Starting phenix.real_space_refine on Mon Sep 14 23:50:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5ftj_3295/09_2026/5ftj_3295.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ftj_3295/09_2026/5ftj_3295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5ftj_3295/09_2026/5ftj_3295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ftj_3295/09_2026/5ftj_3295.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5ftj_3295/09_2026/5ftj_3295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ftj_3295/09_2026/5ftj_3295.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5ftj_3295/09_2026/5ftj_3295.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5ftj_3295/09_2026/5ftj_3295.cif" } resolution = 2.3 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= 0.011 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 24 5.49 5 S 180 5.16 5 C 21654 2.51 5 N 6066 2.21 5 O 6672 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34602 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 36, 'TRANS': 682} Chain breaks: 1 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {'ADP': 2, 'OJA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "F" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 7.30, per 1000 atoms: 0.21 Number of scatterers: 34602 At special positions: 0 Unit cell: (168.805, 180.271, 98.735, 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 180 16.00 P 24 15.00 F 6 9.00 O 6672 8.00 N 6066 7.00 C 21654 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: 2.79 Conformation dependent library (CDL) restraints added in 1.7 seconds 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8100 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 36 sheets defined 44.1% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 134 through 139 removed outlier: 4.434A pdb=" N TYR A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.525A pdb=" N ILE A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 5.318A 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 228 through 233 removed outlier: 3.676A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.629A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.685A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 4.018A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.543A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 334 removed outlier: 3.938A pdb=" N ARG A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.533A pdb=" N ARG A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 4.589A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.604A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 removed outlier: 3.812A pdb=" N ALA A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 482 through 506 Proline residue: A 496 - end of helix Proline residue: A 500 - end of helix removed outlier: 3.559A pdb=" N LYS A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.516A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 598 through 610 removed outlier: 3.542A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.685A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 671 through 679 removed outlier: 4.028A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 707 removed outlier: 3.550A pdb=" N ILE A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 742 removed outlier: 3.958A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 763 removed outlier: 3.609A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 134 through 139 removed outlier: 4.434A pdb=" N TYR B 138 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.524A pdb=" N ILE B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 5.318A 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 228 through 233 removed outlier: 3.675A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 removed outlier: 3.629A pdb=" N ALA B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.685A pdb=" N LYS B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 removed outlier: 4.018A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 289 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.543A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 334 removed outlier: 3.938A pdb=" N ARG B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.533A pdb=" N ARG B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 removed outlier: 4.589A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.605A pdb=" N GLU B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.812A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 482 through 506 Proline residue: B 496 - end of helix Proline residue: B 500 - end of helix removed outlier: 3.559A pdb=" N LYS B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.516A pdb=" N ILE B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 580 through 587 Processing helix chain 'B' and resid 598 through 610 removed outlier: 3.542A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.684A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 671 through 679 removed outlier: 4.028A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 707 removed outlier: 3.550A pdb=" N ILE B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 707 " --> pdb=" O ILE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 742 removed outlier: 3.959A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 763 removed outlier: 3.609A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 763 " --> pdb=" O ALA B 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 134 through 139 removed outlier: 4.434A pdb=" N TYR C 138 " --> pdb=" O TYR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 212 through 226 removed outlier: 3.525A pdb=" N ILE C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) removed outlier: 5.319A 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 228 through 233 removed outlier: 3.677A pdb=" N ALA C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 removed outlier: 3.629A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 277 removed outlier: 3.685A pdb=" N LYS C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 4.018A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 289 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.543A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 334 removed outlier: 3.938A pdb=" N ARG C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.533A pdb=" N ARG C 358 " --> pdb=" O PRO C 355 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 removed outlier: 4.589A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 removed outlier: 3.604A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 426 removed outlier: 3.812A pdb=" N ALA C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 482 through 506 Proline residue: C 496 - end of helix Proline residue: C 500 - end of helix removed outlier: 3.558A pdb=" N LYS C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.517A pdb=" N ILE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 580 through 587 Processing helix chain 'C' and resid 598 through 610 removed outlier: 3.542A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.685A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 671 through 679 removed outlier: 4.028A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 707 removed outlier: 3.549A pdb=" N ILE C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 707 " --> pdb=" O ILE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 742 removed outlier: 3.958A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 removed outlier: 3.609A pdb=" N ILE C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN C 763 " --> pdb=" O ALA C 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 93 Processing helix chain 'D' and resid 134 through 139 removed outlier: 4.435A pdb=" N TYR D 138 " --> pdb=" O TYR D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 212 through 226 removed outlier: 3.525A pdb=" N ILE D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET D 219 " --> pdb=" O GLN D 215 " (cutoff:3.500A) removed outlier: 5.318A 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 228 through 233 removed outlier: 3.677A pdb=" N ALA D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 removed outlier: 3.629A pdb=" N ALA D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 removed outlier: 3.686A pdb=" N LYS D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 removed outlier: 4.018A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 289 " --> pdb=" O ASN D 285 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.543A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 334 removed outlier: 3.937A pdb=" N ARG D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.533A pdb=" N ARG D 358 " --> pdb=" O PRO D 355 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 removed outlier: 4.588A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 403 removed outlier: 3.604A pdb=" N GLU D 402 " --> pdb=" O GLN D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 426 removed outlier: 3.812A pdb=" N ALA D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 482 through 506 Proline residue: D 496 - end of helix Proline residue: D 500 - end of helix removed outlier: 3.559A pdb=" N LYS D 505 " --> pdb=" O ASP D 501 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.516A pdb=" N ILE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 558 through 569 Processing helix chain 'D' and resid 580 through 587 Processing helix chain 'D' and resid 598 through 610 removed outlier: 3.542A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.684A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 662 Processing helix chain 'D' and resid 671 through 679 removed outlier: 4.028A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 707 removed outlier: 3.549A pdb=" N ILE D 690 " --> pdb=" O ASP D 686 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 707 " --> pdb=" O ILE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 742 removed outlier: 3.959A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 763 removed outlier: 3.609A pdb=" N ILE D 752 " --> pdb=" O SER D 748 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN D 763 " --> pdb=" O ALA D 759 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 134 through 139 removed outlier: 4.434A pdb=" N TYR E 138 " --> pdb=" O TYR E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 212 through 226 removed outlier: 3.524A pdb=" N ILE E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET E 219 " --> pdb=" O GLN E 215 " (cutoff:3.500A) removed outlier: 5.318A 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 228 through 233 removed outlier: 3.676A pdb=" N ALA E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 removed outlier: 3.629A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 277 removed outlier: 3.685A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 removed outlier: 4.018A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 289 " --> pdb=" O ASN E 285 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.542A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 334 removed outlier: 3.938A pdb=" N ARG E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.533A pdb=" N ARG E 358 " --> pdb=" O PRO E 355 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 removed outlier: 4.588A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE E 380 " --> pdb=" O GLY E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 403 removed outlier: 3.605A pdb=" N GLU E 402 " --> pdb=" O GLN E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 426 removed outlier: 3.813A pdb=" N ALA E 422 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 482 through 506 Proline residue: E 496 - end of helix Proline residue: E 500 - end of helix removed outlier: 3.559A pdb=" N LYS E 505 " --> pdb=" O ASP E 501 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.516A pdb=" N ILE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 558 through 569 Processing helix chain 'E' and resid 580 through 587 Processing helix chain 'E' and resid 598 through 610 removed outlier: 3.541A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.685A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 662 Processing helix chain 'E' and resid 671 through 679 removed outlier: 4.028A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA E 676 " --> pdb=" O LEU E 672 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 707 removed outlier: 3.549A pdb=" N ILE E 690 " --> pdb=" O ASP E 686 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 707 " --> pdb=" O ILE E 703 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 742 removed outlier: 3.958A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 763 removed outlier: 3.609A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN E 763 " --> pdb=" O ALA E 759 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'F' and resid 134 through 139 removed outlier: 4.434A pdb=" N TYR F 138 " --> pdb=" O TYR F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 212 through 226 removed outlier: 3.525A pdb=" N ILE F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET F 219 " --> pdb=" O GLN F 215 " (cutoff:3.500A) removed outlier: 5.319A 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 228 through 233 removed outlier: 3.676A pdb=" N ALA F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 removed outlier: 3.629A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 277 removed outlier: 3.685A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 removed outlier: 4.018A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA F 289 " --> pdb=" O ASN F 285 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.543A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 334 removed outlier: 3.937A pdb=" N ARG F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.533A pdb=" N ARG F 358 " --> pdb=" O PRO F 355 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG F 359 " --> pdb=" O ALA F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 removed outlier: 4.589A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE F 380 " --> pdb=" O GLY F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 403 removed outlier: 3.604A pdb=" N GLU F 402 " --> pdb=" O GLN F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 426 removed outlier: 3.813A pdb=" N ALA F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 482 through 506 Proline residue: F 496 - end of helix Proline residue: F 500 - end of helix removed outlier: 3.559A pdb=" N LYS F 505 " --> pdb=" O ASP F 501 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.517A pdb=" N ILE F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 558 through 569 Processing helix chain 'F' and resid 580 through 587 Processing helix chain 'F' and resid 598 through 610 removed outlier: 3.542A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.684A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 Processing helix chain 'F' and resid 671 through 679 removed outlier: 4.028A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA F 676 " --> pdb=" O LEU F 672 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 707 removed outlier: 3.549A pdb=" N ILE F 690 " --> pdb=" O ASP F 686 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 707 " --> pdb=" O ILE F 703 " (cutoff:3.500A) Processing helix chain 'F' and resid 734 through 742 removed outlier: 3.958A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 763 removed outlier: 3.609A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN F 763 " --> pdb=" O ALA F 759 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AB, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.857A pdb=" N CYS A 69 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 57 " --> pdb=" O CYS A 69 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.675A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.850A pdb=" N CYS A 174 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'A' and resid 265 through 270 removed outlier: 3.506A pdb=" N ASP A 304 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.662A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=BB, first strand: chain 'B' and resid 38 through 40 removed outlier: 3.857A pdb=" N CYS B 69 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 57 " --> pdb=" O CYS B 69 " (cutoff:3.500A) Processing sheet with id=BC, first strand: chain 'B' and resid 117 through 118 removed outlier: 3.675A pdb=" N VAL B 161 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing sheet with id=BD, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.850A pdb=" N CYS B 174 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing sheet with id=BE, first strand: chain 'B' and resid 265 through 270 removed outlier: 3.507A pdb=" N ASP B 304 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing sheet with id=BF, first strand: chain 'B' and resid 538 through 542 removed outlier: 3.662A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 28 through 29 Processing sheet with id=CB, first strand: chain 'C' and resid 38 through 40 removed outlier: 3.857A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL C 57 " --> pdb=" O CYS C 69 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'C' and resid 117 through 118 removed outlier: 3.675A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing sheet with id=CD, first strand: chain 'C' and resid 146 through 147 removed outlier: 3.850A pdb=" N CYS C 174 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing sheet with id=CE, first strand: chain 'C' and resid 265 through 270 removed outlier: 3.507A pdb=" N ASP C 304 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing sheet with id=CF, first strand: chain 'C' and resid 538 through 542 removed outlier: 3.662A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 28 through 29 Processing sheet with id=DB, first strand: chain 'D' and resid 38 through 40 removed outlier: 3.857A pdb=" N CYS D 69 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 57 " --> pdb=" O CYS D 69 " (cutoff:3.500A) Processing sheet with id=DC, first strand: chain 'D' and resid 117 through 118 removed outlier: 3.675A pdb=" N VAL D 161 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id=DD, first strand: chain 'D' and resid 146 through 147 removed outlier: 3.850A pdb=" N CYS D 174 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing sheet with id=DE, first strand: chain 'D' and resid 265 through 270 removed outlier: 3.506A pdb=" N ASP D 304 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing sheet with id=DF, first strand: chain 'D' and resid 538 through 542 removed outlier: 3.661A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=EA, first strand: chain 'E' and resid 28 through 29 Processing sheet with id=EB, first strand: chain 'E' and resid 38 through 40 removed outlier: 3.857A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL E 57 " --> pdb=" O CYS E 69 " (cutoff:3.500A) Processing sheet with id=EC, first strand: chain 'E' and resid 117 through 118 removed outlier: 3.675A pdb=" N VAL E 161 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing sheet with id=ED, first strand: chain 'E' and resid 146 through 147 removed outlier: 3.850A pdb=" N CYS E 174 " --> pdb=" O ILE E 146 " (cutoff:3.500A) Processing sheet with id=EE, first strand: chain 'E' and resid 265 through 270 removed outlier: 3.507A pdb=" N ASP E 304 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) Processing sheet with id=EF, first strand: chain 'E' and resid 538 through 542 removed outlier: 3.662A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=FA, first strand: chain 'F' and resid 28 through 29 Processing sheet with id=FB, first strand: chain 'F' and resid 38 through 40 removed outlier: 3.857A pdb=" N CYS F 69 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL F 57 " --> pdb=" O CYS F 69 " (cutoff:3.500A) Processing sheet with id=FC, first strand: chain 'F' and resid 117 through 118 removed outlier: 3.674A pdb=" N VAL F 161 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id=FD, first strand: chain 'F' and resid 146 through 147 removed outlier: 3.850A pdb=" N CYS F 174 " --> pdb=" O ILE F 146 " (cutoff:3.500A) Processing sheet with id=FE, first strand: chain 'F' and resid 265 through 270 removed outlier: 3.506A pdb=" N ASP F 304 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=FF, first strand: chain 'F' and resid 538 through 542 removed outlier: 3.662A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) 1272 hydrogen bonds defined for protein. 3654 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11253 1.34 - 1.46: 5447 1.46 - 1.58: 18058 1.58 - 1.70: 36 1.70 - 1.82: 288 Bond restraints: 35082 Sorted by residual: bond pdb=" C GLY D 271 " pdb=" N PRO D 272 " ideal model delta sigma weight residual 1.332 1.388 -0.056 8.20e-03 1.49e+04 4.71e+01 bond pdb=" C GLY A 271 " pdb=" N PRO A 272 " ideal model delta sigma weight residual 1.332 1.388 -0.056 8.20e-03 1.49e+04 4.70e+01 bond pdb=" C GLY F 271 " pdb=" N PRO F 272 " ideal model delta sigma weight residual 1.332 1.388 -0.056 8.20e-03 1.49e+04 4.69e+01 bond pdb=" C GLY B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 1.332 1.388 -0.056 8.20e-03 1.49e+04 4.66e+01 bond pdb=" C GLY E 271 " pdb=" N PRO E 272 " ideal model delta sigma weight residual 1.332 1.388 -0.056 8.20e-03 1.49e+04 4.66e+01 ... (remaining 35077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 45386 2.85 - 5.70: 1780 5.70 - 8.55: 234 8.55 - 11.40: 36 11.40 - 14.25: 24 Bond angle restraints: 47460 Sorted by residual: angle pdb=" N ARG C 599 " pdb=" CA ARG C 599 " pdb=" C ARG C 599 " ideal model delta sigma weight residual 111.28 120.40 -9.12 1.09e+00 8.42e-01 7.01e+01 angle pdb=" N ARG E 599 " pdb=" CA ARG E 599 " pdb=" C ARG E 599 " ideal model delta sigma weight residual 111.28 120.36 -9.08 1.09e+00 8.42e-01 6.94e+01 angle pdb=" N SER D 459 " pdb=" CA SER D 459 " pdb=" C SER D 459 " ideal model delta sigma weight residual 111.28 120.16 -8.88 1.09e+00 8.42e-01 6.64e+01 angle pdb=" N SER A 459 " pdb=" CA SER A 459 " pdb=" C SER A 459 " ideal model delta sigma weight residual 111.28 120.14 -8.86 1.09e+00 8.42e-01 6.61e+01 angle pdb=" N SER C 459 " pdb=" CA SER C 459 " pdb=" C SER C 459 " ideal model delta sigma weight residual 111.28 120.14 -8.86 1.09e+00 8.42e-01 6.61e+01 ... (remaining 47455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.49: 21252 34.49 - 68.99: 324 68.99 - 103.48: 48 103.48 - 137.97: 42 137.97 - 172.47: 6 Dihedral angle restraints: 21672 sinusoidal: 9180 harmonic: 12492 Sorted by residual: dihedral pdb=" O2A ADP E 807 " pdb=" O3A ADP E 807 " pdb=" PA ADP E 807 " pdb=" PB ADP E 807 " ideal model delta sinusoidal sigma weight residual -60.00 112.47 -172.47 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP B 807 " pdb=" O3A ADP B 807 " pdb=" PA ADP B 807 " pdb=" PB ADP B 807 " ideal model delta sinusoidal sigma weight residual -60.00 112.45 -172.45 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP A 807 " pdb=" O3A ADP A 807 " pdb=" PA ADP A 807 " pdb=" PB ADP A 807 " ideal model delta sinusoidal sigma weight residual -60.00 112.44 -172.44 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 21669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3962 0.077 - 0.154: 1173 0.154 - 0.231: 133 0.231 - 0.308: 48 0.308 - 0.385: 6 Chirality restraints: 5322 Sorted by residual: chirality pdb=" CA ARG B 599 " pdb=" N ARG B 599 " pdb=" C ARG B 599 " pdb=" CB ARG B 599 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA ARG C 599 " pdb=" N ARG C 599 " pdb=" C ARG C 599 " pdb=" CB ARG C 599 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA ARG E 599 " pdb=" N ARG E 599 " pdb=" C ARG E 599 " pdb=" CB ARG E 599 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 5319 not shown) Planarity restraints: 6198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 728 " -0.050 5.00e-02 4.00e+02 7.61e-02 9.26e+00 pdb=" N PRO A 729 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 729 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 729 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 728 " -0.050 5.00e-02 4.00e+02 7.60e-02 9.24e+00 pdb=" N PRO C 729 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 729 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 729 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 728 " 0.050 5.00e-02 4.00e+02 7.60e-02 9.24e+00 pdb=" N PRO D 729 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 729 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 729 " 0.042 5.00e-02 4.00e+02 ... (remaining 6195 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 300 2.47 - 3.08: 25401 3.08 - 3.68: 52873 3.68 - 4.29: 78188 4.29 - 4.90: 123106 Nonbonded interactions: 279868 Sorted by model distance: nonbonded pdb=" CD2 LEU D 26 " pdb=" O ILE D 100 " model vdw 1.862 3.460 nonbonded pdb=" CD2 LEU E 26 " pdb=" O ILE E 100 " model vdw 1.862 3.460 nonbonded pdb=" CD2 LEU A 26 " pdb=" O ILE A 100 " model vdw 1.863 3.460 nonbonded pdb=" CD2 LEU F 26 " pdb=" O ILE F 100 " model vdw 1.863 3.460 nonbonded pdb=" CD2 LEU C 26 " pdb=" O ILE C 100 " model vdw 1.863 3.460 ... (remaining 279863 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: 0.010 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.000 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.099 35082 Z= 0.456 Angle : 1.303 14.252 47460 Z= 0.736 Chirality : 0.072 0.385 5322 Planarity : 0.008 0.076 6198 Dihedral : 14.886 172.467 13572 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 40.79 Ramachandran Plot: Outliers : 0.97 % Allowed : 5.70 % Favored : 93.32 % Rotamer: Outliers : 0.81 % Allowed : 2.93 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % 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: -3.32 (0.10), residues: 4314 helix: -2.64 (0.10), residues: 1596 sheet: -1.66 (0.18), residues: 546 loop : -1.91 (0.11), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG F 147 TYR 0.036 0.005 TYR C 644 PHE 0.047 0.005 PHE C 360 TRP 0.031 0.003 TRP F 551 HIS 0.020 0.005 HIS F 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00970 / 0.46 (35082) covalent geometry : angle 1.30315 / 0.74 (47460) hydrogen bonds : bond 0.27099 / 18.19 ( 1272) hydrogen bonds : angle 9.20878 / 6.43 ( 3654) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 782 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 GLN cc_start: 0.7359 (tt0) cc_final: 0.7124 (tt0) REVERT: A 222 LEU cc_start: 0.7723 (mt) cc_final: 0.7415 (mm) REVERT: A 236 LYS cc_start: 0.5599 (tptp) cc_final: 0.5292 (tptt) REVERT: A 239 ARG cc_start: 0.5620 (mtt180) cc_final: 0.5145 (mmp-170) REVERT: A 288 LYS cc_start: 0.7113 (ttmt) cc_final: 0.6699 (pttp) REVERT: A 291 GLU cc_start: 0.5898 (tm-30) cc_final: 0.5597 (tm-30) REVERT: A 304 ASP cc_start: 0.7896 (p0) cc_final: 0.7164 (t0) REVERT: A 349 ARG cc_start: 0.6483 (mtt180) cc_final: 0.6163 (mtm-85) REVERT: A 360 PHE cc_start: 0.6345 (t80) cc_final: 0.5989 (t80) REVERT: A 389 LYS cc_start: 0.5271 (tptm) cc_final: 0.4853 (tptt) REVERT: A 397 GLU cc_start: 0.6494 (tt0) cc_final: 0.5974 (tm-30) REVERT: A 470 GLU cc_start: 0.7372 (tt0) cc_final: 0.7130 (pm20) REVERT: A 505 LYS cc_start: 0.6131 (tttm) cc_final: 0.5665 (mmpt) REVERT: A 546 GLU cc_start: 0.8306 (tt0) cc_final: 0.7729 (tp30) REVERT: A 636 PRO cc_start: 0.7356 (Cg_exo) cc_final: 0.7050 (Cg_endo) REVERT: A 638 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6692 (mmt-90) REVERT: A 738 GLU cc_start: 0.6619 (tp30) cc_final: 0.6306 (tt0) REVERT: A 741 ARG cc_start: 0.6288 (mtp-110) cc_final: 0.4841 (tpp-160) REVERT: A 754 LYS cc_start: 0.5869 (mmtt) cc_final: 0.5348 (ptmt) REVERT: B 215 GLN cc_start: 0.7309 (tt0) cc_final: 0.7006 (tt0) REVERT: B 239 ARG cc_start: 0.5667 (mtt180) cc_final: 0.5301 (mmp-170) REVERT: B 288 LYS cc_start: 0.6963 (ttmt) cc_final: 0.6679 (pttp) REVERT: B 291 GLU cc_start: 0.5977 (tm-30) cc_final: 0.5673 (tm-30) REVERT: B 349 ARG cc_start: 0.6494 (mtt180) cc_final: 0.6161 (mtm-85) REVERT: B 397 GLU cc_start: 0.6536 (tt0) cc_final: 0.5942 (tm-30) REVERT: B 465 ARG cc_start: 0.5937 (mmt180) cc_final: 0.5332 (mtt-85) REVERT: B 470 GLU cc_start: 0.7282 (tt0) cc_final: 0.7082 (pm20) REVERT: B 546 GLU cc_start: 0.8313 (tt0) cc_final: 0.7763 (tp30) REVERT: B 636 PRO cc_start: 0.7422 (Cg_exo) cc_final: 0.7120 (Cg_endo) REVERT: B 638 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6797 (mmt-90) REVERT: B 674 PHE cc_start: 0.6233 (t80) cc_final: 0.5957 (t80) REVERT: B 689 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6690 (tm-30) REVERT: B 738 GLU cc_start: 0.6586 (tp30) cc_final: 0.6310 (tt0) REVERT: B 741 ARG cc_start: 0.6253 (mtp-110) cc_final: 0.5665 (mmt-90) REVERT: B 754 LYS cc_start: 0.5778 (mmtt) cc_final: 0.5270 (ptmt) REVERT: C 215 GLN cc_start: 0.7372 (tt0) cc_final: 0.7061 (tt0) REVERT: C 236 LYS cc_start: 0.5821 (tptp) cc_final: 0.5547 (tptt) REVERT: C 239 ARG cc_start: 0.5586 (mtt180) cc_final: 0.5198 (mmp-170) REVERT: C 349 ARG cc_start: 0.6483 (mtt180) cc_final: 0.6078 (mtm-85) REVERT: C 397 GLU cc_start: 0.6537 (tt0) cc_final: 0.5943 (tm-30) REVERT: C 470 GLU cc_start: 0.7348 (tt0) cc_final: 0.7093 (pm20) REVERT: C 495 TYR cc_start: 0.8093 (m-10) cc_final: 0.7832 (m-10) REVERT: C 546 GLU cc_start: 0.8301 (tt0) cc_final: 0.7739 (tp30) REVERT: C 636 PRO cc_start: 0.7515 (Cg_exo) cc_final: 0.7187 (Cg_endo) REVERT: C 638 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6744 (mmt-90) REVERT: C 650 GLU cc_start: 0.5829 (pm20) cc_final: 0.5611 (pm20) REVERT: C 701 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6599 (tp30) REVERT: C 738 GLU cc_start: 0.6621 (tp30) cc_final: 0.6301 (tt0) REVERT: C 741 ARG cc_start: 0.6334 (mtp-110) cc_final: 0.5727 (mmt-90) REVERT: C 754 LYS cc_start: 0.5888 (mmtt) cc_final: 0.5336 (ptmt) REVERT: D 222 LEU cc_start: 0.7803 (mt) cc_final: 0.7477 (mm) REVERT: D 236 LYS cc_start: 0.5627 (tptp) cc_final: 0.5314 (tptt) REVERT: D 239 ARG cc_start: 0.5593 (mtt180) cc_final: 0.5145 (mmp-170) REVERT: D 288 LYS cc_start: 0.7107 (ttmt) cc_final: 0.6708 (pttp) REVERT: D 291 GLU cc_start: 0.5839 (tm-30) cc_final: 0.5525 (tm-30) REVERT: D 304 ASP cc_start: 0.7864 (p0) cc_final: 0.7180 (t0) REVERT: D 321 GLU cc_start: 0.6732 (tp30) cc_final: 0.6088 (pm20) REVERT: D 349 ARG cc_start: 0.6477 (mtt180) cc_final: 0.6138 (mtm-85) REVERT: D 360 PHE cc_start: 0.6412 (t80) cc_final: 0.6044 (t80) REVERT: D 397 GLU cc_start: 0.6575 (tt0) cc_final: 0.6040 (tm-30) REVERT: D 465 ARG cc_start: 0.5956 (mmt180) cc_final: 0.5483 (mtt-85) REVERT: D 470 GLU cc_start: 0.7401 (tt0) cc_final: 0.7166 (pm20) REVERT: D 546 GLU cc_start: 0.8289 (tt0) cc_final: 0.7723 (tp30) REVERT: D 636 PRO cc_start: 0.7338 (Cg_exo) cc_final: 0.7016 (Cg_endo) REVERT: D 638 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.6751 (mmt-90) REVERT: D 738 GLU cc_start: 0.6608 (tp30) cc_final: 0.6326 (tt0) REVERT: D 741 ARG cc_start: 0.6255 (mtp-110) cc_final: 0.4841 (tpp-160) REVERT: D 754 LYS cc_start: 0.5859 (mmtt) cc_final: 0.5341 (ptmt) REVERT: E 215 GLN cc_start: 0.7308 (tt0) cc_final: 0.7001 (tt0) REVERT: E 239 ARG cc_start: 0.5660 (mtt180) cc_final: 0.5293 (mmp-170) REVERT: E 288 LYS cc_start: 0.6981 (ttmt) cc_final: 0.6697 (pttp) REVERT: E 291 GLU cc_start: 0.5952 (tm-30) cc_final: 0.5645 (tm-30) REVERT: E 349 ARG cc_start: 0.6505 (mtt180) cc_final: 0.6172 (mtm-85) REVERT: E 397 GLU cc_start: 0.6537 (tt0) cc_final: 0.5937 (tm-30) REVERT: E 465 ARG cc_start: 0.5929 (mmt180) cc_final: 0.5323 (mtt-85) REVERT: E 546 GLU cc_start: 0.8314 (tt0) cc_final: 0.7760 (tp30) REVERT: E 636 PRO cc_start: 0.7416 (Cg_exo) cc_final: 0.7111 (Cg_endo) REVERT: E 638 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6795 (mmt-90) REVERT: E 650 GLU cc_start: 0.5877 (pm20) cc_final: 0.5672 (pm20) REVERT: E 674 PHE cc_start: 0.6240 (t80) cc_final: 0.5968 (t80) REVERT: E 689 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6696 (tm-30) REVERT: E 738 GLU cc_start: 0.6562 (tp30) cc_final: 0.6333 (tt0) REVERT: E 741 ARG cc_start: 0.6242 (mtp-110) cc_final: 0.5660 (mmt-90) REVERT: E 754 LYS cc_start: 0.5788 (mmtt) cc_final: 0.5536 (ttpt) REVERT: F 215 GLN cc_start: 0.7374 (tt0) cc_final: 0.7064 (tt0) REVERT: F 236 LYS cc_start: 0.5822 (tptp) cc_final: 0.5546 (tptt) REVERT: F 239 ARG cc_start: 0.5599 (mtt180) cc_final: 0.5208 (mmp-170) REVERT: F 288 LYS cc_start: 0.7054 (ttmt) cc_final: 0.6833 (pttt) REVERT: F 291 GLU cc_start: 0.5962 (tm-30) cc_final: 0.5691 (tm-30) REVERT: F 321 GLU cc_start: 0.6487 (tp30) cc_final: 0.5947 (pm20) REVERT: F 349 ARG cc_start: 0.6480 (mtt180) cc_final: 0.6073 (mtm-85) REVERT: F 397 GLU cc_start: 0.6540 (tt0) cc_final: 0.5941 (tm-30) REVERT: F 470 GLU cc_start: 0.7367 (tt0) cc_final: 0.7100 (pm20) REVERT: F 495 TYR cc_start: 0.8095 (m-10) cc_final: 0.7860 (m-10) REVERT: F 546 GLU cc_start: 0.8303 (tt0) cc_final: 0.7737 (tp30) REVERT: F 636 PRO cc_start: 0.7500 (Cg_exo) cc_final: 0.7178 (Cg_endo) REVERT: F 638 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6755 (mmt-90) REVERT: F 650 GLU cc_start: 0.5815 (pm20) cc_final: 0.5576 (pm20) REVERT: F 701 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6630 (tp30) REVERT: F 738 GLU cc_start: 0.6630 (tp30) cc_final: 0.6303 (tt0) REVERT: F 741 ARG cc_start: 0.6331 (mtp-110) cc_final: 0.5729 (mmt-90) REVERT: F 754 LYS cc_start: 0.5917 (mmtt) cc_final: 0.5366 (ptmt) outliers start: 30 outliers final: 15 residues processed: 806 average time/residue: 0.8738 time to fit residues: 814.6441 Evaluate side-chains 534 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 513 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain E residue 669 ASP Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 638 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS A 212 GLN A 460 ASN A 536 GLN A 568 GLN A 603 GLN A 692 GLN A 763 GLN B 115 HIS B 212 GLN B 460 ASN B 536 GLN B 568 GLN B 603 GLN B 692 GLN B 763 GLN C 115 HIS C 212 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 536 GLN C 568 GLN C 603 GLN C 692 GLN C 763 GLN D 115 HIS D 212 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN D 536 GLN D 568 GLN D 603 GLN D 692 GLN D 763 GLN E 115 HIS E 212 GLN E 226 HIS E 460 ASN E 536 GLN E 568 GLN E 603 GLN E 692 GLN E 763 GLN F 115 HIS F 212 GLN F 536 GLN F 568 GLN F 603 GLN F 692 GLN F 763 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.242271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.219173 restraints weight = 41807.271| |-----------------------------------------------------------------------------| r_work (start): 0.4483 rms_B_bonded: 1.45 r_work: 0.4257 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.4169 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35082 Z= 0.177 Angle : 0.853 10.590 47460 Z= 0.426 Chirality : 0.051 0.218 5322 Planarity : 0.006 0.063 6198 Dihedral : 13.973 156.409 4973 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.89 % Favored : 94.83 % Rotamer: Outliers : 3.28 % Allowed : 11.68 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % 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: -2.09 (0.11), residues: 4314 helix: -1.24 (0.11), residues: 1650 sheet: -0.86 (0.20), residues: 564 loop : -1.58 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 210 TYR 0.014 0.002 TYR E 495 PHE 0.027 0.002 PHE F 139 TRP 0.009 0.002 TRP C 551 HIS 0.010 0.002 HIS E 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (35082) covalent geometry : angle 0.85272 / 0.43 (47460) hydrogen bonds : bond 0.05455 / 3.68 ( 1272) hydrogen bonds : angle 5.70851 / 3.96 ( 3654) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 663 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 GLN cc_start: 0.7115 (tt0) cc_final: 0.6899 (tt0) REVERT: A 401 ASN cc_start: 0.5939 (m-40) cc_final: 0.5673 (m110) REVERT: A 440 GLU cc_start: 0.4636 (tm-30) cc_final: 0.4384 (mt-10) REVERT: A 451 ASP cc_start: 0.6744 (m-30) cc_final: 0.6365 (m-30) REVERT: A 550 MET cc_start: 0.7417 (mtm) cc_final: 0.7186 (mtm) REVERT: A 633 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.7113 (mm) REVERT: A 636 PRO cc_start: 0.6839 (Cg_exo) cc_final: 0.6622 (Cg_endo) REVERT: A 638 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.5822 (mmt-90) REVERT: A 689 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6603 (tm-30) REVERT: A 741 ARG cc_start: 0.6109 (mtp-110) cc_final: 0.5782 (mmt-90) REVERT: B 556 GLU cc_start: 0.7014 (pm20) cc_final: 0.6670 (pm20) REVERT: B 638 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6480 (mmt-90) REVERT: B 741 ARG cc_start: 0.6124 (mtp-110) cc_final: 0.5875 (mmt-90) REVERT: C 291 GLU cc_start: 0.5715 (tm-30) cc_final: 0.5489 (tm-30) REVERT: C 401 ASN cc_start: 0.6183 (m-40) cc_final: 0.5974 (m110) REVERT: C 451 ASP cc_start: 0.6746 (m-30) cc_final: 0.6540 (m-30) REVERT: C 465 ARG cc_start: 0.6229 (mmt90) cc_final: 0.5605 (mtt-85) REVERT: C 636 PRO cc_start: 0.6900 (Cg_exo) cc_final: 0.6664 (Cg_endo) REVERT: C 638 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6510 (mmt-90) REVERT: C 675 LEU cc_start: 0.6992 (tt) cc_final: 0.6780 (tp) REVERT: D 401 ASN cc_start: 0.5981 (m-40) cc_final: 0.5747 (m110) REVERT: D 451 ASP cc_start: 0.6625 (m-30) cc_final: 0.6371 (m-30) REVERT: D 550 MET cc_start: 0.7422 (mtm) cc_final: 0.7151 (mtm) REVERT: D 633 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.7095 (mm) REVERT: D 636 PRO cc_start: 0.6857 (Cg_exo) cc_final: 0.6635 (Cg_endo) REVERT: D 638 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.5824 (mmt-90) REVERT: D 649 ASP cc_start: 0.5145 (m-30) cc_final: 0.4764 (m-30) REVERT: D 741 ARG cc_start: 0.6103 (mtp-110) cc_final: 0.5778 (mmt-90) REVERT: E 215 GLN cc_start: 0.7201 (tt0) cc_final: 0.6932 (tt0) REVERT: E 465 ARG cc_start: 0.6177 (mmt180) cc_final: 0.5744 (mtt-85) REVERT: E 556 GLU cc_start: 0.6989 (pm20) cc_final: 0.6682 (pm20) REVERT: E 638 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6506 (mmt-90) REVERT: E 741 ARG cc_start: 0.6135 (mtp-110) cc_final: 0.5862 (mmt-90) REVERT: E 758 PHE cc_start: 0.6773 (t80) cc_final: 0.6538 (t80) REVERT: F 288 LYS cc_start: 0.7184 (ttmt) cc_final: 0.6965 (tmmt) REVERT: F 451 ASP cc_start: 0.6713 (m-30) cc_final: 0.6503 (m-30) REVERT: F 465 ARG cc_start: 0.6236 (mmt90) cc_final: 0.5590 (mtt-85) REVERT: F 636 PRO cc_start: 0.6909 (Cg_exo) cc_final: 0.6676 (Cg_endo) REVERT: F 638 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.5812 (mmt-90) REVERT: F 675 LEU cc_start: 0.6994 (tt) cc_final: 0.6756 (tp) outliers start: 121 outliers final: 27 residues processed: 739 average time/residue: 0.8119 time to fit residues: 705.0559 Evaluate side-chains 533 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 498 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 638 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 147 optimal weight: 20.0000 chunk 129 optimal weight: 30.0000 chunk 225 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 190 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 348 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 389 optimal weight: 3.9990 chunk 338 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 ASN A 533 ASN A 616 ASN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN B 382 GLN B 401 ASN B 460 ASN B 533 ASN B 616 ASN C 226 HIS ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 616 ASN D 382 GLN D 460 ASN D 533 ASN D 616 ASN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN E 382 GLN E 401 ASN E 460 ASN E 533 ASN E 616 ASN F 129 ASN F 226 HIS F 401 ASN ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN F 616 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.237784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.214524 restraints weight = 41922.197| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 1.50 r_work: 0.4219 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.4124 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 35082 Z= 0.248 Angle : 0.919 10.815 47460 Z= 0.457 Chirality : 0.054 0.238 5322 Planarity : 0.006 0.065 6198 Dihedral : 13.992 146.937 4956 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.26 % Favored : 93.60 % Rotamer: Outliers : 4.80 % Allowed : 15.15 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % 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: -1.74 (0.12), residues: 4314 helix: -0.64 (0.12), residues: 1614 sheet: -0.70 (0.21), residues: 582 loop : -1.66 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 147 TYR 0.016 0.003 TYR E 495 PHE 0.031 0.003 PHE D 360 TRP 0.009 0.002 TRP E 551 HIS 0.011 0.002 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.25 (35082) covalent geometry : angle 0.91930 / 0.46 (47460) hydrogen bonds : bond 0.05876 / 3.94 ( 1272) hydrogen bonds : angle 5.59711 / 3.87 ( 3654) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 515 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.7644 (tmmt) cc_final: 0.7412 (ptmm) REVERT: A 627 ASP cc_start: 0.6769 (OUTLIER) cc_final: 0.6258 (m-30) REVERT: A 633 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7153 (mm) REVERT: A 638 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6432 (mmt-90) REVERT: A 741 ARG cc_start: 0.6345 (mtp-110) cc_final: 0.5899 (mmt-90) REVERT: A 754 LYS cc_start: 0.5721 (ttpt) cc_final: 0.5457 (tmmm) REVERT: B 89 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.4199 (ttp80) REVERT: B 315 LYS cc_start: 0.3369 (OUTLIER) cc_final: 0.3083 (pttp) REVERT: B 397 GLU cc_start: 0.5843 (OUTLIER) cc_final: 0.5584 (tm-30) REVERT: B 401 ASN cc_start: 0.6093 (m-40) cc_final: 0.5843 (m110) REVERT: B 556 GLU cc_start: 0.7191 (pm20) cc_final: 0.6811 (pm20) REVERT: B 627 ASP cc_start: 0.6706 (OUTLIER) cc_final: 0.6131 (m-30) REVERT: B 634 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7844 (mt) REVERT: B 638 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6488 (mmt-90) REVERT: B 741 ARG cc_start: 0.6488 (mtp-110) cc_final: 0.6045 (mmt-90) REVERT: C 382 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6649 (mt0) REVERT: C 465 ARG cc_start: 0.6245 (mmt90) cc_final: 0.5874 (mtt-85) REVERT: C 638 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6445 (mmt-90) REVERT: C 669 ASP cc_start: 0.3897 (t0) cc_final: 0.3308 (OUTLIER) REVERT: C 757 MET cc_start: 0.6414 (OUTLIER) cc_final: 0.6092 (ptp) REVERT: D 288 LYS cc_start: 0.7686 (tmmt) cc_final: 0.7447 (ptmm) REVERT: D 294 GLU cc_start: 0.6079 (mm-30) cc_final: 0.5876 (tp30) REVERT: D 627 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.6240 (m-30) REVERT: D 633 ILE cc_start: 0.7386 (OUTLIER) cc_final: 0.7149 (mm) REVERT: D 638 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6460 (mmt-90) REVERT: D 669 ASP cc_start: 0.3939 (t0) cc_final: 0.3428 (OUTLIER) REVERT: D 741 ARG cc_start: 0.6374 (mtp-110) cc_final: 0.5974 (mmt-90) REVERT: E 89 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.4208 (ttp80) REVERT: E 215 GLN cc_start: 0.7243 (tt0) cc_final: 0.7030 (tt0) REVERT: E 294 GLU cc_start: 0.6342 (mm-30) cc_final: 0.6111 (tp30) REVERT: E 397 GLU cc_start: 0.5711 (OUTLIER) cc_final: 0.5449 (tm-30) REVERT: E 401 ASN cc_start: 0.6034 (m-40) cc_final: 0.5755 (m110) REVERT: E 556 GLU cc_start: 0.7219 (pm20) cc_final: 0.6827 (pm20) REVERT: E 627 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6223 (m-30) REVERT: E 634 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7886 (mt) REVERT: E 638 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6491 (mmt-90) REVERT: E 741 ARG cc_start: 0.6381 (mtp-110) cc_final: 0.5997 (mmt-90) REVERT: E 754 LYS cc_start: 0.5726 (OUTLIER) cc_final: 0.5190 (ptmt) REVERT: F 359 ARG cc_start: 0.6359 (ttm170) cc_final: 0.6045 (mmt90) REVERT: F 382 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6640 (mt0) REVERT: F 401 ASN cc_start: 0.6087 (m-40) cc_final: 0.5823 (m110) REVERT: F 638 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6477 (mmt-90) outliers start: 177 outliers final: 65 residues processed: 638 average time/residue: 0.7208 time to fit residues: 547.7934 Evaluate side-chains 547 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 461 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 754 LYS Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 638 ARG Chi-restraints excluded: chain F residue 669 ASP Chi-restraints excluded: chain F residue 678 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 326 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 377 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 426 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 chunk 308 optimal weight: 0.6980 chunk 239 optimal weight: 5.9990 chunk 271 optimal weight: 7.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN A 460 ASN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN D 401 ASN D 460 ASN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.238419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.214917 restraints weight = 41799.308| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 1.52 r_work: 0.4234 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.4136 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 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 : 0.004 0.043 35082 Z= 0.195 Angle : 0.817 9.821 47460 Z= 0.406 Chirality : 0.050 0.247 5322 Planarity : 0.005 0.063 6198 Dihedral : 13.467 134.145 4956 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.05 % Favored : 93.81 % Rotamer: Outliers : 4.50 % Allowed : 16.75 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % 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: -1.41 (0.12), residues: 4314 helix: -0.25 (0.13), residues: 1614 sheet: -0.70 (0.22), residues: 564 loop : -1.52 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 147 TYR 0.017 0.002 TYR F 244 PHE 0.028 0.002 PHE A 360 TRP 0.008 0.002 TRP E 551 HIS 0.010 0.002 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (35082) covalent geometry : angle 0.81746 / 0.41 (47460) hydrogen bonds : bond 0.05065 / 3.40 ( 1272) hydrogen bonds : angle 5.26717 / 3.65 ( 3654) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 495 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.7721 (tmmt) cc_final: 0.7390 (ptmm) REVERT: A 304 ASP cc_start: 0.7005 (t0) cc_final: 0.6735 (t0) REVERT: A 315 LYS cc_start: 0.3048 (OUTLIER) cc_final: 0.2683 (ptpt) REVERT: A 397 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.5382 (tm-30) REVERT: A 440 GLU cc_start: 0.4789 (tm-30) cc_final: 0.4431 (mt-10) REVERT: A 449 MET cc_start: 0.5504 (tpt) cc_final: 0.5258 (tpt) REVERT: A 633 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.7133 (mm) REVERT: A 638 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6164 (mmt-90) REVERT: A 741 ARG cc_start: 0.6419 (mtp-110) cc_final: 0.5909 (mmt-90) REVERT: A 757 MET cc_start: 0.6055 (OUTLIER) cc_final: 0.5779 (ptp) REVERT: A 758 PHE cc_start: 0.6900 (t80) cc_final: 0.6667 (t80) REVERT: B 340 HIS cc_start: 0.5739 (OUTLIER) cc_final: 0.5516 (m-70) REVERT: B 445 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5398 (tp) REVERT: B 470 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6448 (pp20) REVERT: B 556 GLU cc_start: 0.7105 (pm20) cc_final: 0.6737 (pm20) REVERT: B 627 ASP cc_start: 0.6622 (OUTLIER) cc_final: 0.6061 (m-30) REVERT: B 633 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7254 (mm) REVERT: B 634 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7782 (mt) REVERT: B 638 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6546 (mmt-90) REVERT: B 741 ARG cc_start: 0.6546 (mtp-110) cc_final: 0.6074 (mmt-90) REVERT: C 224 LEU cc_start: 0.6792 (pp) cc_final: 0.6545 (pp) REVERT: C 322 ARG cc_start: 0.6818 (mpt90) cc_final: 0.6555 (mpt-90) REVERT: C 359 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.6250 (ttm170) REVERT: C 382 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6594 (mt0) REVERT: C 550 MET cc_start: 0.7452 (mtm) cc_final: 0.7057 (mtm) REVERT: C 556 GLU cc_start: 0.7083 (pm20) cc_final: 0.6785 (pm20) REVERT: C 638 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6550 (mmt-90) REVERT: C 754 LYS cc_start: 0.5596 (ttpt) cc_final: 0.5393 (tmmm) REVERT: D 288 LYS cc_start: 0.7714 (tmmt) cc_final: 0.7390 (ptmm) REVERT: D 315 LYS cc_start: 0.3031 (OUTLIER) cc_final: 0.2685 (ptpt) REVERT: D 445 LEU cc_start: 0.5677 (OUTLIER) cc_final: 0.5145 (tp) REVERT: D 556 GLU cc_start: 0.7211 (pm20) cc_final: 0.6900 (pm20) REVERT: D 633 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7171 (mm) REVERT: D 638 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6174 (mmt-90) REVERT: D 741 ARG cc_start: 0.6436 (mtp-110) cc_final: 0.5957 (mmt-90) REVERT: D 757 MET cc_start: 0.6016 (OUTLIER) cc_final: 0.5737 (ptp) REVERT: E 89 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.4289 (ttp80) REVERT: E 215 GLN cc_start: 0.7208 (tt0) cc_final: 0.7005 (tt0) REVERT: E 340 HIS cc_start: 0.5697 (OUTLIER) cc_final: 0.5480 (m-70) REVERT: E 445 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5368 (tp) REVERT: E 556 GLU cc_start: 0.7102 (pm20) cc_final: 0.6741 (pm20) REVERT: E 627 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.6052 (m-30) REVERT: E 633 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7254 (mm) REVERT: E 634 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7783 (mt) REVERT: E 638 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6550 (mmt-90) REVERT: E 741 ARG cc_start: 0.6524 (mtp-110) cc_final: 0.6060 (mmt-90) REVERT: E 754 LYS cc_start: 0.5734 (OUTLIER) cc_final: 0.5203 (ptmt) REVERT: F 224 LEU cc_start: 0.6759 (pp) cc_final: 0.6476 (pp) REVERT: F 322 ARG cc_start: 0.6803 (mpt90) cc_final: 0.6570 (mpt-90) REVERT: F 382 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6552 (mt0) REVERT: F 556 GLU cc_start: 0.7129 (pm20) cc_final: 0.6758 (pm20) REVERT: F 638 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6542 (mmt-90) REVERT: F 757 MET cc_start: 0.6282 (OUTLIER) cc_final: 0.5990 (ptp) outliers start: 166 outliers final: 61 residues processed: 603 average time/residue: 0.7287 time to fit residues: 522.4149 Evaluate side-chains 522 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 430 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 754 LYS Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 638 ARG Chi-restraints excluded: chain F residue 678 MET Chi-restraints excluded: chain F residue 704 GLU Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 158 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 409 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 379 optimal weight: 8.9990 chunk 326 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 ASN B 351 ASN B 382 GLN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN D 460 ASN E 382 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.237729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.214436 restraints weight = 41901.501| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 1.44 r_work: 0.4227 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4134 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 35082 Z= 0.210 Angle : 0.845 10.092 47460 Z= 0.422 Chirality : 0.051 0.258 5322 Planarity : 0.006 0.065 6198 Dihedral : 13.550 132.069 4956 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.91 % Favored : 92.95 % Rotamer: Outliers : 5.07 % Allowed : 17.05 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % 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: -1.35 (0.12), residues: 4314 helix: -0.21 (0.12), residues: 1662 sheet: -0.72 (0.22), residues: 564 loop : -1.48 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 653 TYR 0.015 0.002 TYR B 495 PHE 0.029 0.003 PHE C 139 TRP 0.008 0.002 TRP C 476 HIS 0.011 0.002 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (35082) covalent geometry : angle 0.84537 / 0.42 (47460) hydrogen bonds : bond 0.05263 / 3.52 ( 1272) hydrogen bonds : angle 5.30590 / 3.69 ( 3654) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 462 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.7676 (tmmt) cc_final: 0.7365 (ptmm) REVERT: A 304 ASP cc_start: 0.7060 (t0) cc_final: 0.6835 (t0) REVERT: A 315 LYS cc_start: 0.2907 (OUTLIER) cc_final: 0.2556 (ptpt) REVERT: A 445 LEU cc_start: 0.5663 (OUTLIER) cc_final: 0.5081 (tp) REVERT: A 627 ASP cc_start: 0.6907 (OUTLIER) cc_final: 0.6466 (p0) REVERT: A 633 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7216 (mm) REVERT: A 638 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6229 (mmt-90) REVERT: A 650 GLU cc_start: 0.5528 (mp0) cc_final: 0.5314 (mt-10) REVERT: A 674 PHE cc_start: 0.6443 (t80) cc_final: 0.6154 (t80) REVERT: A 741 ARG cc_start: 0.6449 (mtp-110) cc_final: 0.5955 (mmt-90) REVERT: B 89 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.4168 (ttp80) REVERT: B 198 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5683 (mm) REVERT: B 322 ARG cc_start: 0.6771 (ttp-110) cc_final: 0.6325 (mmt180) REVERT: B 445 LEU cc_start: 0.5837 (OUTLIER) cc_final: 0.5448 (tp) REVERT: B 556 GLU cc_start: 0.7185 (pm20) cc_final: 0.6793 (pm20) REVERT: B 627 ASP cc_start: 0.6670 (OUTLIER) cc_final: 0.6088 (m-30) REVERT: B 633 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7316 (mm) REVERT: B 634 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7816 (mt) REVERT: B 638 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6402 (mmt-90) REVERT: B 650 GLU cc_start: 0.5691 (mp0) cc_final: 0.5181 (mt-10) REVERT: B 741 ARG cc_start: 0.6568 (mtp-110) cc_final: 0.6102 (mmt-90) REVERT: B 754 LYS cc_start: 0.5629 (OUTLIER) cc_final: 0.4359 (ttpt) REVERT: C 322 ARG cc_start: 0.6831 (mpt90) cc_final: 0.6430 (mpt-90) REVERT: C 359 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.6237 (ttm170) REVERT: C 382 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6594 (mt0) REVERT: C 445 LEU cc_start: 0.5605 (OUTLIER) cc_final: 0.5122 (tp) REVERT: C 550 MET cc_start: 0.7536 (mtm) cc_final: 0.7205 (mtm) REVERT: C 556 GLU cc_start: 0.7110 (pm20) cc_final: 0.6828 (pm20) REVERT: C 638 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6403 (mmt-90) REVERT: C 754 LYS cc_start: 0.5565 (ttpt) cc_final: 0.5313 (tmmm) REVERT: C 757 MET cc_start: 0.6161 (OUTLIER) cc_final: 0.5873 (ptp) REVERT: D 288 LYS cc_start: 0.7669 (tmmt) cc_final: 0.7364 (ptmm) REVERT: D 315 LYS cc_start: 0.2875 (OUTLIER) cc_final: 0.2528 (ptpt) REVERT: D 445 LEU cc_start: 0.5563 (OUTLIER) cc_final: 0.5061 (tp) REVERT: D 556 GLU cc_start: 0.7292 (pm20) cc_final: 0.7001 (pm20) REVERT: D 627 ASP cc_start: 0.6851 (OUTLIER) cc_final: 0.6414 (p0) REVERT: D 633 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7201 (mm) REVERT: D 638 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6219 (mmt-90) REVERT: D 741 ARG cc_start: 0.6482 (mtp-110) cc_final: 0.5896 (mmm160) REVERT: D 757 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.5839 (ptp) REVERT: E 89 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.4294 (ttp80) REVERT: E 198 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5709 (mm) REVERT: E 225 ARG cc_start: 0.6669 (tmt-80) cc_final: 0.6372 (tpt90) REVERT: E 322 ARG cc_start: 0.6768 (ttp-110) cc_final: 0.6324 (mmt180) REVERT: E 445 LEU cc_start: 0.5833 (OUTLIER) cc_final: 0.5432 (tp) REVERT: E 556 GLU cc_start: 0.7171 (pm20) cc_final: 0.6793 (pm20) REVERT: E 627 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.6102 (m-30) REVERT: E 633 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7309 (mm) REVERT: E 634 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7823 (mt) REVERT: E 638 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6437 (mmt-90) REVERT: E 650 GLU cc_start: 0.5651 (mp0) cc_final: 0.5145 (mt-10) REVERT: E 741 ARG cc_start: 0.6556 (mtp-110) cc_final: 0.6088 (mmt-90) REVERT: E 754 LYS cc_start: 0.5732 (OUTLIER) cc_final: 0.5173 (ptmt) REVERT: F 322 ARG cc_start: 0.6880 (mpt90) cc_final: 0.6482 (mpt-90) REVERT: F 359 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.6194 (ttm170) REVERT: F 382 GLN cc_start: 0.6944 (OUTLIER) cc_final: 0.6535 (mt0) REVERT: F 445 LEU cc_start: 0.5612 (OUTLIER) cc_final: 0.5133 (tp) REVERT: F 638 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6466 (mmt-90) REVERT: F 649 ASP cc_start: 0.5058 (m-30) cc_final: 0.4751 (m-30) REVERT: F 669 ASP cc_start: 0.4294 (t0) cc_final: 0.3606 (p0) outliers start: 187 outliers final: 70 residues processed: 596 average time/residue: 0.7173 time to fit residues: 510.9927 Evaluate side-chains 524 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 418 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 754 LYS Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 638 ARG Chi-restraints excluded: chain F residue 678 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 188 optimal weight: 4.9990 chunk 324 optimal weight: 9.9990 chunk 317 optimal weight: 30.0000 chunk 231 optimal weight: 0.6980 chunk 389 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 190 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 358 optimal weight: 6.9990 chunk 377 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN A 568 GLN B 382 GLN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 538 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.240687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.215718 restraints weight = 41803.502| |-----------------------------------------------------------------------------| r_work (start): 0.4449 rms_B_bonded: 1.64 r_work: 0.4252 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4156 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35082 Z= 0.136 Angle : 0.726 8.960 47460 Z= 0.356 Chirality : 0.047 0.224 5322 Planarity : 0.005 0.058 6198 Dihedral : 12.683 112.821 4956 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.59 % Favored : 94.18 % Rotamer: Outliers : 4.09 % Allowed : 18.24 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % 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: -0.98 (0.12), residues: 4314 helix: 0.09 (0.13), residues: 1692 sheet: -0.58 (0.22), residues: 546 loop : -1.24 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 25 TYR 0.013 0.002 TYR E 244 PHE 0.028 0.002 PHE D 674 TRP 0.007 0.001 TRP F 476 HIS 0.009 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (35082) covalent geometry : angle 0.72649 / 0.36 (47460) hydrogen bonds : bond 0.04204 / 2.83 ( 1272) hydrogen bonds : angle 4.91212 / 3.41 ( 3654) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 467 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.2999 (OUTLIER) cc_final: 0.2656 (p) REVERT: A 288 LYS cc_start: 0.7597 (tmmt) cc_final: 0.7351 (ptmm) REVERT: A 315 LYS cc_start: 0.2933 (OUTLIER) cc_final: 0.2566 (ptpt) REVERT: A 322 ARG cc_start: 0.6663 (ttp-110) cc_final: 0.6284 (mmt180) REVERT: A 440 GLU cc_start: 0.4773 (tm-30) cc_final: 0.4473 (mt-10) REVERT: A 445 LEU cc_start: 0.5566 (OUTLIER) cc_final: 0.4925 (tp) REVERT: A 449 MET cc_start: 0.5519 (tpt) cc_final: 0.5305 (tpt) REVERT: A 470 GLU cc_start: 0.6912 (pm20) cc_final: 0.6515 (pp20) REVERT: A 627 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6440 (p0) REVERT: A 633 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.7194 (mm) REVERT: A 638 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6352 (mmt-90) REVERT: A 674 PHE cc_start: 0.6369 (t80) cc_final: 0.6079 (t80) REVERT: A 696 LYS cc_start: 0.7090 (ttpt) cc_final: 0.6852 (tttt) REVERT: A 741 ARG cc_start: 0.6312 (mtp-110) cc_final: 0.5820 (mmt-90) REVERT: A 757 MET cc_start: 0.6009 (OUTLIER) cc_final: 0.5768 (ptp) REVERT: B 89 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.4236 (ttp80) REVERT: B 427 MET cc_start: 0.4077 (tpt) cc_final: 0.3545 (tpt) REVERT: B 445 LEU cc_start: 0.5734 (OUTLIER) cc_final: 0.5330 (tp) REVERT: B 470 GLU cc_start: 0.6974 (pm20) cc_final: 0.6506 (pp20) REVERT: B 556 GLU cc_start: 0.6857 (pm20) cc_final: 0.6649 (pm20) REVERT: B 633 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7253 (mm) REVERT: B 634 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7666 (mt) REVERT: B 638 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6552 (mmt-90) REVERT: B 741 ARG cc_start: 0.6487 (mtp-110) cc_final: 0.6004 (mmt-90) REVERT: C 56 THR cc_start: 0.3117 (OUTLIER) cc_final: 0.2821 (p) REVERT: C 236 LYS cc_start: 0.6211 (tptt) cc_final: 0.5879 (tttm) REVERT: C 322 ARG cc_start: 0.6668 (mpt90) cc_final: 0.6353 (mpt-90) REVERT: C 359 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.6195 (ttm170) REVERT: C 470 GLU cc_start: 0.6865 (pm20) cc_final: 0.6487 (pp20) REVERT: C 550 MET cc_start: 0.7428 (mtm) cc_final: 0.7040 (mtm) REVERT: C 556 GLU cc_start: 0.6881 (pm20) cc_final: 0.6564 (pm20) REVERT: C 638 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.5951 (mmt-90) REVERT: C 757 MET cc_start: 0.6023 (OUTLIER) cc_final: 0.5802 (ptp) REVERT: D 288 LYS cc_start: 0.7625 (tmmt) cc_final: 0.7378 (ptmm) REVERT: D 315 LYS cc_start: 0.2868 (OUTLIER) cc_final: 0.2535 (ptpt) REVERT: D 445 LEU cc_start: 0.5423 (OUTLIER) cc_final: 0.4982 (tp) REVERT: D 470 GLU cc_start: 0.6881 (pm20) cc_final: 0.6588 (pp20) REVERT: D 556 GLU cc_start: 0.6990 (pm20) cc_final: 0.6729 (pm20) REVERT: D 627 ASP cc_start: 0.6838 (OUTLIER) cc_final: 0.6421 (p0) REVERT: D 633 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7163 (mm) REVERT: D 638 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6345 (mmt-90) REVERT: D 674 PHE cc_start: 0.6369 (t80) cc_final: 0.6114 (t80) REVERT: D 696 LYS cc_start: 0.7154 (ttpt) cc_final: 0.6925 (tttt) REVERT: D 741 ARG cc_start: 0.6380 (mtp-110) cc_final: 0.5901 (mmp-170) REVERT: D 757 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.5832 (ptp) REVERT: E 225 ARG cc_start: 0.6706 (tmt-80) cc_final: 0.6474 (tpt90) REVERT: E 427 MET cc_start: 0.4073 (tpt) cc_final: 0.3541 (tpt) REVERT: E 445 LEU cc_start: 0.5714 (OUTLIER) cc_final: 0.5303 (tp) REVERT: E 470 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6496 (pp20) REVERT: E 556 GLU cc_start: 0.6840 (pm20) cc_final: 0.6633 (pm20) REVERT: E 633 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7256 (mm) REVERT: E 634 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7676 (mt) REVERT: E 638 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6527 (mmt-90) REVERT: E 741 ARG cc_start: 0.6528 (mtp-110) cc_final: 0.5983 (mmt-90) REVERT: F 56 THR cc_start: 0.3111 (OUTLIER) cc_final: 0.2807 (p) REVERT: F 236 LYS cc_start: 0.6262 (tptt) cc_final: 0.5909 (tttm) REVERT: F 322 ARG cc_start: 0.6725 (mpt90) cc_final: 0.6384 (mpt-90) REVERT: F 359 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.6137 (ttt180) REVERT: F 470 GLU cc_start: 0.6860 (pm20) cc_final: 0.6479 (pp20) REVERT: F 556 GLU cc_start: 0.6847 (pm20) cc_final: 0.6483 (pm20) REVERT: F 638 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.5992 (mmt-90) REVERT: F 696 LYS cc_start: 0.7071 (ttpt) cc_final: 0.6826 (tttt) REVERT: F 757 MET cc_start: 0.5998 (OUTLIER) cc_final: 0.5759 (ptp) outliers start: 151 outliers final: 50 residues processed: 577 average time/residue: 0.6925 time to fit residues: 478.5311 Evaluate side-chains 510 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 429 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 638 ARG Chi-restraints excluded: chain F residue 678 MET Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 315 optimal weight: 20.0000 chunk 206 optimal weight: 6.9990 chunk 210 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 425 optimal weight: 8.9990 chunk 329 optimal weight: 0.0570 chunk 201 optimal weight: 30.0000 chunk 347 optimal weight: 20.0000 chunk 334 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 396 optimal weight: 20.0000 overall best weight: 6.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN F 538 ASN F 568 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.237369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.214277 restraints weight = 41722.703| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 1.47 r_work: 0.4224 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4134 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 35082 Z= 0.210 Angle : 0.833 13.147 47460 Z= 0.412 Chirality : 0.051 0.226 5322 Planarity : 0.006 0.055 6198 Dihedral : 13.309 126.449 4956 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.79 % Favored : 92.98 % Rotamer: Outliers : 3.88 % Allowed : 19.11 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % 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: -1.12 (0.12), residues: 4314 helix: 0.04 (0.13), residues: 1656 sheet: -0.60 (0.22), residues: 564 loop : -1.40 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 653 TYR 0.017 0.002 TYR A 495 PHE 0.027 0.002 PHE F 139 TRP 0.007 0.002 TRP C 476 HIS 0.011 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (35082) covalent geometry : angle 0.83339 / 0.41 (47460) hydrogen bonds : bond 0.05114 / 3.42 ( 1272) hydrogen bonds : angle 5.17331 / 3.59 ( 3654) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 451 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5175 (tp) REVERT: A 633 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.7133 (mm) REVERT: A 638 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6238 (mmt-90) REVERT: A 674 PHE cc_start: 0.6491 (t80) cc_final: 0.6164 (t80) REVERT: A 701 GLU cc_start: 0.6412 (tp30) cc_final: 0.6195 (tp30) REVERT: A 741 ARG cc_start: 0.6409 (mtp-110) cc_final: 0.5947 (mmt-90) REVERT: B 198 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5699 (mm) REVERT: B 427 MET cc_start: 0.4085 (tpt) cc_final: 0.3527 (tpt) REVERT: B 556 GLU cc_start: 0.7184 (pm20) cc_final: 0.6818 (pm20) REVERT: B 627 ASP cc_start: 0.6740 (OUTLIER) cc_final: 0.6278 (p0) REVERT: B 633 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7285 (mm) REVERT: B 634 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7862 (mt) REVERT: B 638 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6491 (mmt-90) REVERT: B 741 ARG cc_start: 0.6506 (mtp-110) cc_final: 0.6117 (mmp-170) REVERT: C 198 LEU cc_start: 0.6115 (OUTLIER) cc_final: 0.5719 (mm) REVERT: C 322 ARG cc_start: 0.6827 (mpt90) cc_final: 0.6499 (mpt-90) REVERT: C 359 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.6233 (ttm170) REVERT: C 465 ARG cc_start: 0.6215 (mmt90) cc_final: 0.5838 (mtt-85) REVERT: C 638 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6105 (mmt-90) REVERT: C 757 MET cc_start: 0.6269 (OUTLIER) cc_final: 0.5984 (ptp) REVERT: D 445 LEU cc_start: 0.5800 (OUTLIER) cc_final: 0.5318 (tp) REVERT: D 556 GLU cc_start: 0.7276 (pm20) cc_final: 0.6948 (pm20) REVERT: D 633 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.7100 (mm) REVERT: D 634 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7800 (mt) REVERT: D 638 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6231 (mmt-90) REVERT: D 650 GLU cc_start: 0.5691 (mp0) cc_final: 0.5198 (mt-10) REVERT: D 674 PHE cc_start: 0.6496 (t80) cc_final: 0.6171 (t80) REVERT: D 741 ARG cc_start: 0.6398 (mtp-110) cc_final: 0.5971 (mmt-90) REVERT: D 757 MET cc_start: 0.6188 (OUTLIER) cc_final: 0.5931 (ptp) REVERT: E 89 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.4261 (ttp80) REVERT: E 198 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5701 (mm) REVERT: E 225 ARG cc_start: 0.6739 (tmt-80) cc_final: 0.6492 (tpt90) REVERT: E 427 MET cc_start: 0.4080 (tpt) cc_final: 0.3538 (tpt) REVERT: E 470 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6467 (pp20) REVERT: E 556 GLU cc_start: 0.7130 (pm20) cc_final: 0.6782 (pm20) REVERT: E 627 ASP cc_start: 0.6756 (OUTLIER) cc_final: 0.6285 (p0) REVERT: E 633 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7278 (mm) REVERT: E 634 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7865 (mt) REVERT: E 638 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6495 (mmt-90) REVERT: E 649 ASP cc_start: 0.5110 (m-30) cc_final: 0.4885 (m-30) REVERT: E 741 ARG cc_start: 0.6486 (mtp-110) cc_final: 0.6091 (mmp-170) REVERT: F 198 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5709 (mm) REVERT: F 322 ARG cc_start: 0.6865 (mpt90) cc_final: 0.6306 (mmt90) REVERT: F 359 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.6156 (ttm170) REVERT: F 465 ARG cc_start: 0.6190 (mmt90) cc_final: 0.5823 (mtt-85) REVERT: F 556 GLU cc_start: 0.7142 (pm20) cc_final: 0.6776 (pm20) REVERT: F 638 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6159 (mmt-90) REVERT: F 689 GLU cc_start: 0.7207 (tm-30) cc_final: 0.7003 (tm-30) REVERT: F 757 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.5974 (ptp) outliers start: 143 outliers final: 59 residues processed: 551 average time/residue: 0.7178 time to fit residues: 471.7446 Evaluate side-chains 507 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 420 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 638 ARG Chi-restraints excluded: chain F residue 678 MET Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 153 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 223 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 421 optimal weight: 5.9990 chunk 278 optimal weight: 8.9990 chunk 229 optimal weight: 20.0000 chunk 202 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 385 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.238549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.215500 restraints weight = 41764.949| |-----------------------------------------------------------------------------| r_work (start): 0.4448 rms_B_bonded: 1.43 r_work: 0.4232 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4134 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35082 Z= 0.180 Angle : 0.791 13.075 47460 Z= 0.391 Chirality : 0.049 0.212 5322 Planarity : 0.005 0.058 6198 Dihedral : 13.093 122.543 4956 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.42 % Favored : 93.35 % Rotamer: Outliers : 3.52 % Allowed : 20.16 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % 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: -1.10 (0.12), residues: 4314 helix: 0.04 (0.13), residues: 1686 sheet: -0.56 (0.23), residues: 546 loop : -1.40 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 744 TYR 0.020 0.002 TYR A 495 PHE 0.025 0.002 PHE B 139 TRP 0.008 0.001 TRP E 551 HIS 0.010 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (35082) covalent geometry : angle 0.79103 / 0.39 (47460) hydrogen bonds : bond 0.04786 / 3.20 ( 1272) hydrogen bonds : angle 5.10037 / 3.54 ( 3654) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 431 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5607 (mm) REVERT: A 288 LYS cc_start: 0.7643 (tmmt) cc_final: 0.7354 (ptmm) REVERT: A 445 LEU cc_start: 0.5634 (OUTLIER) cc_final: 0.5022 (tp) REVERT: A 449 MET cc_start: 0.5506 (tpt) cc_final: 0.5293 (tpt) REVERT: A 465 ARG cc_start: 0.6119 (mmt90) cc_final: 0.5756 (mtt-85) REVERT: A 633 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7194 (mm) REVERT: A 638 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6274 (mmt-90) REVERT: A 673 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5658 (mp0) REVERT: A 674 PHE cc_start: 0.6448 (t80) cc_final: 0.6037 (t80) REVERT: A 741 ARG cc_start: 0.6421 (mtp-110) cc_final: 0.5917 (mmt-90) REVERT: A 757 MET cc_start: 0.6158 (OUTLIER) cc_final: 0.5810 (ptp) REVERT: B 556 GLU cc_start: 0.7129 (pm20) cc_final: 0.6732 (pm20) REVERT: B 627 ASP cc_start: 0.6751 (OUTLIER) cc_final: 0.6247 (p0) REVERT: B 633 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7308 (mm) REVERT: B 634 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7769 (mt) REVERT: B 638 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6492 (mmt-90) REVERT: B 741 ARG cc_start: 0.6601 (mtp-110) cc_final: 0.6123 (mmp-170) REVERT: B 757 MET cc_start: 0.6271 (OUTLIER) cc_final: 0.5997 (ptp) REVERT: C 56 THR cc_start: 0.3043 (OUTLIER) cc_final: 0.2727 (p) REVERT: C 198 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5673 (mm) REVERT: C 359 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6229 (ttm170) REVERT: C 465 ARG cc_start: 0.6132 (mmt90) cc_final: 0.5688 (mtt-85) REVERT: C 550 MET cc_start: 0.7534 (mtm) cc_final: 0.7173 (mtm) REVERT: C 627 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6423 (p0) REVERT: C 638 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6088 (mmt-90) REVERT: C 696 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6715 (ttmt) REVERT: C 757 MET cc_start: 0.6278 (OUTLIER) cc_final: 0.5953 (ptp) REVERT: D 56 THR cc_start: 0.3081 (OUTLIER) cc_final: 0.2730 (p) REVERT: D 135 LEU cc_start: 0.4903 (OUTLIER) cc_final: 0.4623 (mp) REVERT: D 288 LYS cc_start: 0.7650 (tmmt) cc_final: 0.7360 (ptmm) REVERT: D 445 LEU cc_start: 0.5656 (OUTLIER) cc_final: 0.5204 (tp) REVERT: D 556 GLU cc_start: 0.7207 (pm20) cc_final: 0.6895 (pm20) REVERT: D 633 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7180 (mm) REVERT: D 638 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6253 (mmt-90) REVERT: D 650 GLU cc_start: 0.5707 (mp0) cc_final: 0.5265 (mt-10) REVERT: D 674 PHE cc_start: 0.6427 (t80) cc_final: 0.6103 (t80) REVERT: D 741 ARG cc_start: 0.6419 (mtp-110) cc_final: 0.5920 (mmt-90) REVERT: D 757 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5902 (ptp) REVERT: E 89 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.4297 (ttp80) REVERT: E 225 ARG cc_start: 0.6742 (tmt-80) cc_final: 0.6488 (tpt90) REVERT: E 470 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6627 (pp20) REVERT: E 556 GLU cc_start: 0.7091 (pm20) cc_final: 0.6702 (pm20) REVERT: E 627 ASP cc_start: 0.6771 (OUTLIER) cc_final: 0.6268 (p0) REVERT: E 633 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7290 (mm) REVERT: E 634 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7743 (mt) REVERT: E 638 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6012 (mmt-90) REVERT: E 741 ARG cc_start: 0.6614 (mtp-110) cc_final: 0.6113 (mmp-170) REVERT: F 198 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5647 (mm) REVERT: F 322 ARG cc_start: 0.6853 (mpt90) cc_final: 0.6328 (mmt90) REVERT: F 359 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.6185 (ttm170) REVERT: F 465 ARG cc_start: 0.6098 (mmt90) cc_final: 0.5666 (mtt-85) REVERT: F 556 GLU cc_start: 0.7047 (pm20) cc_final: 0.6687 (pm20) REVERT: F 627 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6447 (p0) REVERT: F 638 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6143 (mmt-90) REVERT: F 696 LYS cc_start: 0.7019 (ttpt) cc_final: 0.6764 (tttt) REVERT: F 757 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5883 (ptp) outliers start: 130 outliers final: 54 residues processed: 517 average time/residue: 0.7091 time to fit residues: 439.2931 Evaluate side-chains 501 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 412 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 696 LYS Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 638 ARG Chi-restraints excluded: chain F residue 678 MET Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 349 optimal weight: 10.0000 chunk 313 optimal weight: 0.7980 chunk 389 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 312 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 310 optimal weight: 5.9990 chunk 379 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 538 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.240715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.216816 restraints weight = 41442.949| |-----------------------------------------------------------------------------| r_work (start): 0.4456 rms_B_bonded: 1.48 r_work: 0.4245 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4151 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35082 Z= 0.137 Angle : 0.727 12.578 47460 Z= 0.356 Chirality : 0.047 0.196 5322 Planarity : 0.005 0.054 6198 Dihedral : 12.554 110.567 4956 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.07 % Favored : 93.65 % Rotamer: Outliers : 2.90 % Allowed : 20.68 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % 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: -0.79 (0.13), residues: 4314 helix: 0.33 (0.13), residues: 1686 sheet: -0.54 (0.23), residues: 510 loop : -1.20 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 322 TYR 0.019 0.001 TYR A 495 PHE 0.022 0.002 PHE B 139 TRP 0.007 0.001 TRP C 476 HIS 0.009 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (35082) covalent geometry : angle 0.72731 / 0.36 (47460) hydrogen bonds : bond 0.04125 / 2.75 ( 1272) hydrogen bonds : angle 4.88469 / 3.40 ( 3654) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 448 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: A 56 THR cc_start: 0.2979 (OUTLIER) cc_final: 0.2635 (p) REVERT: A 198 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5526 (mm) REVERT: A 440 GLU cc_start: 0.4740 (tm-30) cc_final: 0.4460 (mt-10) REVERT: A 445 LEU cc_start: 0.5554 (OUTLIER) cc_final: 0.4930 (tp) REVERT: A 449 MET cc_start: 0.5545 (tpt) cc_final: 0.5268 (tpt) REVERT: A 470 GLU cc_start: 0.6930 (pm20) cc_final: 0.6519 (pp20) REVERT: A 627 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6560 (p0) REVERT: A 633 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7189 (mm) REVERT: A 638 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6447 (mmt-90) REVERT: A 673 GLU cc_start: 0.5990 (OUTLIER) cc_final: 0.5736 (mp0) REVERT: A 674 PHE cc_start: 0.6362 (t80) cc_final: 0.6056 (t80) REVERT: A 696 LYS cc_start: 0.7141 (ttpt) cc_final: 0.6933 (tttt) REVERT: A 741 ARG cc_start: 0.6357 (mtp-110) cc_final: 0.5868 (mmp-170) REVERT: B 89 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.4149 (ttp80) REVERT: B 198 LEU cc_start: 0.5948 (OUTLIER) cc_final: 0.5612 (mm) REVERT: B 427 MET cc_start: 0.4075 (tpt) cc_final: 0.3521 (tpt) REVERT: B 470 GLU cc_start: 0.6965 (pm20) cc_final: 0.6496 (pp20) REVERT: B 556 GLU cc_start: 0.6951 (pm20) cc_final: 0.6542 (pm20) REVERT: B 633 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7302 (mm) REVERT: B 634 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7718 (mt) REVERT: B 638 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6736 (mmt-90) REVERT: B 741 ARG cc_start: 0.6354 (mtp-110) cc_final: 0.5866 (mmt-90) REVERT: B 753 ARG cc_start: 0.5222 (mtp180) cc_final: 0.4757 (mmm-85) REVERT: B 757 MET cc_start: 0.6119 (OUTLIER) cc_final: 0.5903 (ptp) REVERT: C 56 THR cc_start: 0.3038 (OUTLIER) cc_final: 0.2705 (p) REVERT: C 161 VAL cc_start: 0.4623 (p) cc_final: 0.4387 (t) REVERT: C 198 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5641 (mm) REVERT: C 236 LYS cc_start: 0.6169 (tptt) cc_final: 0.5801 (tttm) REVERT: C 359 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.6175 (ttt180) REVERT: C 379 GLU cc_start: 0.5674 (pm20) cc_final: 0.5464 (pt0) REVERT: C 470 GLU cc_start: 0.6998 (pm20) cc_final: 0.6450 (pp20) REVERT: C 550 MET cc_start: 0.7493 (mtm) cc_final: 0.7132 (mtm) REVERT: C 627 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6356 (p0) REVERT: C 638 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6093 (mmt-90) REVERT: C 696 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6678 (ttmt) REVERT: D 56 THR cc_start: 0.2987 (OUTLIER) cc_final: 0.2640 (p) REVERT: D 445 LEU cc_start: 0.5597 (OUTLIER) cc_final: 0.5086 (tp) REVERT: D 470 GLU cc_start: 0.6982 (pm20) cc_final: 0.6596 (pp20) REVERT: D 556 GLU cc_start: 0.7083 (pm20) cc_final: 0.6764 (pm20) REVERT: D 627 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.6496 (p0) REVERT: D 633 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.7145 (mm) REVERT: D 638 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6392 (mmt-90) REVERT: D 674 PHE cc_start: 0.6339 (t80) cc_final: 0.5996 (t80) REVERT: D 696 LYS cc_start: 0.7150 (ttpt) cc_final: 0.6946 (tttt) REVERT: D 741 ARG cc_start: 0.6377 (mtp-110) cc_final: 0.5909 (mmp-170) REVERT: D 757 MET cc_start: 0.6109 (OUTLIER) cc_final: 0.5858 (ptp) REVERT: E 89 ARG cc_start: 0.6517 (OUTLIER) cc_final: 0.4266 (ttp80) REVERT: E 198 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5598 (mm) REVERT: E 225 ARG cc_start: 0.6640 (tmt-80) cc_final: 0.6365 (tpt90) REVERT: E 427 MET cc_start: 0.4090 (tpt) cc_final: 0.3544 (tpt) REVERT: E 470 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6641 (pp20) REVERT: E 556 GLU cc_start: 0.6904 (pm20) cc_final: 0.6508 (pm20) REVERT: E 633 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7303 (mm) REVERT: E 634 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7735 (mt) REVERT: E 638 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6767 (mmt-90) REVERT: E 741 ARG cc_start: 0.6368 (mtp-110) cc_final: 0.5872 (mmt-90) REVERT: E 753 ARG cc_start: 0.5205 (mtp180) cc_final: 0.4784 (mmm-85) REVERT: F 56 THR cc_start: 0.3041 (OUTLIER) cc_final: 0.2706 (p) REVERT: F 161 VAL cc_start: 0.4600 (p) cc_final: 0.4380 (t) REVERT: F 236 LYS cc_start: 0.6199 (tptt) cc_final: 0.5836 (tttm) REVERT: F 359 ARG cc_start: 0.6562 (OUTLIER) cc_final: 0.6093 (mmt90) REVERT: F 470 GLU cc_start: 0.6975 (pm20) cc_final: 0.6422 (pp20) REVERT: F 556 GLU cc_start: 0.6946 (pm20) cc_final: 0.6594 (pm20) REVERT: F 627 ASP cc_start: 0.6843 (OUTLIER) cc_final: 0.6332 (p0) REVERT: F 638 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6176 (mmt-90) REVERT: F 696 LYS cc_start: 0.7059 (ttpt) cc_final: 0.6843 (tttt) REVERT: F 753 ARG cc_start: 0.5175 (mtp180) cc_final: 0.4767 (mmm-85) REVERT: F 757 MET cc_start: 0.6043 (OUTLIER) cc_final: 0.5810 (ptp) outliers start: 107 outliers final: 56 residues processed: 523 average time/residue: 0.7110 time to fit residues: 445.1700 Evaluate side-chains 501 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 409 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 696 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 638 ARG Chi-restraints excluded: chain F residue 678 MET Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 300 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 185 optimal weight: 0.2980 chunk 126 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 326 optimal weight: 30.0000 chunk 337 optimal weight: 0.9980 chunk 265 optimal weight: 9.9990 chunk 218 optimal weight: 0.8980 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.240544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.216218 restraints weight = 41739.994| |-----------------------------------------------------------------------------| r_work (start): 0.4455 rms_B_bonded: 1.53 r_work: 0.4252 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4155 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35082 Z= 0.146 Angle : 0.740 12.360 47460 Z= 0.363 Chirality : 0.048 0.185 5322 Planarity : 0.005 0.053 6198 Dihedral : 12.555 111.095 4956 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.07 % Favored : 93.79 % Rotamer: Outliers : 2.57 % Allowed : 21.41 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % 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: -0.70 (0.13), residues: 4314 helix: 0.40 (0.13), residues: 1686 sheet: -0.51 (0.23), residues: 516 loop : -1.14 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 322 TYR 0.020 0.002 TYR A 495 PHE 0.024 0.002 PHE B 139 TRP 0.009 0.001 TRP B 454 HIS 0.009 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (35082) covalent geometry : angle 0.74017 / 0.36 (47460) hydrogen bonds : bond 0.04179 / 2.79 ( 1272) hydrogen bonds : angle 4.86490 / 3.38 ( 3654) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 434 time to evaluate : 1.300 Fit side-chains REVERT: A 56 THR cc_start: 0.2943 (OUTLIER) cc_final: 0.2597 (p) REVERT: A 198 LEU cc_start: 0.5846 (OUTLIER) cc_final: 0.5524 (mm) REVERT: A 440 GLU cc_start: 0.4776 (tm-30) cc_final: 0.4489 (mt-10) REVERT: A 445 LEU cc_start: 0.5565 (OUTLIER) cc_final: 0.4957 (tp) REVERT: A 449 MET cc_start: 0.5503 (tpt) cc_final: 0.5205 (tpt) REVERT: A 465 ARG cc_start: 0.6076 (mmt90) cc_final: 0.5710 (mtt-85) REVERT: A 470 GLU cc_start: 0.6908 (pm20) cc_final: 0.6503 (pp20) REVERT: A 627 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6453 (p0) REVERT: A 633 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7196 (mm) REVERT: A 638 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6513 (mmt-90) REVERT: A 673 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5736 (mp0) REVERT: A 674 PHE cc_start: 0.6361 (t80) cc_final: 0.6041 (t80) REVERT: A 741 ARG cc_start: 0.6402 (mtp-110) cc_final: 0.5875 (mmp-170) REVERT: A 753 ARG cc_start: 0.5421 (mmm-85) cc_final: 0.5150 (mtp-110) REVERT: A 757 MET cc_start: 0.6072 (OUTLIER) cc_final: 0.5381 (ptm) REVERT: B 89 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.4229 (ttp80) REVERT: B 198 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5659 (mm) REVERT: B 236 LYS cc_start: 0.6429 (tptt) cc_final: 0.5955 (tttm) REVERT: B 427 MET cc_start: 0.4198 (tpt) cc_final: 0.3616 (tpt) REVERT: B 449 MET cc_start: 0.5236 (tpp) cc_final: 0.5004 (mmt) REVERT: B 470 GLU cc_start: 0.6968 (pm20) cc_final: 0.6502 (pp20) REVERT: B 556 GLU cc_start: 0.6979 (pm20) cc_final: 0.6619 (pm20) REVERT: B 633 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7335 (mm) REVERT: B 634 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7713 (mt) REVERT: B 638 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6757 (mmt-90) REVERT: B 740 MET cc_start: 0.7232 (tpp) cc_final: 0.7005 (tpt) REVERT: B 741 ARG cc_start: 0.6422 (mtp-110) cc_final: 0.5872 (mmp-170) REVERT: B 753 ARG cc_start: 0.5176 (mtp180) cc_final: 0.4770 (mmm-85) REVERT: B 757 MET cc_start: 0.6129 (OUTLIER) cc_final: 0.5917 (ptp) REVERT: C 161 VAL cc_start: 0.4643 (p) cc_final: 0.4393 (t) REVERT: C 198 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5638 (mm) REVERT: C 236 LYS cc_start: 0.6168 (tptt) cc_final: 0.5820 (tttm) REVERT: C 322 ARG cc_start: 0.6790 (mmt180) cc_final: 0.6540 (mpt-90) REVERT: C 359 ARG cc_start: 0.6591 (OUTLIER) cc_final: 0.6167 (ttt180) REVERT: C 550 MET cc_start: 0.7511 (mtm) cc_final: 0.7146 (mtm) REVERT: C 627 ASP cc_start: 0.6810 (OUTLIER) cc_final: 0.6309 (p0) REVERT: C 638 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6064 (mmt-90) REVERT: C 696 LYS cc_start: 0.6988 (OUTLIER) cc_final: 0.6637 (ttmt) REVERT: D 56 THR cc_start: 0.2958 (OUTLIER) cc_final: 0.2599 (p) REVERT: D 427 MET cc_start: 0.4293 (tpt) cc_final: 0.3742 (tpt) REVERT: D 445 LEU cc_start: 0.5612 (OUTLIER) cc_final: 0.5164 (tp) REVERT: D 470 GLU cc_start: 0.6966 (pm20) cc_final: 0.6580 (pp20) REVERT: D 556 GLU cc_start: 0.7009 (pm20) cc_final: 0.6696 (pm20) REVERT: D 627 ASP cc_start: 0.6916 (OUTLIER) cc_final: 0.6507 (p0) REVERT: D 638 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6490 (mmt-90) REVERT: D 650 GLU cc_start: 0.5618 (mp0) cc_final: 0.5305 (mt-10) REVERT: D 741 ARG cc_start: 0.6406 (mtp-110) cc_final: 0.5886 (mmp-170) REVERT: D 757 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5858 (ptp) REVERT: E 89 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.4336 (ttp80) REVERT: E 198 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5661 (mm) REVERT: E 225 ARG cc_start: 0.6665 (tmt-80) cc_final: 0.6383 (tpt90) REVERT: E 236 LYS cc_start: 0.6445 (tptt) cc_final: 0.6008 (tttm) REVERT: E 427 MET cc_start: 0.4201 (tpt) cc_final: 0.3622 (tpt) REVERT: E 470 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6622 (pp20) REVERT: E 556 GLU cc_start: 0.6922 (pm20) cc_final: 0.6560 (pm20) REVERT: E 633 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7355 (mm) REVERT: E 634 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7728 (mt) REVERT: E 638 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6773 (mmt-90) REVERT: E 741 ARG cc_start: 0.6590 (mtp-110) cc_final: 0.6067 (mmt-90) REVERT: E 753 ARG cc_start: 0.5145 (mtp180) cc_final: 0.4762 (mmm-85) REVERT: F 56 THR cc_start: 0.2995 (OUTLIER) cc_final: 0.2655 (p) REVERT: F 161 VAL cc_start: 0.4648 (p) cc_final: 0.4425 (t) REVERT: F 236 LYS cc_start: 0.6141 (tptt) cc_final: 0.5817 (tttm) REVERT: F 322 ARG cc_start: 0.6801 (mmt180) cc_final: 0.6499 (mpt-90) REVERT: F 359 ARG cc_start: 0.6544 (OUTLIER) cc_final: 0.6139 (ttt180) REVERT: F 556 GLU cc_start: 0.6911 (pm20) cc_final: 0.6565 (pm20) REVERT: F 627 ASP cc_start: 0.6785 (OUTLIER) cc_final: 0.6273 (p0) REVERT: F 638 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6138 (mmt-90) REVERT: F 696 LYS cc_start: 0.7040 (ttpt) cc_final: 0.6817 (tttt) REVERT: F 753 ARG cc_start: 0.5242 (mtp180) cc_final: 0.4775 (mmm-85) REVERT: F 754 LYS cc_start: 0.5367 (OUTLIER) cc_final: 0.4263 (ttpt) REVERT: F 757 MET cc_start: 0.6024 (OUTLIER) cc_final: 0.5793 (ptp) outliers start: 95 outliers final: 54 residues processed: 503 average time/residue: 0.7294 time to fit residues: 439.2240 Evaluate side-chains 510 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 420 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 696 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 638 ARG Chi-restraints excluded: chain F residue 678 MET Chi-restraints excluded: chain F residue 754 LYS Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 107 optimal weight: 6.9990 chunk 267 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 225 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 297 optimal weight: 0.8980 chunk 383 optimal weight: 9.9990 chunk 401 optimal weight: 30.0000 chunk 38 optimal weight: 30.0000 chunk 138 optimal weight: 20.0000 chunk 351 optimal weight: 3.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN B 421 GLN B 460 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.237899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.215136 restraints weight = 41534.511| |-----------------------------------------------------------------------------| r_work (start): 0.4447 rms_B_bonded: 1.44 r_work: 0.4233 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4142 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35082 Z= 0.190 Angle : 0.805 12.756 47460 Z= 0.398 Chirality : 0.050 0.181 5322 Planarity : 0.005 0.054 6198 Dihedral : 12.960 118.807 4956 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.98 % Favored : 92.93 % Rotamer: Outliers : 3.06 % Allowed : 21.22 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % 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: -0.94 (0.12), residues: 4314 helix: 0.18 (0.13), residues: 1680 sheet: -0.51 (0.22), residues: 552 loop : -1.29 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 322 TYR 0.023 0.002 TYR A 495 PHE 0.041 0.002 PHE D 674 TRP 0.009 0.002 TRP B 454 HIS 0.011 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (35082) covalent geometry : angle 0.80529 / 0.40 (47460) hydrogen bonds : bond 0.04762 / 3.17 ( 1272) hydrogen bonds : angle 5.09722 / 3.54 ( 3654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16757.61 seconds wall clock time: 284 minutes 41.82 seconds (17081.82 seconds total)