (t80) outliers start: 46 outliers final: 31 residues processed: 271 average time/residue: 0.1756 time to fit residues: 82.3193 Evaluate side-chains 263 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 563 PHE 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 509 THR 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 388 MET 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 402 GLU Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 PHE 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 332 MET 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 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: 50.0000 chunk 322 optimal weight: 4.9990 chunk 385 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 226 optimal weight: 30.0000 chunk 422 optimal weight: 9.9990 chunk 359 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 349 optimal weight: 9.9990 chunk 230 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 ASN B 337 GLN C 296 ASN C 337 GLN D 296 ASN D 337 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.144532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.093159 restraints weight = 76577.803| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.80 r_work: 0.2871 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 35514 Z= 0.198 Angle : 0.614 10.529 48042 Z= 0.290 Chirality : 0.045 0.148 5436 Planarity : 0.004 0.052 6288 Dihedral : 6.913 48.148 5022 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.54 % Allowed : 12.43 % Favored : 86.02 % 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: -0.22 (0.13), residues: 4398 helix: 1.48 (0.13), residues: 1698 sheet: 1.11 (0.27), residues: 390 loop : -1.74 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 586 TYR 0.008 0.001 TYR C 244 PHE 0.013 0.001 PHE C 563 TRP 0.025 0.002 TRP B 551 HIS 0.004 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00465 (35514) covalent geometry : angle 0.61399 (48042) hydrogen bonds : bond 0.03544 ( 984) hydrogen bonds : angle 3.66246 ( 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 271 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LYS cc_start: 0.9170 (pttm) cc_final: 0.8825 (pttp) REVERT: A 454 TRP cc_start: 0.9424 (t-100) cc_final: 0.9179 (t-100) REVERT: A 551 TRP cc_start: 0.8328 (t-100) cc_final: 0.7581 (t-100) REVERT: A 689 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8743 (tm-30) REVERT: B 454 TRP cc_start: 0.9427 (t-100) cc_final: 0.8741 (t-100) REVERT: B 678 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7992 (pmm) REVERT: B 689 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8635 (tm-30) REVERT: C 315 LYS cc_start: 0.9254 (ptpp) cc_final: 0.8757 (pttp) REVERT: C 449 MET cc_start: 0.9199 (tpp) cc_final: 0.8900 (tpp) REVERT: C 466 GLU cc_start: 0.8838 (mp0) cc_final: 0.8491 (mp0) REVERT: C 492 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9328 (tt) REVERT: C 561 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: C 563 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.8302 (t80) REVERT: C 678 MET cc_start: 0.8388 (pmm) cc_final: 0.8135 (pmm) REVERT: D 203 TYR cc_start: 0.9211 (m-10) cc_final: 0.8827 (m-10) REVERT: D 449 MET cc_start: 0.9111 (mmm) cc_final: 0.8735 (tpp) REVERT: D 551 TRP cc_start: 0.8192 (t-100) cc_final: 0.7447 (t-100) REVERT: D 608 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8917 (ptm) REVERT: D 678 MET cc_start: 0.8212 (pmm) cc_final: 0.7842 (pmm) REVERT: E 203 TYR cc_start: 0.9360 (m-10) cc_final: 0.8903 (m-80) REVERT: E 449 MET cc_start: 0.9197 (mmm) cc_final: 0.8661 (tpp) REVERT: E 464 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9425 (mm) REVERT: E 689 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8562 (tm-30) REVERT: F 466 GLU cc_start: 0.8763 (mp0) cc_final: 0.8498 (mp0) REVERT: F 546 GLU cc_start: 0.9214 (tt0) cc_final: 0.8877 (mt-10) REVERT: F 551 TRP cc_start: 0.8387 (t-100) cc_final: 0.8037 (t-100) REVERT: F 561 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7703 (pm20) REVERT: F 563 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.8371 (t80) outliers start: 58 outliers final: 42 residues processed: 257 average time/residue: 0.1999 time to fit residues: 87.1793 Evaluate side-chains 255 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 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 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 442 MET Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR 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 402 GLU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 562 ILE 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 332 MET 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 504 LEU Chi-restraints excluded: chain F residue 561 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 426 optimal weight: 0.9990 chunk 302 optimal weight: 0.8980 chunk 323 optimal weight: 6.9990 chunk 328 optimal weight: 0.9980 chunk 263 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 353 optimal weight: 0.0270 chunk 273 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 410 optimal weight: 2.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 GLN E 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.145560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.094664 restraints weight = 75562.881| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.79 r_work: 0.2883 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3575 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= 0.111 Angle : 0.541 9.604 48042 Z= 0.254 Chirality : 0.044 0.147 5436 Planarity : 0.003 0.053 6288 Dihedral : 6.715 47.025 5022 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.30 % Allowed : 12.86 % Favored : 85.84 % 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: -0.20 (0.13), residues: 4398 helix: 1.50 (0.13), residues: 1698 sheet: 1.09 (0.26), residues: 390 loop : -1.72 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 424 TYR 0.015 0.001 TYR A 203 PHE 0.012 0.001 PHE C 563 TRP 0.032 0.002 TRP E 551 HIS 0.002 0.000 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00268 (35514) covalent geometry : angle 0.54088 (48042) hydrogen bonds : bond 0.02859 ( 984) hydrogen bonds : angle 3.53093 ( 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 263 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 214 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.2168 (pmm) cc_final: 0.1898 (pmm) REVERT: A 315 LYS cc_start: 0.9177 (pttm) cc_final: 0.8850 (pttp) REVERT: A 454 TRP cc_start: 0.9410 (t-100) cc_final: 0.9114 (t-100) REVERT: A 551 TRP cc_start: 0.8239 (t-100) cc_final: 0.7576 (t-100) REVERT: A 563 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8412 (m-80) REVERT: A 689 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8715 (tm-30) REVERT: B 454 TRP cc_start: 0.9425 (t-100) cc_final: 0.8697 (t-100) REVERT: B 464 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9416 (mm) REVERT: B 563 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.8584 (t80) REVERT: B 678 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8081 (pmm) REVERT: B 689 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8618 (tm-30) REVERT: C 315 LYS cc_start: 0.9262 (ptpp) cc_final: 0.8636 (pttp) REVERT: C 466 GLU cc_start: 0.8790 (mp0) cc_final: 0.8449 (mp0) REVERT: C 492 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9290 (tt) REVERT: C 561 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7556 (pm20) REVERT: C 563 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.8223 (t80) REVERT: C 678 MET cc_start: 0.8414 (pmm) cc_final: 0.8134 (pmm) REVERT: D 449 MET cc_start: 0.9144 (mmm) cc_final: 0.8875 (tpp) REVERT: D 551 TRP cc_start: 0.8156 (t-100) cc_final: 0.7470 (t-100) REVERT: D 608 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8735 (ptm) REVERT: D 678 MET cc_start: 0.8281 (pmm) cc_final: 0.7944 (pmm) REVERT: E 158 MET cc_start: 0.2783 (pmm) cc_final: 0.2499 (pmm) REVERT: E 203 TYR cc_start: 0.9359 (m-10) cc_final: 0.8866 (m-80) REVERT: E 315 LYS cc_start: 0.9187 (ptpp) cc_final: 0.8872 (pttp) REVERT: E 449 MET cc_start: 0.9200 (mmm) cc_final: 0.8659 (tpp) REVERT: E 563 PHE cc_start: 0.9449 (OUTLIER) cc_final: 0.8710 (t80) REVERT: E 689 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8565 (tm-30) REVERT: F 466 GLU cc_start: 0.8710 (mp0) cc_final: 0.8443 (mp0) REVERT: F 546 GLU cc_start: 0.9215 (tt0) cc_final: 0.8881 (mt-10) REVERT: F 563 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8214 (t80) outliers start: 49 outliers final: 37 residues processed: 252 average time/residue: 0.1947 time to fit residues: 83.6676 Evaluate side-chains 249 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 562 ILE Chi-restraints excluded: chain A residue 563 PHE 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 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 509 THR 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 492 LEU Chi-restraints excluded: chain C residue 509 THR 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 402 GLU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 562 ILE 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 332 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 116 optimal weight: 7.9990 chunk 423 optimal weight: 10.0000 chunk 342 optimal weight: 2.9990 chunk 422 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 391 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 226 optimal weight: 40.0000 chunk 253 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.145231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.093921 restraints weight = 75758.390| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.76 r_work: 0.2877 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35514 Z= 0.142 Angle : 0.555 9.852 48042 Z= 0.260 Chirality : 0.044 0.144 5436 Planarity : 0.003 0.050 6288 Dihedral : 6.610 46.994 5022 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.52 % Allowed : 12.67 % Favored : 85.81 % 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: -0.13 (0.13), residues: 4398 helix: 1.57 (0.13), residues: 1698 sheet: 1.07 (0.26), residues: 390 loop : -1.67 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 465 TYR 0.008 0.001 TYR C 244 PHE 0.012 0.001 PHE C 563 TRP 0.034 0.002 TRP B 551 HIS 0.003 0.000 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00341 (35514) covalent geometry : angle 0.55532 (48042) hydrogen bonds : bond 0.02966 ( 984) hydrogen bonds : angle 3.50155 ( 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 266 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.2260 (pmm) cc_final: 0.2018 (pmm) REVERT: A 315 LYS cc_start: 0.9194 (pttm) cc_final: 0.8842 (pttp) REVERT: A 449 MET cc_start: 0.9056 (mmm) cc_final: 0.8659 (tpp) REVERT: A 454 TRP cc_start: 0.9412 (t-100) cc_final: 0.9130 (t-100) REVERT: A 551 TRP cc_start: 0.8238 (t-100) cc_final: 0.7695 (t-100) REVERT: A 563 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: A 678 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8048 (pmm) REVERT: A 689 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8710 (tm-30) REVERT: B 392 ASP cc_start: 0.9191 (p0) cc_final: 0.8955 (p0) REVERT: B 454 TRP cc_start: 0.9441 (t-100) cc_final: 0.8749 (t-100) REVERT: B 464 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9391 (mm) REVERT: B 563 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.8563 (t80) REVERT: B 678 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7969 (pmm) REVERT: B 689 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8606 (tm-30) REVERT: C 315 LYS cc_start: 0.9281 (ptpp) cc_final: 0.8773 (pttp) REVERT: C 466 GLU cc_start: 0.8849 (mp0) cc_final: 0.8476 (mp0) REVERT: C 492 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9300 (tt) REVERT: C 551 TRP cc_start: 0.8198 (t-100) cc_final: 0.7647 (t-100) REVERT: C 561 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: C 563 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8170 (t80) REVERT: C 678 MET cc_start: 0.8408 (pmm) cc_final: 0.8156 (pmm) REVERT: D 449 MET cc_start: 0.9164 (mmm) cc_final: 0.8575 (tpp) REVERT: D 551 TRP cc_start: 0.8188 (t-100) cc_final: 0.7566 (t-100) REVERT: D 678 MET cc_start: 0.8281 (pmm) cc_final: 0.7956 (pmm) REVERT: E 158 MET cc_start: 0.2819 (pmm) cc_final: 0.2529 (pmm) REVERT: E 203 TYR cc_start: 0.9358 (m-10) cc_final: 0.8852 (m-80) REVERT: E 315 LYS cc_start: 0.9178 (ptpp) cc_final: 0.8943 (pttp) REVERT: E 392 ASP cc_start: 0.9219 (p0) cc_final: 0.8993 (p0) REVERT: E 449 MET cc_start: 0.9197 (mmm) cc_final: 0.8766 (tpp) REVERT: E 563 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.8723 (t80) REVERT: F 546 GLU cc_start: 0.9179 (tt0) cc_final: 0.8816 (mt-10) REVERT: F 551 TRP cc_start: 0.8306 (t-100) cc_final: 0.7956 (t-100) REVERT: F 561 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7771 (pm20) REVERT: F 563 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8251 (t80) outliers start: 57 outliers final: 38 residues processed: 254 average time/residue: 0.2129 time to fit residues: 92.2915 Evaluate side-chains 253 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 504 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 563 PHE 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 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 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 396 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 509 THR 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 402 GLU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 562 ILE 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 332 MET 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 509 THR 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 Chi-restraints excluded: chain F residue 678 MET 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: 0.7980 chunk 399 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 405 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 169 optimal weight: 0.0370 chunk 119 optimal weight: 0.0270 chunk 413 optimal weight: 0.1980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.146312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.095478 restraints weight = 75385.229| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.79 r_work: 0.2899 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35514 Z= 0.096 Angle : 0.537 9.562 48042 Z= 0.252 Chirality : 0.043 0.156 5436 Planarity : 0.003 0.068 6288 Dihedral : 6.373 47.099 5022 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.20 % Allowed : 12.99 % Favored : 85.81 % 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: -0.13 (0.13), residues: 4398 helix: 1.60 (0.13), residues: 1692 sheet: 1.04 (0.26), residues: 390 loop : -1.68 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 465 TYR 0.009 0.001 TYR C 244 PHE 0.012 0.001 PHE C 563 TRP 0.044 0.002 TRP E 551 HIS 0.002 0.000 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00230 (35514) covalent geometry : angle 0.53661 (48042) hydrogen bonds : bond 0.02616 ( 984) hydrogen bonds : angle 3.40377 ( 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 265 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LYS cc_start: 0.9155 (pttm) cc_final: 0.8882 (pttp) REVERT: A 454 TRP cc_start: 0.9411 (t-100) cc_final: 0.9106 (t-100) REVERT: A 551 TRP cc_start: 0.8039 (t-100) cc_final: 0.7553 (t-100) REVERT: A 563 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8573 (m-80) REVERT: B 392 ASP cc_start: 0.9347 (p0) cc_final: 0.9117 (p0) REVERT: B 454 TRP cc_start: 0.9419 (t-100) cc_final: 0.8691 (t-100) REVERT: B 563 PHE cc_start: 0.9467 (OUTLIER) cc_final: 0.8750 (t80) REVERT: B 678 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7874 (pmm) REVERT: C 315 LYS cc_start: 0.9282 (ptpp) cc_final: 0.8657 (pttp) REVERT: C 466 GLU cc_start: 0.8781 (mp0) cc_final: 0.8491 (mp0) REVERT: C 551 TRP cc_start: 0.8071 (t-100) cc_final: 0.7428 (t-100) REVERT: C 561 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: C 563 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.8129 (t80) REVERT: C 611 MET cc_start: 0.8442 (mmm) cc_final: 0.7993 (mmm) REVERT: C 678 MET cc_start: 0.8357 (pmm) cc_final: 0.8111 (pmm) REVERT: D 449 MET cc_start: 0.9140 (mmm) cc_final: 0.8671 (tpp) REVERT: D 551 TRP cc_start: 0.8011 (t-100) cc_final: 0.7379 (t-100) REVERT: D 678 MET cc_start: 0.8196 (pmm) cc_final: 0.7871 (pmm) REVERT: E 158 MET cc_start: 0.2805 (pmm) cc_final: 0.2559 (pmm) REVERT: E 203 TYR cc_start: 0.9353 (m-10) cc_final: 0.8804 (m-80) REVERT: E 315 LYS cc_start: 0.9166 (ptpp) cc_final: 0.8939 (pttp) REVERT: E 392 ASP cc_start: 0.9355 (p0) cc_final: 0.9136 (p0) REVERT: E 449 MET cc_start: 0.9198 (mmm) cc_final: 0.8864 (tpp) REVERT: E 549 THR cc_start: 0.8120 (t) cc_final: 0.7769 (p) REVERT: E 563 PHE cc_start: 0.9516 (OUTLIER) cc_final: 0.8917 (t80) REVERT: E 678 MET cc_start: 0.8156 (pmm) cc_final: 0.7899 (pmm) REVERT: E 689 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8545 (tm-30) REVERT: F 546 GLU cc_start: 0.9211 (tt0) cc_final: 0.8851 (mt-10) REVERT: F 551 TRP cc_start: 0.8103 (t-100) cc_final: 0.7605 (t-100) REVERT: F 561 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: F 563 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8094 (t80) REVERT: F 599 ARG cc_start: 0.7450 (ptp90) cc_final: 0.7213 (ptt-90) REVERT: F 618 PHE cc_start: 0.8434 (t80) cc_final: 0.8084 (t80) outliers start: 45 outliers final: 31 residues processed: 256 average time/residue: 0.2120 time to fit residues: 92.3650 Evaluate side-chains 255 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 1.339 ------------------------------------------------------------------------------- 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 563 PHE 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 509 THR 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 509 THR 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 402 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 332 MET 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 509 THR 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 Chi-restraints excluded: chain F residue 678 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 309 optimal weight: 8.9990 chunk 436 optimal weight: 0.0970 chunk 242 optimal weight: 5.9990 chunk 426 optimal weight: 0.0670 chunk 205 optimal weight: 4.9990 chunk 2 optimal weight: 0.0170 chunk 430 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.147834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.097279 restraints weight = 75417.196| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.79 r_work: 0.2924 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 35514 Z= 0.094 Angle : 0.537 10.400 48042 Z= 0.250 Chirality : 0.043 0.144 5436 Planarity : 0.003 0.053 6288 Dihedral : 6.127 46.175 5022 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.99 % Allowed : 13.53 % Favored : 85.49 % 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: -0.14 (0.13), residues: 4398 helix: 1.51 (0.13), residues: 1728 sheet: 1.07 (0.26), residues: 390 loop : -1.68 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 560 TYR 0.008 0.001 TYR C 517 PHE 0.012 0.001 PHE C 563 TRP 0.046 0.002 TRP E 551 HIS 0.002 0.000 HIS D 406 Details of bonding type rmsd covalent geometry : bond 0.00228 (35514) covalent geometry : angle 0.53698 (48042) hydrogen bonds : bond 0.02498 ( 984) hydrogen bonds : angle 3.33280 ( 2844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9620.25 seconds wall clock time: 164 minutes 54.81 seconds (9894.81 seconds total)