Starting phenix.real_space_refine on Tue Aug 26 06:20:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ftj_3295/08_2025/5ftj_3295.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ftj_3295/08_2025/5ftj_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_3295/08_2025/5ftj_3295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ftj_3295/08_2025/5ftj_3295.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5ftj_3295/08_2025/5ftj_3295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ftj_3295/08_2025/5ftj_3295.map" } 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-2.0-5787/lib/python3.9/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: 6.55, per 1000 atoms: 0.19 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: 2.94 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.32 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: 6.85 Time building geometry restraints manager: 3.91 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: 21258 34.49 - 68.99: 366 68.99 - 103.48: 60 103.48 - 137.97: 42 137.97 - 172.47: 6 Dihedral angle restraints: 21732 sinusoidal: 9240 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 21729 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 30.340 Find NCS groups from input model: 0.330 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:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 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 : 15.430 172.467 13632 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 aren 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 covalent geometry : bond 0.00970 (35082) covalent geometry : angle 1.30315 (47460) hydrogen bonds : bond 0.27099 ( 1272) hydrogen bonds : angle 9.20878 ( 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 : 1.191 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: 0.8605 time to fit residues: 797.1607 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 : 1.176 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.242195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.217755 restraints weight = 41801.252| |-----------------------------------------------------------------------------| r_work (start): 0.4468 rms_B_bonded: 1.58 r_work: 0.4258 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4160 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35082 Z= 0.177 Angle : 0.859 10.536 47460 Z= 0.427 Chirality : 0.050 0.191 5322 Planarity : 0.006 0.063 6198 Dihedral : 14.328 156.918 5033 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.89 % Favored : 94.83 % Rotamer: Outliers : 3.28 % Allowed : 11.73 % Favored : 84.99 % 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 aren not related in a simple way. whole: -2.11 (0.11), residues: 4314 helix: -1.25 (0.11), residues: 1650 sheet: -0.86 (0.20), residues: 564 loop : -1.59 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 B 340 Details of bonding type rmsd covalent geometry : bond 0.00380 (35082) covalent geometry : angle 0.85945 (47460) hydrogen bonds : bond 0.05528 ( 1272) hydrogen bonds : angle 5.71920 ( 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 783 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 662 time to evaluate : 1.351 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: 0.7133 (tt0) cc_final: 0.6873 (tt0) REVERT: A 401 ASN cc_start: 0.5955 (m-40) cc_final: 0.5670 (m110) REVERT: A 440 GLU cc_start: 0.4642 (tm-30) cc_final: 0.4386 (mt-10) REVERT: A 451 ASP cc_start: 0.6791 (m-30) cc_final: 0.6405 (m-30) REVERT: A 550 MET cc_start: 0.7443 (mtm) cc_final: 0.7209 (mtm) REVERT: A 633 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.7126 (mm) REVERT: A 636 PRO cc_start: 0.6874 (Cg_exo) cc_final: 0.6648 (Cg_endo) REVERT: A 638 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.5862 (mmt-90) REVERT: A 649 ASP cc_start: 0.5107 (m-30) cc_final: 0.4715 (m-30) REVERT: A 689 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6726 (tm-30) REVERT: A 741 ARG cc_start: 0.6096 (mtp-110) cc_final: 0.5792 (mmt-90) REVERT: B 465 ARG cc_start: 0.6172 (mmt180) cc_final: 0.5943 (mtt-85) REVERT: B 638 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6423 (mmt-90) REVERT: B 649 ASP cc_start: 0.5436 (m-30) cc_final: 0.5047 (m-30) REVERT: B 741 ARG cc_start: 0.6124 (mtp-110) cc_final: 0.5874 (mmt-90) REVERT: C 291 GLU cc_start: 0.5702 (tm-30) cc_final: 0.5479 (tm-30) REVERT: C 401 ASN cc_start: 0.6216 (m-40) cc_final: 0.6000 (m110) REVERT: C 451 ASP cc_start: 0.6752 (m-30) cc_final: 0.6535 (m-30) REVERT: C 465 ARG cc_start: 0.6250 (mmt90) cc_final: 0.5642 (mtt-85) REVERT: C 636 PRO cc_start: 0.6921 (Cg_exo) cc_final: 0.6690 (Cg_endo) REVERT: C 638 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6525 (mmt-90) REVERT: C 675 LEU cc_start: 0.7022 (tt) cc_final: 0.6799 (tp) REVERT: D 401 ASN cc_start: 0.6004 (m-40) cc_final: 0.5780 (m110) REVERT: D 451 ASP cc_start: 0.6649 (m-30) cc_final: 0.6388 (m-30) REVERT: D 550 MET cc_start: 0.7444 (mtm) cc_final: 0.7189 (mtm) REVERT: D 633 ILE cc_start: 0.7349 (OUTLIER) cc_final: 0.7122 (mm) REVERT: D 636 PRO cc_start: 0.6905 (Cg_exo) cc_final: 0.6678 (Cg_endo) REVERT: D 638 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.5876 (mmt-90) REVERT: D 649 ASP cc_start: 0.5159 (m-30) cc_final: 0.4785 (m-30) REVERT: D 741 ARG cc_start: 0.6087 (mtp-110) cc_final: 0.5783 (mmt-90) REVERT: E 215 GLN cc_start: 0.7217 (tt0) cc_final: 0.6946 (tt0) REVERT: E 465 ARG cc_start: 0.6185 (mmt180) cc_final: 0.5954 (mtt-85) REVERT: E 556 GLU cc_start: 0.7034 (pm20) cc_final: 0.6720 (pm20) REVERT: E 638 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6466 (mmt-90) REVERT: E 741 ARG cc_start: 0.6136 (mtp-110) cc_final: 0.5864 (mmt-90) REVERT: E 758 PHE cc_start: 0.6799 (t80) cc_final: 0.6269 (t80) REVERT: F 288 LYS cc_start: 0.7171 (ttmt) cc_final: 0.6917 (tmmt) REVERT: F 451 ASP cc_start: 0.6728 (m-30) cc_final: 0.6515 (m-30) REVERT: F 465 ARG cc_start: 0.6243 (mmt90) cc_final: 0.5593 (mtt-85) REVERT: F 636 PRO cc_start: 0.6946 (Cg_exo) cc_final: 0.6707 (Cg_endo) REVERT: F 638 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6504 (mmt-90) REVERT: F 675 LEU cc_start: 0.7016 (tt) cc_final: 0.6775 (tp) REVERT: F 741 ARG cc_start: 0.5953 (mtp-110) cc_final: 0.5747 (mmt-90) outliers start: 121 outliers final: 27 residues processed: 738 average time/residue: 0.7618 time to fit residues: 656.3478 Evaluate side-chains 527 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 492 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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: 0.6980 chunk 173 optimal weight: 5.9990 chunk 190 optimal weight: 20.0000 chunk 119 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 348 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 389 optimal weight: 5.9990 chunk 338 optimal weight: 10.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN A 533 ASN A 616 ASN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN B 460 ASN B 533 ASN B 616 ASN C 460 ASN C 533 ASN C 616 ASN D 460 ASN D 533 ASN D 616 ASN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN E 460 ASN E 533 ASN E 616 ASN 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.240224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.218100 restraints weight = 41974.405| |-----------------------------------------------------------------------------| r_work (start): 0.4476 rms_B_bonded: 1.42 r_work: 0.4242 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.4154 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 35082 Z= 0.185 Angle : 0.817 9.898 47460 Z= 0.404 Chirality : 0.051 0.226 5322 Planarity : 0.005 0.059 6198 Dihedral : 13.786 143.795 5016 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.91 % Favored : 93.95 % Rotamer: Outliers : 4.34 % Allowed : 15.61 % 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 aren not related in a simple way. whole: -1.50 (0.12), residues: 4314 helix: -0.50 (0.12), residues: 1644 sheet: -0.63 (0.22), residues: 582 loop : -1.47 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 465 TYR 0.015 0.002 TYR E 495 PHE 0.027 0.002 PHE D 139 TRP 0.008 0.001 TRP E 551 HIS 0.010 0.002 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00416 (35082) covalent geometry : angle 0.81701 (47460) hydrogen bonds : bond 0.05135 ( 1272) hydrogen bonds : angle 5.29958 ( 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 688 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 528 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: A 215 GLN cc_start: 0.7195 (tt0) cc_final: 0.6994 (tt0) REVERT: A 224 LEU cc_start: 0.6751 (pp) cc_final: 0.6470 (mt) REVERT: A 294 GLU cc_start: 0.5993 (mm-30) cc_final: 0.5746 (tp30) REVERT: A 440 GLU cc_start: 0.4752 (tm-30) cc_final: 0.4493 (mt-10) REVERT: A 449 MET cc_start: 0.5423 (tpt) cc_final: 0.5210 (tpt) REVERT: A 451 ASP cc_start: 0.6738 (m-30) cc_final: 0.6515 (m-30) REVERT: A 478 ASP cc_start: 0.6905 (m-30) cc_final: 0.6689 (m-30) REVERT: A 627 ASP cc_start: 0.6593 (OUTLIER) cc_final: 0.6074 (m-30) REVERT: A 633 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.7088 (mm) REVERT: A 638 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6366 (mmt-90) REVERT: A 741 ARG cc_start: 0.6175 (mtp-110) cc_final: 0.5802 (mmt-90) REVERT: A 757 MET cc_start: 0.5938 (OUTLIER) cc_final: 0.5696 (ptp) REVERT: B 397 GLU cc_start: 0.5720 (OUTLIER) cc_final: 0.5467 (tm-30) REVERT: B 401 ASN cc_start: 0.6007 (m-40) cc_final: 0.5701 (m110) REVERT: B 449 MET cc_start: 0.5410 (tpt) cc_final: 0.5208 (tpt) REVERT: B 627 ASP cc_start: 0.6606 (OUTLIER) cc_final: 0.6072 (m-30) REVERT: B 634 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7668 (mt) REVERT: B 638 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6267 (mmt-90) REVERT: B 741 ARG cc_start: 0.6385 (mtp-110) cc_final: 0.5956 (mmt-90) REVERT: C 224 LEU cc_start: 0.6617 (pp) cc_final: 0.6402 (mt) REVERT: C 322 ARG cc_start: 0.6640 (mpt90) cc_final: 0.5324 (ttm110) REVERT: C 451 ASP cc_start: 0.6755 (m-30) cc_final: 0.6481 (m-30) REVERT: C 556 GLU cc_start: 0.7061 (pm20) cc_final: 0.6729 (pm20) REVERT: C 638 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6637 (mmt-90) REVERT: C 757 MET cc_start: 0.6131 (OUTLIER) cc_final: 0.5874 (ptp) REVERT: D 294 GLU cc_start: 0.6047 (mm-30) cc_final: 0.5811 (tp30) REVERT: D 451 ASP cc_start: 0.6604 (m-30) cc_final: 0.6397 (m-30) REVERT: D 627 ASP cc_start: 0.6618 (OUTLIER) cc_final: 0.6085 (m-30) REVERT: D 633 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.7135 (mm) REVERT: D 638 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6382 (mmt-90) REVERT: D 741 ARG cc_start: 0.6165 (mtp-110) cc_final: 0.5834 (mmt-90) REVERT: D 757 MET cc_start: 0.5925 (OUTLIER) cc_final: 0.5670 (ptp) REVERT: E 215 GLN cc_start: 0.7203 (tt0) cc_final: 0.6975 (tt0) REVERT: E 397 GLU cc_start: 0.5736 (OUTLIER) cc_final: 0.5516 (tm-30) REVERT: E 401 ASN cc_start: 0.6012 (m-40) cc_final: 0.5702 (m110) REVERT: E 556 GLU cc_start: 0.7080 (pm20) cc_final: 0.6667 (pm20) REVERT: E 627 ASP cc_start: 0.6643 (OUTLIER) cc_final: 0.6131 (m-30) REVERT: E 634 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7663 (mt) REVERT: E 638 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6275 (mmt-90) REVERT: E 741 ARG cc_start: 0.6174 (mtp-110) cc_final: 0.5864 (mmt-90) REVERT: F 224 LEU cc_start: 0.6593 (pp) cc_final: 0.6376 (mt) REVERT: F 288 LYS cc_start: 0.7145 (ttmt) cc_final: 0.6938 (tmmt) REVERT: F 322 ARG cc_start: 0.6654 (mpt90) cc_final: 0.5318 (ttm110) REVERT: F 401 ASN cc_start: 0.6112 (m-40) cc_final: 0.5826 (m110) REVERT: F 638 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.5858 (mmt-90) REVERT: F 741 ARG cc_start: 0.6242 (mtp-110) cc_final: 0.5904 (mmt-90) REVERT: F 757 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5887 (ptp) outliers start: 160 outliers final: 59 residues processed: 631 average time/residue: 0.8419 time to fit residues: 625.4532 Evaluate side-chains 546 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 467 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 371 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 757 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 268 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 397 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 508 MET 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 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 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 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 371 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 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 268 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 397 GLU 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 634 LEU Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 122 THR 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 371 ILE 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 Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 326 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 188 optimal weight: 20.0000 chunk 377 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 426 optimal weight: 20.0000 chunk 332 optimal weight: 3.9990 chunk 308 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN B 129 ASN B 382 GLN C 129 ASN D 382 GLN D 401 ASN D 460 ASN E 129 ASN E 382 GLN F 129 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.239320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.215507 restraints weight = 41804.540| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 1.55 r_work: 0.4237 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4138 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.3694 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= 0.182 Angle : 0.792 9.753 47460 Z= 0.393 Chirality : 0.049 0.231 5322 Planarity : 0.005 0.059 6198 Dihedral : 13.318 132.560 5016 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.12 % Favored : 93.74 % Rotamer: Outliers : 4.34 % Allowed : 16.31 % Favored : 79.35 % 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 aren not related in a simple way. whole: -1.21 (0.12), residues: 4314 helix: -0.12 (0.13), residues: 1614 sheet: -0.50 (0.22), residues: 582 loop : -1.40 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 210 TYR 0.028 0.002 TYR F 244 PHE 0.026 0.002 PHE F 139 TRP 0.007 0.001 TRP B 551 HIS 0.010 0.001 HIS C 340 Details of bonding type rmsd covalent geometry : bond 0.00409 (35082) covalent geometry : angle 0.79245 (47460) hydrogen bonds : bond 0.04880 ( 1272) hydrogen bonds : angle 5.14194 ( 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 662 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 502 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 GLN cc_start: 0.7255 (tt0) cc_final: 0.7043 (tt0) REVERT: A 224 LEU cc_start: 0.6718 (pp) cc_final: 0.6510 (mt) REVERT: A 304 ASP cc_start: 0.6945 (t0) cc_final: 0.6724 (t0) REVERT: A 315 LYS cc_start: 0.2896 (OUTLIER) cc_final: 0.2489 (ptpt) REVERT: A 401 ASN cc_start: 0.6174 (m-40) cc_final: 0.5954 (m110) REVERT: A 440 GLU cc_start: 0.4857 (tm-30) cc_final: 0.4488 (mt-10) REVERT: A 449 MET cc_start: 0.5446 (tpt) cc_final: 0.5238 (tpt) REVERT: A 451 ASP cc_start: 0.6833 (m-30) cc_final: 0.6617 (m-30) REVERT: A 478 ASP cc_start: 0.7022 (m-30) cc_final: 0.6761 (m-30) REVERT: A 633 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.7107 (mm) REVERT: A 638 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6181 (mmt-90) REVERT: A 650 GLU cc_start: 0.5405 (mp0) cc_final: 0.5191 (mt-10) REVERT: A 741 ARG cc_start: 0.6259 (mtp-110) cc_final: 0.5822 (mmt-90) REVERT: A 757 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.5760 (ptp) REVERT: B 89 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.6336 (ttp80) REVERT: B 315 LYS cc_start: 0.3094 (OUTLIER) cc_final: 0.2546 (pttm) REVERT: B 322 ARG cc_start: 0.6769 (ttp-110) cc_final: 0.6307 (mmt180) REVERT: B 340 HIS cc_start: 0.5655 (OUTLIER) cc_final: 0.5446 (m-70) REVERT: B 397 GLU cc_start: 0.5858 (OUTLIER) cc_final: 0.5545 (tm-30) REVERT: B 445 LEU cc_start: 0.5791 (OUTLIER) cc_final: 0.5305 (tp) REVERT: B 470 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6599 (pp20) REVERT: B 627 ASP cc_start: 0.6631 (OUTLIER) cc_final: 0.6072 (m-30) REVERT: B 633 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7240 (mm) REVERT: B 634 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7741 (mt) REVERT: B 638 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6633 (mmt-90) REVERT: B 741 ARG cc_start: 0.6450 (mtp-110) cc_final: 0.6015 (mmt-90) REVERT: B 753 ARG cc_start: 0.5262 (mtp180) cc_final: 0.4800 (mmm-85) REVERT: C 451 ASP cc_start: 0.6763 (m-30) cc_final: 0.6492 (m-30) REVERT: C 550 MET cc_start: 0.7449 (mtm) cc_final: 0.7078 (mtm) REVERT: C 627 ASP cc_start: 0.6704 (OUTLIER) cc_final: 0.6215 (m-30) REVERT: C 638 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6590 (mmt-90) REVERT: C 649 ASP cc_start: 0.5078 (m-30) cc_final: 0.4706 (m-30) REVERT: C 757 MET cc_start: 0.6300 (OUTLIER) cc_final: 0.6022 (ptp) REVERT: D 304 ASP cc_start: 0.7029 (t0) cc_final: 0.6805 (t0) REVERT: D 315 LYS cc_start: 0.2919 (OUTLIER) cc_final: 0.2504 (ptpt) REVERT: D 401 ASN cc_start: 0.6168 (m-40) cc_final: 0.5959 (m110) REVERT: D 445 LEU cc_start: 0.5665 (OUTLIER) cc_final: 0.5128 (tp) REVERT: D 470 GLU cc_start: 0.6968 (pm20) cc_final: 0.6598 (pp20) REVERT: D 633 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7153 (mm) REVERT: D 638 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6137 (mmt-90) REVERT: D 741 ARG cc_start: 0.6332 (mtp-110) cc_final: 0.5868 (mmt-90) REVERT: D 757 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.5794 (ptp) REVERT: E 89 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.6366 (ttp80) REVERT: E 215 GLN cc_start: 0.7219 (tt0) cc_final: 0.7016 (tt0) REVERT: E 322 ARG cc_start: 0.6775 (ttp-110) cc_final: 0.6320 (mmt180) REVERT: E 445 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5293 (tp) REVERT: E 556 GLU cc_start: 0.7069 (pm20) cc_final: 0.6681 (pm20) REVERT: E 627 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.6113 (m-30) REVERT: E 633 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7229 (mm) REVERT: E 634 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7716 (mt) REVERT: E 638 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6616 (mmt-90) REVERT: E 741 ARG cc_start: 0.6415 (mtp-110) cc_final: 0.5978 (mmt-90) REVERT: E 753 ARG cc_start: 0.5162 (mtp180) cc_final: 0.4772 (mmm-85) REVERT: F 288 LYS cc_start: 0.7192 (ttmt) cc_final: 0.6906 (pttm) REVERT: F 322 ARG cc_start: 0.6781 (mpt90) cc_final: 0.6412 (mpt-90) REVERT: F 550 MET cc_start: 0.7449 (mtm) cc_final: 0.7088 (mtm) REVERT: F 556 GLU cc_start: 0.7035 (pm20) cc_final: 0.6719 (pm20) REVERT: F 627 ASP cc_start: 0.6680 (OUTLIER) cc_final: 0.6171 (m-30) REVERT: F 638 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6564 (mmt-90) REVERT: F 649 ASP cc_start: 0.5155 (m-30) cc_final: 0.4809 (m-30) REVERT: F 741 ARG cc_start: 0.6352 (mtp-110) cc_final: 0.5948 (mmt-90) REVERT: F 757 MET cc_start: 0.6219 (OUTLIER) cc_final: 0.5952 (ptp) outliers start: 160 outliers final: 66 residues processed: 602 average time/residue: 0.7317 time to fit residues: 522.1311 Evaluate side-chains 533 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 436 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 371 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 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 166 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 340 HIS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 397 GLU 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 27 ILE Chi-restraints excluded: chain C residue 82 ILE 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 508 MET 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 757 MET Chi-restraints excluded: chain D residue 27 ILE 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 371 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 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 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 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 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 F residue 27 ILE Chi-restraints excluded: chain F residue 82 ILE 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 371 ILE Chi-restraints excluded: chain F residue 508 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 757 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 158 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 409 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 254 optimal weight: 6.9990 chunk 379 optimal weight: 10.0000 chunk 326 optimal weight: 30.0000 chunk 138 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 ASN C 226 HIS C 404 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN E 351 ASN F 226 HIS F 404 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.237289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.215502 restraints weight = 41886.438| |-----------------------------------------------------------------------------| r_work (start): 0.4453 rms_B_bonded: 1.40 r_work: 0.4221 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.4130 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 35082 Z= 0.222 Angle : 0.855 10.187 47460 Z= 0.427 Chirality : 0.051 0.246 5322 Planarity : 0.006 0.064 6198 Dihedral : 13.360 128.458 5016 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.65 % Favored : 93.21 % Rotamer: Outliers : 4.82 % Allowed : 16.80 % Favored : 78.37 % 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 aren not related in a simple way. whole: -1.37 (0.12), residues: 4314 helix: -0.20 (0.12), residues: 1626 sheet: -0.61 (0.22), residues: 564 loop : -1.53 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 653 TYR 0.016 0.002 TYR B 495 PHE 0.028 0.003 PHE C 139 TRP 0.008 0.002 TRP E 551 HIS 0.011 0.002 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00508 (35082) covalent geometry : angle 0.85526 (47460) hydrogen bonds : bond 0.05331 ( 1272) hydrogen bonds : angle 5.31112 ( 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 647 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 469 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 ASP cc_start: 0.6920 (t0) cc_final: 0.6684 (t0) REVERT: A 445 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5203 (tp) REVERT: A 449 MET cc_start: 0.5488 (tpt) cc_final: 0.5263 (tpt) REVERT: A 478 ASP cc_start: 0.6987 (m-30) cc_final: 0.6667 (m-30) REVERT: A 627 ASP cc_start: 0.6944 (OUTLIER) cc_final: 0.6558 (p0) REVERT: A 633 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.7102 (mm) REVERT: A 638 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6571 (mmt-90) REVERT: A 674 PHE cc_start: 0.6543 (t80) cc_final: 0.6284 (t80) REVERT: A 741 ARG cc_start: 0.6367 (mtp-110) cc_final: 0.5964 (mmt-90) REVERT: A 757 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5825 (ptp) REVERT: B 322 ARG cc_start: 0.6751 (ttp-110) cc_final: 0.6346 (mmt180) REVERT: B 445 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5460 (tp) REVERT: B 627 ASP cc_start: 0.6678 (OUTLIER) cc_final: 0.6125 (m-30) REVERT: B 633 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7265 (mm) REVERT: B 634 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7818 (mt) REVERT: B 638 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6347 (mmt-90) REVERT: B 650 GLU cc_start: 0.5739 (mp0) cc_final: 0.5292 (mt-10) REVERT: B 741 ARG cc_start: 0.6516 (mtp-110) cc_final: 0.6097 (mmt-90) REVERT: B 753 ARG cc_start: 0.5198 (mtp180) cc_final: 0.4860 (mmm-85) REVERT: C 322 ARG cc_start: 0.6814 (mpt180) cc_final: 0.5543 (ttp-110) REVERT: C 359 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.6269 (ttm170) REVERT: C 382 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6631 (mt0) REVERT: C 445 LEU cc_start: 0.5699 (OUTLIER) cc_final: 0.5206 (tp) REVERT: C 550 MET cc_start: 0.7476 (mtm) cc_final: 0.7137 (mtm) REVERT: C 638 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6314 (mmt-90) REVERT: C 649 ASP cc_start: 0.4949 (m-30) cc_final: 0.4659 (m-30) REVERT: C 689 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6995 (tm-30) REVERT: C 757 MET cc_start: 0.6308 (OUTLIER) cc_final: 0.6033 (ptp) REVERT: D 304 ASP cc_start: 0.6985 (t0) cc_final: 0.6755 (t0) REVERT: D 445 LEU cc_start: 0.5709 (OUTLIER) cc_final: 0.5242 (tp) REVERT: D 627 ASP cc_start: 0.6894 (OUTLIER) cc_final: 0.6503 (p0) REVERT: D 633 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.7119 (mm) REVERT: D 638 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6131 (mmt-90) REVERT: D 650 GLU cc_start: 0.5812 (mp0) cc_final: 0.5441 (mt-10) REVERT: D 741 ARG cc_start: 0.6414 (mtp-110) cc_final: 0.5992 (mmt-90) REVERT: D 757 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.5850 (ptp) REVERT: E 89 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.4417 (ttp80) REVERT: E 322 ARG cc_start: 0.6756 (ttp-110) cc_final: 0.6351 (mmt180) REVERT: E 445 LEU cc_start: 0.5845 (OUTLIER) cc_final: 0.5437 (tp) REVERT: E 502 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6722 (tppt) REVERT: E 556 GLU cc_start: 0.7166 (pm20) cc_final: 0.6717 (pm20) REVERT: E 627 ASP cc_start: 0.6697 (OUTLIER) cc_final: 0.6152 (m-30) REVERT: E 633 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7270 (mm) REVERT: E 634 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7800 (mt) REVERT: E 638 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6362 (mmt-90) REVERT: E 649 ASP cc_start: 0.5205 (m-30) cc_final: 0.4915 (m-30) REVERT: E 650 GLU cc_start: 0.5697 (mp0) cc_final: 0.5192 (mt-10) REVERT: E 741 ARG cc_start: 0.6484 (mtp-110) cc_final: 0.6077 (mmt-90) REVERT: E 753 ARG cc_start: 0.5147 (mtp180) cc_final: 0.4834 (mmm-85) REVERT: F 322 ARG cc_start: 0.6803 (mpt90) cc_final: 0.6460 (mpt-90) REVERT: F 382 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6565 (mt0) REVERT: F 445 LEU cc_start: 0.5689 (OUTLIER) cc_final: 0.5238 (tp) REVERT: F 638 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6309 (mmt-90) REVERT: F 649 ASP cc_start: 0.5011 (m-30) cc_final: 0.4694 (m-30) REVERT: F 689 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6999 (tm-30) REVERT: F 741 ARG cc_start: 0.6456 (mtp-110) cc_final: 0.6097 (mmt-90) REVERT: F 757 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.6013 (ptp) outliers start: 178 outliers final: 70 residues processed: 592 average time/residue: 0.7464 time to fit residues: 523.9504 Evaluate side-chains 522 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 421 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 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 460 ASN 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 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 292 GLU 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 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 678 MET Chi-restraints excluded: chain C residue 27 ILE 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 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 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 242 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 383 ILE Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 502 LYS 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 E residue 678 MET Chi-restraints excluded: chain F residue 27 ILE 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 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 Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 188 optimal weight: 1.9990 chunk 324 optimal weight: 9.9990 chunk 317 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 389 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 190 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 358 optimal weight: 20.0000 chunk 377 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN ** 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** D 568 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.238309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.214962 restraints weight = 41649.657| |-----------------------------------------------------------------------------| r_work (start): 0.4442 rms_B_bonded: 1.48 r_work: 0.4227 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4129 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 35082 Z= 0.196 Angle : 0.806 9.679 47460 Z= 0.401 Chirality : 0.050 0.173 5322 Planarity : 0.006 0.062 6198 Dihedral : 12.417 125.563 5016 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.77 % Favored : 93.02 % Rotamer: Outliers : 4.69 % Allowed : 17.62 % Favored : 77.70 % 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 aren not related in a simple way. whole: -1.32 (0.12), residues: 4314 helix: -0.20 (0.12), residues: 1692 sheet: -0.59 (0.22), residues: 564 loop : -1.50 (0.12), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 653 TYR 0.015 0.002 TYR E 495 PHE 0.026 0.002 PHE E 139 TRP 0.007 0.002 TRP C 476 HIS 0.011 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00446 (35082) covalent geometry : angle 0.80577 (47460) hydrogen bonds : bond 0.05027 ( 1272) hydrogen bonds : angle 5.16506 ( 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 625 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 452 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.2998 (OUTLIER) cc_final: 0.2636 (p) REVERT: A 440 GLU cc_start: 0.4772 (tm-30) cc_final: 0.4435 (mt-10) REVERT: A 445 LEU cc_start: 0.5612 (OUTLIER) cc_final: 0.5017 (tp) REVERT: A 556 GLU cc_start: 0.7187 (pm20) cc_final: 0.6920 (pm20) REVERT: A 633 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.7172 (mm) REVERT: A 638 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6258 (mmt-90) REVERT: A 650 GLU cc_start: 0.5717 (mp0) cc_final: 0.5392 (mt-10) REVERT: A 674 PHE cc_start: 0.6499 (t80) cc_final: 0.6159 (t80) REVERT: A 741 ARG cc_start: 0.6427 (mtp-110) cc_final: 0.5938 (mmt-90) REVERT: B 89 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.4184 (ttp80) REVERT: B 445 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.5404 (tp) REVERT: B 470 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6448 (pp20) REVERT: B 627 ASP cc_start: 0.6728 (OUTLIER) cc_final: 0.6178 (m-30) REVERT: B 633 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7294 (mm) REVERT: B 634 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7784 (mt) REVERT: B 638 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6477 (mmt-90) REVERT: B 650 GLU cc_start: 0.5600 (mp0) cc_final: 0.5211 (mt-10) REVERT: B 741 ARG cc_start: 0.6606 (mtp-110) cc_final: 0.6121 (mmp-170) REVERT: B 753 ARG cc_start: 0.5208 (mtp180) cc_final: 0.4825 (mmm-85) REVERT: C 56 THR cc_start: 0.3134 (OUTLIER) cc_final: 0.2808 (p) REVERT: C 322 ARG cc_start: 0.6828 (mpt180) cc_final: 0.5564 (ttp-110) REVERT: C 359 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.6236 (ttm170) REVERT: C 550 MET cc_start: 0.7576 (mtm) cc_final: 0.7218 (mtm) REVERT: C 638 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6496 (mmt-90) REVERT: C 649 ASP cc_start: 0.4969 (m-30) cc_final: 0.4660 (m-30) REVERT: C 757 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.6063 (ptp) REVERT: D 304 ASP cc_start: 0.7056 (t0) cc_final: 0.6839 (t0) REVERT: D 445 LEU cc_start: 0.5549 (OUTLIER) cc_final: 0.5028 (tp) REVERT: D 633 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7175 (mm) REVERT: D 638 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6236 (mmt-90) REVERT: D 674 PHE cc_start: 0.6421 (t80) cc_final: 0.6101 (t80) REVERT: D 741 ARG cc_start: 0.6448 (mtp-110) cc_final: 0.5919 (mmt-90) REVERT: D 757 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.5964 (ptp) REVERT: E 89 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.4402 (ttp80) REVERT: E 445 LEU cc_start: 0.5820 (OUTLIER) cc_final: 0.5424 (tp) REVERT: E 556 GLU cc_start: 0.7080 (pm20) cc_final: 0.6708 (pm20) REVERT: E 627 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.6144 (m-30) REVERT: E 633 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7281 (mm) REVERT: E 634 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7761 (mt) REVERT: E 638 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6506 (mmt-90) REVERT: E 649 ASP cc_start: 0.5227 (m-30) cc_final: 0.4964 (m-30) REVERT: E 650 GLU cc_start: 0.5574 (mp0) cc_final: 0.5157 (mt-10) REVERT: E 741 ARG cc_start: 0.6567 (mtp-110) cc_final: 0.6065 (mmp-170) REVERT: E 753 ARG cc_start: 0.5152 (mtp180) cc_final: 0.4820 (mmm-85) REVERT: F 56 THR cc_start: 0.3122 (OUTLIER) cc_final: 0.2798 (p) REVERT: F 322 ARG cc_start: 0.6790 (mpt90) cc_final: 0.6483 (mpt-90) REVERT: F 359 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.5894 (mmm160) REVERT: F 445 LEU cc_start: 0.5593 (OUTLIER) cc_final: 0.5095 (tp) REVERT: F 465 ARG cc_start: 0.6157 (mmt90) cc_final: 0.5797 (mtt-85) REVERT: F 550 MET cc_start: 0.7530 (mtm) cc_final: 0.7158 (mtm) REVERT: F 556 GLU cc_start: 0.7033 (pm20) cc_final: 0.6695 (pm20) REVERT: F 627 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.6352 (p0) REVERT: F 638 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6540 (mmt-90) REVERT: F 649 ASP cc_start: 0.5044 (m-30) cc_final: 0.4769 (m-30) REVERT: F 741 ARG cc_start: 0.6539 (mtp-110) cc_final: 0.6057 (mmp-170) REVERT: F 757 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.6051 (ptp) outliers start: 173 outliers final: 68 residues processed: 580 average time/residue: 0.7430 time to fit residues: 511.9796 Evaluate side-chains 510 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 411 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 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 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 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 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 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 678 MET Chi-restraints excluded: chain C residue 27 ILE 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 184 CYS 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 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 57 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 LEU 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 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 748 SER 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 383 ILE Chi-restraints excluded: chain E residue 445 LEU 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 E residue 678 MET Chi-restraints excluded: chain F residue 27 ILE 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 184 CYS 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 445 LEU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 514 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 315 optimal weight: 8.9990 chunk 206 optimal weight: 30.0000 chunk 210 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 chunk 425 optimal weight: 9.9990 chunk 329 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 347 optimal weight: 0.9990 chunk 334 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 396 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4651 r_free = 0.4651 target = 0.237654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.214953 restraints weight = 41724.511| |-----------------------------------------------------------------------------| r_work (start): 0.4446 rms_B_bonded: 1.50 r_work: 0.4207 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.4154 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= 0.190 Angle : 0.801 9.579 47460 Z= 0.398 Chirality : 0.050 0.219 5322 Planarity : 0.005 0.060 6198 Dihedral : 11.644 125.432 5016 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.00 % Favored : 92.79 % Rotamer: Outliers : 4.31 % Allowed : 18.46 % Favored : 77.24 % 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 aren not related in a simple way. whole: -1.23 (0.12), residues: 4314 helix: -0.10 (0.12), residues: 1698 sheet: -0.56 (0.23), residues: 546 loop : -1.47 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 653 TYR 0.014 0.002 TYR B 495 PHE 0.026 0.002 PHE F 139 TRP 0.008 0.002 TRP C 476 HIS 0.011 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00432 (35082) covalent geometry : angle 0.80126 (47460) hydrogen bonds : bond 0.04967 ( 1272) hydrogen bonds : angle 5.11291 ( 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 609 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 450 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.3001 (OUTLIER) cc_final: 0.2673 (p) REVERT: A 440 GLU cc_start: 0.4766 (tm-30) cc_final: 0.4477 (mt-10) REVERT: A 445 LEU cc_start: 0.5593 (OUTLIER) cc_final: 0.4983 (tp) REVERT: A 449 MET cc_start: 0.5503 (tpt) cc_final: 0.5299 (tpt) REVERT: A 614 LYS cc_start: 0.4764 (OUTLIER) cc_final: 0.4365 (pttp) REVERT: A 627 ASP cc_start: 0.6705 (OUTLIER) cc_final: 0.6234 (p0) REVERT: A 633 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.7131 (mm) REVERT: A 638 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6184 (mmt-90) REVERT: A 674 PHE cc_start: 0.6409 (t80) cc_final: 0.6095 (t80) REVERT: A 741 ARG cc_start: 0.6441 (mtp-110) cc_final: 0.5930 (mmt-90) REVERT: B 89 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.4092 (ttp80) REVERT: B 198 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5807 (mm) REVERT: B 470 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6262 (pp20) REVERT: B 627 ASP cc_start: 0.6446 (OUTLIER) cc_final: 0.5870 (m-30) REVERT: B 633 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7221 (mm) REVERT: B 634 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7698 (mt) REVERT: B 638 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6415 (mmt-90) REVERT: B 741 ARG cc_start: 0.6608 (mtp-110) cc_final: 0.6104 (mmp-170) REVERT: B 753 ARG cc_start: 0.5231 (mtp180) cc_final: 0.4818 (mmm-85) REVERT: C 56 THR cc_start: 0.3059 (OUTLIER) cc_final: 0.2762 (p) REVERT: C 359 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6107 (ttm170) REVERT: C 550 MET cc_start: 0.7430 (mtm) cc_final: 0.7115 (mtm) REVERT: C 638 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.5935 (mmt-90) REVERT: C 757 MET cc_start: 0.6131 (OUTLIER) cc_final: 0.5898 (ptp) REVERT: D 56 THR cc_start: 0.3046 (OUTLIER) cc_final: 0.2727 (p) REVERT: D 304 ASP cc_start: 0.6899 (t0) cc_final: 0.6650 (t0) REVERT: D 445 LEU cc_start: 0.5587 (OUTLIER) cc_final: 0.5090 (tp) REVERT: D 614 LYS cc_start: 0.4827 (OUTLIER) cc_final: 0.4457 (pttp) REVERT: D 627 ASP cc_start: 0.6695 (OUTLIER) cc_final: 0.6228 (p0) REVERT: D 633 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.7122 (mm) REVERT: D 638 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6202 (mmt-90) REVERT: D 674 PHE cc_start: 0.6368 (t80) cc_final: 0.5967 (t80) REVERT: D 701 GLU cc_start: 0.6401 (tp30) cc_final: 0.6177 (tp30) REVERT: D 741 ARG cc_start: 0.6464 (mtp-110) cc_final: 0.5952 (mmt-90) REVERT: D 757 MET cc_start: 0.6084 (OUTLIER) cc_final: 0.5856 (ptp) REVERT: E 89 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.4320 (ttp80) REVERT: E 198 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5786 (mm) REVERT: E 556 GLU cc_start: 0.6749 (pm20) cc_final: 0.6544 (pm20) REVERT: E 627 ASP cc_start: 0.6466 (OUTLIER) cc_final: 0.5897 (m-30) REVERT: E 633 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7240 (mm) REVERT: E 634 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7713 (mt) REVERT: E 638 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6467 (mmt-90) REVERT: E 741 ARG cc_start: 0.6568 (mtp-110) cc_final: 0.6075 (mmt-90) REVERT: E 753 ARG cc_start: 0.5193 (mtp180) cc_final: 0.4811 (mmm-85) REVERT: F 56 THR cc_start: 0.3052 (OUTLIER) cc_final: 0.2759 (p) REVERT: F 322 ARG cc_start: 0.6822 (mpt90) cc_final: 0.6259 (mmt90) REVERT: F 359 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.5762 (mmm160) REVERT: F 465 ARG cc_start: 0.5966 (mmt90) cc_final: 0.5582 (mtt-85) REVERT: F 550 MET cc_start: 0.7410 (mtm) cc_final: 0.6989 (mtm) REVERT: F 638 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.5999 (mmt-90) REVERT: F 741 ARG cc_start: 0.6445 (mtp-110) cc_final: 0.6018 (mmt-90) outliers start: 159 outliers final: 68 residues processed: 568 average time/residue: 0.7166 time to fit residues: 486.4885 Evaluate side-chains 522 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 421 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU 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 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 491 GLU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 614 LYS 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 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 383 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 678 MET Chi-restraints excluded: chain C residue 27 ILE 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 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 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 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 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 614 LYS 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 748 SER 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 383 ILE 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 E residue 678 MET Chi-restraints excluded: chain F residue 27 ILE 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 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 508 MET Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 638 ARG Chi-restraints excluded: chain F residue 678 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 153 optimal weight: 10.0000 chunk 308 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 421 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 202 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 385 optimal weight: 0.6980 chunk 262 optimal weight: 5.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4661 r_free = 0.4661 target = 0.238699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.215047 restraints weight = 41826.291| |-----------------------------------------------------------------------------| r_work (start): 0.4440 rms_B_bonded: 1.48 r_work: 0.4228 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4135 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.4282 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= 0.178 Angle : 0.782 9.680 47460 Z= 0.388 Chirality : 0.049 0.185 5322 Planarity : 0.005 0.058 6198 Dihedral : 10.987 122.158 5016 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.95 % Favored : 92.81 % Rotamer: Outliers : 3.98 % Allowed : 19.35 % Favored : 76.67 % 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 aren not related in a simple way. whole: -1.13 (0.12), residues: 4314 helix: 0.01 (0.13), residues: 1692 sheet: -0.53 (0.23), residues: 546 loop : -1.42 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 653 TYR 0.014 0.002 TYR B 495 PHE 0.025 0.002 PHE B 139 TRP 0.007 0.001 TRP C 476 HIS 0.010 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00404 (35082) covalent geometry : angle 0.78186 (47460) hydrogen bonds : bond 0.04766 ( 1272) hydrogen bonds : angle 5.07565 ( 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 596 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 449 time to evaluate : 1.476 Fit side-chains revert: symmetry clash REVERT: A 56 THR cc_start: 0.2983 (OUTLIER) cc_final: 0.2636 (p) REVERT: A 440 GLU cc_start: 0.4735 (tm-30) cc_final: 0.4444 (mt-10) REVERT: A 445 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5006 (tp) REVERT: A 449 MET cc_start: 0.5615 (tpt) cc_final: 0.5381 (tpt) REVERT: A 465 ARG cc_start: 0.6136 (mmt90) cc_final: 0.5780 (mtt-85) REVERT: A 614 LYS cc_start: 0.4961 (OUTLIER) cc_final: 0.4411 (pttp) REVERT: A 633 ILE cc_start: 0.7415 (OUTLIER) cc_final: 0.7169 (mm) REVERT: A 638 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6358 (mmt-90) REVERT: A 673 GLU cc_start: 0.5890 (OUTLIER) cc_final: 0.5560 (mp0) REVERT: A 674 PHE cc_start: 0.6401 (t80) cc_final: 0.6070 (t80) REVERT: A 741 ARG cc_start: 0.6391 (mtp-110) cc_final: 0.5912 (mmt-90) REVERT: A 757 MET cc_start: 0.6206 (OUTLIER) cc_final: 0.5858 (ptp) REVERT: B 89 ARG cc_start: 0.6544 (OUTLIER) cc_final: 0.4249 (ttp80) REVERT: B 198 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5690 (mm) REVERT: B 427 MET cc_start: 0.4165 (tpt) cc_final: 0.3618 (tpt) REVERT: B 470 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6635 (pp20) REVERT: B 627 ASP cc_start: 0.6629 (OUTLIER) cc_final: 0.6085 (m-30) REVERT: B 633 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7295 (mm) REVERT: B 634 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7781 (mt) REVERT: B 638 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6466 (mmt-90) REVERT: B 741 ARG cc_start: 0.6534 (mtp-110) cc_final: 0.6058 (mmp-170) REVERT: B 753 ARG cc_start: 0.5231 (mtp180) cc_final: 0.4855 (mmm-85) REVERT: C 56 THR cc_start: 0.3000 (OUTLIER) cc_final: 0.2688 (p) REVERT: C 198 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5661 (mm) REVERT: C 359 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.6212 (ttt180) REVERT: C 550 MET cc_start: 0.7632 (mtm) cc_final: 0.7277 (mtm) REVERT: C 627 ASP cc_start: 0.6882 (OUTLIER) cc_final: 0.6367 (p0) REVERT: C 638 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6121 (mmt-90) REVERT: C 757 MET cc_start: 0.6277 (OUTLIER) cc_final: 0.6027 (ptp) REVERT: D 56 THR cc_start: 0.2971 (OUTLIER) cc_final: 0.2625 (p) REVERT: D 445 LEU cc_start: 0.5510 (OUTLIER) cc_final: 0.4977 (tp) REVERT: D 614 LYS cc_start: 0.4941 (OUTLIER) cc_final: 0.4551 (pttp) REVERT: D 627 ASP cc_start: 0.6882 (OUTLIER) cc_final: 0.6459 (p0) REVERT: D 633 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7164 (mm) REVERT: D 638 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6405 (mmt-90) REVERT: D 649 ASP cc_start: 0.4989 (m-30) cc_final: 0.4772 (m-30) REVERT: D 650 GLU cc_start: 0.5760 (mp0) cc_final: 0.5379 (mt-10) REVERT: D 674 PHE cc_start: 0.6420 (t80) cc_final: 0.5998 (t80) REVERT: D 701 GLU cc_start: 0.6437 (tp30) cc_final: 0.6235 (tp30) REVERT: D 741 ARG cc_start: 0.6427 (mtp-110) cc_final: 0.5978 (mmp-170) REVERT: E 89 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.4422 (ttp80) REVERT: E 198 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5667 (mm) REVERT: E 427 MET cc_start: 0.4161 (tpt) cc_final: 0.3608 (tpt) REVERT: E 556 GLU cc_start: 0.6996 (pm20) cc_final: 0.6619 (pm20) REVERT: E 627 ASP cc_start: 0.6663 (OUTLIER) cc_final: 0.6129 (m-30) REVERT: E 633 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7281 (mm) REVERT: E 634 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7715 (mt) REVERT: E 638 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6465 (mmt-90) REVERT: E 741 ARG cc_start: 0.6580 (mtp-110) cc_final: 0.6099 (mmt-90) REVERT: E 753 ARG cc_start: 0.5162 (mtp180) cc_final: 0.4851 (mmm-85) REVERT: F 56 THR cc_start: 0.3016 (OUTLIER) cc_final: 0.2706 (p) REVERT: F 198 LEU cc_start: 0.6121 (OUTLIER) cc_final: 0.5699 (mm) REVERT: F 359 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.5926 (mmm160) REVERT: F 550 MET cc_start: 0.7558 (mtm) cc_final: 0.7210 (mtm) REVERT: F 638 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6119 (mmt-90) REVERT: F 741 ARG cc_start: 0.6551 (mtp-110) cc_final: 0.6073 (mmp-170) REVERT: F 757 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.5953 (ptp) outliers start: 147 outliers final: 63 residues processed: 551 average time/residue: 0.7527 time to fit residues: 495.6618 Evaluate side-chains 524 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 424 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 99 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 491 GLU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 614 LYS 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 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 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 678 MET Chi-restraints excluded: chain C residue 27 ILE 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 333 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 514 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 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 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 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 614 LYS 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 748 SER 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 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 E residue 678 MET Chi-restraints excluded: chain F residue 27 ILE 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 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 333 ASP Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 508 MET 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: 10.0000 chunk 389 optimal weight: 0.4980 chunk 128 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 312 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 310 optimal weight: 6.9990 chunk 379 optimal weight: 7.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4667 r_free = 0.4667 target = 0.239275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.216408 restraints weight = 41457.359| |-----------------------------------------------------------------------------| r_work (start): 0.4455 rms_B_bonded: 1.39 r_work: 0.4242 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4146 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.4382 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= 0.165 Angle : 0.766 13.662 47460 Z= 0.379 Chirality : 0.048 0.171 5322 Planarity : 0.005 0.056 6198 Dihedral : 10.108 119.922 5016 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.63 % Favored : 93.16 % Rotamer: Outliers : 3.31 % Allowed : 20.41 % Favored : 76.29 % 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 aren not related in a simple way. whole: -1.02 (0.12), residues: 4314 helix: 0.11 (0.13), residues: 1692 sheet: -0.52 (0.23), residues: 546 loop : -1.35 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 322 TYR 0.015 0.002 TYR A 495 PHE 0.024 0.002 PHE E 139 TRP 0.008 0.001 TRP B 551 HIS 0.010 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00371 (35082) covalent geometry : angle 0.76596 (47460) hydrogen bonds : bond 0.04572 ( 1272) hydrogen bonds : angle 5.01497 ( 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 564 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 442 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 56 THR cc_start: 0.2934 (OUTLIER) cc_final: 0.2598 (p) REVERT: A 135 LEU cc_start: 0.4717 (OUTLIER) cc_final: 0.4505 (mp) REVERT: A 440 GLU cc_start: 0.4729 (tm-30) cc_final: 0.4456 (mt-10) REVERT: A 445 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.5012 (tp) REVERT: A 449 MET cc_start: 0.5598 (tpt) cc_final: 0.5354 (tpt) REVERT: A 465 ARG cc_start: 0.6128 (mmt90) cc_final: 0.5775 (mtt-85) REVERT: A 614 LYS cc_start: 0.4915 (OUTLIER) cc_final: 0.4509 (pttm) REVERT: A 627 ASP cc_start: 0.6932 (OUTLIER) cc_final: 0.6505 (p0) REVERT: A 633 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7165 (mm) REVERT: A 638 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6364 (mmt-90) REVERT: A 673 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5583 (mp0) REVERT: A 674 PHE cc_start: 0.6406 (t80) cc_final: 0.6057 (t80) REVERT: A 696 LYS cc_start: 0.7051 (ttpt) cc_final: 0.6822 (tttt) REVERT: A 741 ARG cc_start: 0.6379 (mtp-110) cc_final: 0.5889 (mmt-90) REVERT: A 757 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.5863 (ptp) REVERT: B 89 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.4258 (ttp80) REVERT: B 198 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5725 (mm) REVERT: B 470 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6610 (pp20) REVERT: B 633 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7292 (mm) REVERT: B 634 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7771 (mt) REVERT: B 638 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6611 (mmt-90) REVERT: B 741 ARG cc_start: 0.6508 (mtp-110) cc_final: 0.6081 (mmp-170) REVERT: B 753 ARG cc_start: 0.5160 (mtp180) cc_final: 0.4785 (mmm-85) REVERT: C 56 THR cc_start: 0.3016 (OUTLIER) cc_final: 0.2695 (p) REVERT: C 135 LEU cc_start: 0.4969 (OUTLIER) cc_final: 0.4765 (mp) REVERT: C 359 ARG cc_start: 0.6567 (OUTLIER) cc_final: 0.6162 (ttt180) REVERT: C 550 MET cc_start: 0.7584 (mtm) cc_final: 0.7213 (mtm) REVERT: C 627 ASP cc_start: 0.6909 (OUTLIER) cc_final: 0.6393 (p0) REVERT: C 638 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6113 (mmt-90) REVERT: C 696 LYS cc_start: 0.7082 (ttpt) cc_final: 0.6856 (tttt) REVERT: C 757 MET cc_start: 0.6289 (OUTLIER) cc_final: 0.6042 (ptp) REVERT: D 56 THR cc_start: 0.2996 (OUTLIER) cc_final: 0.2655 (p) REVERT: D 427 MET cc_start: 0.4128 (tpt) cc_final: 0.3594 (tpt) REVERT: D 445 LEU cc_start: 0.5522 (OUTLIER) cc_final: 0.5020 (tp) REVERT: D 556 GLU cc_start: 0.7236 (pm20) cc_final: 0.6972 (pm20) REVERT: D 614 LYS cc_start: 0.4975 (OUTLIER) cc_final: 0.4586 (pttp) REVERT: D 633 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.7173 (mm) REVERT: D 638 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6382 (mmt-90) REVERT: D 650 GLU cc_start: 0.5710 (mp0) cc_final: 0.5356 (mt-10) REVERT: D 674 PHE cc_start: 0.6444 (t80) cc_final: 0.5991 (t80) REVERT: D 696 LYS cc_start: 0.7076 (ttpt) cc_final: 0.6855 (tttt) REVERT: D 741 ARG cc_start: 0.6369 (mtp-110) cc_final: 0.5938 (mmp-170) REVERT: D 757 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5866 (ptp) REVERT: E 89 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.4440 (ttp80) REVERT: E 198 LEU cc_start: 0.6068 (OUTLIER) cc_final: 0.5719 (mm) REVERT: E 236 LYS cc_start: 0.6436 (tptt) cc_final: 0.6012 (tttm) REVERT: E 556 GLU cc_start: 0.6969 (pm20) cc_final: 0.6617 (pm20) REVERT: E 633 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7290 (mm) REVERT: E 634 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7747 (mt) REVERT: E 638 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6627 (mmt-90) REVERT: E 741 ARG cc_start: 0.6533 (mtp-110) cc_final: 0.6108 (mmp-170) REVERT: E 753 ARG cc_start: 0.5072 (mtp180) cc_final: 0.4782 (mmm-85) REVERT: F 56 THR cc_start: 0.3015 (OUTLIER) cc_final: 0.2694 (p) REVERT: F 135 LEU cc_start: 0.4982 (OUTLIER) cc_final: 0.4776 (mp) REVERT: F 359 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.6349 (ttm170) REVERT: F 465 ARG cc_start: 0.6114 (mmt90) cc_final: 0.5661 (mtt-85) REVERT: F 550 MET cc_start: 0.7513 (mtm) cc_final: 0.7159 (mtm) REVERT: F 627 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6355 (p0) REVERT: F 638 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6165 (mmt-90) REVERT: F 696 LYS cc_start: 0.7113 (ttpt) cc_final: 0.6877 (tttt) REVERT: F 741 ARG cc_start: 0.6577 (mtp-110) cc_final: 0.6123 (mmp-170) REVERT: F 757 MET cc_start: 0.6240 (OUTLIER) cc_final: 0.5953 (ptp) outliers start: 122 outliers final: 58 residues processed: 521 average time/residue: 0.7726 time to fit residues: 478.7222 Evaluate side-chains 524 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 428 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 99 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 135 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 491 GLU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 614 LYS 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 27 ILE 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 213 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 470 GLU Chi-restraints excluded: chain B residue 508 MET 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 678 MET Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 135 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 333 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 514 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 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 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 444 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 614 LYS 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 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 508 MET 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 E residue 678 MET Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 135 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 333 ASP Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 514 VAL 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: 0.6980 chunk 235 optimal weight: 0.9980 chunk 179 optimal weight: 0.0050 chunk 185 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 326 optimal weight: 6.9990 chunk 337 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 218 optimal weight: 20.0000 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN ** 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 129 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 538 ASN F 568 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.241848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.218402 restraints weight = 41820.016| |-----------------------------------------------------------------------------| r_work (start): 0.4473 rms_B_bonded: 1.44 r_work: 0.4269 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4166 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35082 Z= 0.129 Angle : 0.701 13.148 47460 Z= 0.346 Chirality : 0.047 0.156 5322 Planarity : 0.005 0.055 6198 Dihedral : 9.129 104.292 5016 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.73 % Favored : 94.14 % Rotamer: Outliers : 2.60 % Allowed : 21.00 % Favored : 76.40 % 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 aren not related in a simple way. whole: -0.72 (0.13), residues: 4314 helix: 0.38 (0.13), residues: 1692 sheet: -0.57 (0.23), residues: 510 loop : -1.12 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 322 TYR 0.018 0.001 TYR A 495 PHE 0.022 0.002 PHE B 139 TRP 0.008 0.001 TRP C 476 HIS 0.008 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00274 (35082) covalent geometry : angle 0.70113 (47460) hydrogen bonds : bond 0.03880 ( 1272) hydrogen bonds : angle 4.79154 ( 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 577 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 481 time to evaluate : 1.423 Fit side-chains REVERT: A 56 THR cc_start: 0.2937 (OUTLIER) cc_final: 0.2600 (p) REVERT: A 225 ARG cc_start: 0.6545 (tpt90) cc_final: 0.6119 (tpt90) REVERT: A 278 LEU cc_start: 0.5827 (mm) cc_final: 0.4941 (tt) REVERT: A 449 MET cc_start: 0.5545 (tpt) cc_final: 0.5298 (tpt) REVERT: A 465 ARG cc_start: 0.6084 (mmt90) cc_final: 0.5690 (mtt-85) REVERT: A 614 LYS cc_start: 0.4922 (OUTLIER) cc_final: 0.4494 (pttm) REVERT: A 627 ASP cc_start: 0.6944 (OUTLIER) cc_final: 0.6562 (p0) REVERT: A 633 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.7136 (mm) REVERT: A 638 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6443 (mmt-90) REVERT: A 673 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.5676 (mp0) REVERT: A 741 ARG cc_start: 0.6308 (mtp-110) cc_final: 0.5800 (mmt-90) REVERT: A 754 LYS cc_start: 0.5410 (ttpt) cc_final: 0.5056 (ttpp) REVERT: A 757 MET cc_start: 0.5986 (OUTLIER) cc_final: 0.5316 (ptm) REVERT: B 198 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5636 (mm) REVERT: B 236 LYS cc_start: 0.6279 (tptt) cc_final: 0.5833 (tttm) REVERT: B 401 ASN cc_start: 0.6473 (t0) cc_final: 0.6241 (m-40) REVERT: B 427 MET cc_start: 0.4209 (tpt) cc_final: 0.3643 (tpt) REVERT: B 470 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6586 (pp20) REVERT: B 633 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7250 (mm) REVERT: B 638 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6767 (mmt-90) REVERT: B 741 ARG cc_start: 0.6465 (mtp-110) cc_final: 0.6011 (mmt-90) REVERT: B 753 ARG cc_start: 0.5250 (mtp180) cc_final: 0.4798 (mmm-85) REVERT: C 56 THR cc_start: 0.2985 (OUTLIER) cc_final: 0.2673 (p) REVERT: C 198 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5624 (mm) REVERT: C 236 LYS cc_start: 0.6271 (tptt) cc_final: 0.5917 (tttm) REVERT: C 359 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.6127 (ttt180) REVERT: C 550 MET cc_start: 0.7535 (mtm) cc_final: 0.7228 (mtm) REVERT: C 627 ASP cc_start: 0.6769 (OUTLIER) cc_final: 0.6245 (p0) REVERT: C 638 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6129 (mmt-90) REVERT: D 56 THR cc_start: 0.3049 (OUTLIER) cc_final: 0.2701 (p) REVERT: D 278 LEU cc_start: 0.5768 (mm) cc_final: 0.4903 (tt) REVERT: D 427 MET cc_start: 0.4003 (tpt) cc_final: 0.3513 (tpt) REVERT: D 445 LEU cc_start: 0.5413 (OUTLIER) cc_final: 0.4905 (tp) REVERT: D 470 GLU cc_start: 0.6918 (pm20) cc_final: 0.6554 (pp20) REVERT: D 556 GLU cc_start: 0.7063 (pm20) cc_final: 0.6792 (pm20) REVERT: D 627 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6456 (p0) REVERT: D 633 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.7142 (mm) REVERT: D 638 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6519 (mmt-90) REVERT: D 674 PHE cc_start: 0.6364 (t80) cc_final: 0.5893 (t80) REVERT: D 733 ARG cc_start: 0.6404 (tpt170) cc_final: 0.6189 (tpt170) REVERT: D 741 ARG cc_start: 0.6304 (mtp-110) cc_final: 0.5767 (mmt-90) REVERT: D 757 MET cc_start: 0.5960 (ptm) cc_final: 0.5716 (ptp) REVERT: E 198 LEU cc_start: 0.5957 (OUTLIER) cc_final: 0.5604 (mm) REVERT: E 236 LYS cc_start: 0.6255 (tptt) cc_final: 0.5807 (tttm) REVERT: E 427 MET cc_start: 0.4220 (tpt) cc_final: 0.3655 (tpt) REVERT: E 470 GLU cc_start: 0.6891 (pm20) cc_final: 0.6589 (pp20) REVERT: E 556 GLU cc_start: 0.6690 (pm20) cc_final: 0.6353 (pm20) REVERT: E 633 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7274 (mm) REVERT: E 638 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6851 (mmt-90) REVERT: E 741 ARG cc_start: 0.6408 (mtp-110) cc_final: 0.5936 (mmt-90) REVERT: E 753 ARG cc_start: 0.5153 (mtp180) cc_final: 0.4769 (mmm-85) REVERT: F 56 THR cc_start: 0.3011 (OUTLIER) cc_final: 0.2688 (p) REVERT: F 198 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5648 (mm) REVERT: F 236 LYS cc_start: 0.6261 (tptt) cc_final: 0.5926 (tttm) REVERT: F 379 GLU cc_start: 0.5599 (pm20) cc_final: 0.5379 (pt0) REVERT: F 470 GLU cc_start: 0.6964 (pm20) cc_final: 0.6466 (pp20) REVERT: F 550 MET cc_start: 0.7421 (mtm) cc_final: 0.7036 (mtm) REVERT: F 638 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6121 (mmt-90) REVERT: F 741 ARG cc_start: 0.6586 (mtp-110) cc_final: 0.6082 (mmt-90) REVERT: F 757 MET cc_start: 0.6032 (OUTLIER) cc_final: 0.5800 (ptp) outliers start: 96 outliers final: 35 residues processed: 545 average time/residue: 0.7793 time to fit residues: 502.8721 Evaluate side-chains 486 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 423 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 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 508 MET Chi-restraints excluded: chain A residue 614 LYS 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 122 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 122 THR 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 342 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 638 ARG 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 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 E residue 57 VAL 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 342 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 198 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 633 ILE Chi-restraints excluded: chain F residue 638 ARG 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: 0.0770 chunk 267 optimal weight: 3.9990 chunk 5 optimal weight: 30.0000 chunk 225 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 297 optimal weight: 0.0030 chunk 383 optimal weight: 9.9990 chunk 401 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 chunk 351 optimal weight: 6.9990 overall best weight: 3.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4680 r_free = 0.4680 target = 0.240784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.217433 restraints weight = 41552.281| |-----------------------------------------------------------------------------| r_work (start): 0.4463 rms_B_bonded: 1.40 r_work: 0.4255 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4158 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35082 Z= 0.150 Angle : 0.730 13.171 47460 Z= 0.361 Chirality : 0.048 0.151 5322 Planarity : 0.005 0.053 6198 Dihedral : 9.328 105.087 5016 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.49 % Favored : 93.37 % Rotamer: Outliers : 2.44 % Allowed : 21.98 % Favored : 75.58 % 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 aren not related in a simple way. whole: -0.69 (0.13), residues: 4314 helix: 0.40 (0.13), residues: 1686 sheet: -0.53 (0.23), residues: 516 loop : -1.11 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 322 TYR 0.013 0.001 TYR E 495 PHE 0.029 0.002 PHE B 674 TRP 0.014 0.001 TRP B 454 HIS 0.009 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00334 (35082) covalent geometry : angle 0.73006 (47460) hydrogen bonds : bond 0.04186 ( 1272) hydrogen bonds : angle 4.85415 ( 3654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17137.89 seconds wall clock time: 291 minutes 34.54 seconds (17494.54 seconds total)